diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
index 03f69a5..0000000
Binary files a/.DS_Store and /dev/null differ
diff --git a/.gitignore b/.gitignore
index 9b00344..5f3d36a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
 .DS_Store
 .Rhistory
 .cache/
+.Rproj.user
+*.Rproj
\ No newline at end of file
diff --git a/001courseLogistics/.DS_Store b/001courseLogistics/.DS_Store
deleted file mode 100644
index f062766..0000000
Binary files a/001courseLogistics/.DS_Store and /dev/null differ
diff --git a/001courseLogistics/.Rhistory b/001courseLogistics/.Rhistory
deleted file mode 100644
index 760dfa5..0000000
--- a/001courseLogistics/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-?symbols
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1),nrow=1),col="gold")
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1),nrow=1),col="gold",add=T)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1,1),nrow=1),col="gold",add=T)
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold")
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-?rect
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runi(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runif(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-rect(xPres-0.5,rep(0,10),xPres+0.5,runif(10,0,1),col=sample(c("blue","red"),size=10,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],rep(0,10),xPres[i]+xWidth[i],runif(10,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],runif(1,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.1*xWidth[i],0,xPres[i]+0.1*xWidth[i],xHeight[i],col="gold")
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample("gold","silver"))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1)
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-?png
-png("xmas.png",height=2*480,width=480)
-<script src="https://gist.github.com/4369771.js"></script>
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-dev.off()
-pvals = runif(10000)
-pvals05 = pvals[pvals < 0.05]
-hist(pvals05)
-data()
-?network
-install.packages("ergm")
-library(ergm)
-?network
-m <- matrix(rbinom(25,1,.4),5,5)
-diag(m) <- 0
-g <- network(m, directed=FALSE)
-summary(g)
-m
-ss = svd(M)
-ss = svd(m)
-plot(ss$v[,1])
-ss$u[,1] %*% t(ss$v[,1])
-ss$d[1]*ss$u[,1] %*% t(ss$v[,1])
-set.seed(31)
-heightsCM = rnorm(10,mean=188, sd=5)
-weightsK = rnorm(10,mean=84,sd=3)
-hasDaughter = sample(c(TRUE,FALSE),size=10,replace=T)
-myDataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-myDataFrame
-set.seed(31)
-heightsCM = rnorm(30,mean=188, sd=5)
-weightsK = rnorm(30,mean=84,sd=3)
-hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T)
-myDataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-set.seed(31)
-heightsCM = rnorm(30,mean=188, sd=5)
-weightsK = rnorm(30,mean=84,sd=3)
-hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T)
-myDataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-set.seed(31)
-heightsCM = rnorm(30,mean=188, sd=5)
-weightsK = rnorm(30,mean=84,sd=3)
-hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T)
-dataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-dataFrame
-set.seed(31)
-heightsCM = rnorm(30,mean=188, sd=5)
-weightsK = rnorm(30,mean=84,sd=3)
-hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T)
-dataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-dataFrame
-set.seed(31)
-heightsCM = rnorm(30,mean=188, sd=5)
-weightsK = rnorm(30,mean=84,sd=3)
-hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T)
-dataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-dataFrameSubset = dataFrame[dataFrame$heightsCM > 188,]
-mean(dataFrameSubset$weightsK)
-mean(dataFrameSubset$weightsK)
-set.seed(31); heightsCM = rnorm(30,mean=188, sd=5); weightsK = rnorm(30,mean=84,sd=3); hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T); dataFrame = data.frame(heightsCM,weightsK,hasDaughter);
-set.seed(31); heightsCM = rnorm(30,mean=188, sd=5); weightsK = rnorm(30,mean=84,sd=3); hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T); dataFrame = data.frame(heightsCM,weightsK,hasDaughter);
-set.seed(31); heightsCM = rnorm(30,mean=188, sd=5); weightsK = rnorm(30,mean=84,sd=3); hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T); dataFrame = data.frame(heightsCM,weightsK,hasDaughter)
-dataFrameSubset = dataFrame[dataFrame$heights > 188,]
-mean(dataFrameSubset$weightsK)
-dataFrameSubset = dataFrame[dataFrame$heights >= 188,]
-mean(dataFrameSubset$weightsK)
-dataFrameSubset = dataFrame[dataFrame$heights < 188,]
-mean(dataFrameSubset$weightsK)
-mean(dataFrame$weightsK)
-set.seed(31); heightsCM = rnorm(30,mean=188, sd=5); weightsK = rnorm(30,mean=84,sd=3); hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T); dataFrame = data.frame(heightsCM,weightsK,hasDaughter);
-dataFrameSubset = dataFrame[dataFrame$heights > 188,]
-mean(dataFrame$weightsK)
-set.seed(31); heightsCM = rnorm(30,mean=188, sd=5); weightsK = rnorm(30,mean=84,sd=3); hasDaughter = sample(c(TRUE,FALSE),size=30,replace=T); dataFrame = data.frame(heightsCM,weightsK,hasDaughter);
-mean(dataFrameSubset$weightsK)
-set.seed(41)
-rcauchy(100)
-set.seed(41)
-cauchyValues = rcauchy(100)
-?cauchyValues
-?rcauchy
-set.seed(41)
-cauchyValues = rcauchy(100)
-set.seed(41)
-sample(cauchyValues,replace=TRUE)
-set.seed(41)
-cauchyValues = rcauchy(100)
-set.seed(41)
-sampledValues = sample(cauchyValues,size=10,replace=TRUE)
-sampledValues[1:3]
-set.seed(41)
-cauchyValues = rcauchy(100)
-set.seed(415)
-sampledValues = sample(cauchyValues,size=10,replace=TRUE)
-sampledValues[1:3]
-set.seed(41)
-cauchyValues = rcauchy(100)
-#set.seed(415)
-sampledValues = sample(cauchyValues,size=10,replace=TRUE)
-sampledValues[1:3]
-set.seed(41)
-cauchyValues = rcauchy(100)
-set.seed(415)
-sampledValues = sample(cauchyValues,size=10,replace=FALSE)
-sampledValues[1:3]
-set.seed(41)
-cauchyValues = rcauchy(100)
-set.seed(41)
-sampledValues = sample(cauchyValues,size=10,replace=TRUE)
-sampledValues[1:3]
-library(kernlab)
-args(predict.kqr)
-args(predict)
-rbinom
-?rnorm
-getwd()
-setwd(file.choose())
-setwd("~/Dropbox/Jeff/teaching/2013/coursera/")
-list.files()
-setwd("week1/")
-setwd("001courseLogistics/")
-?publish
-library(slidify)
-?publish
-publish("001courseLogistics",host="dropbox")
diff --git a/001courseLogistics/assets/.DS_Store b/001courseLogistics/assets/.DS_Store
deleted file mode 100644
index 0895f61..0000000
Binary files a/001courseLogistics/assets/.DS_Store and /dev/null differ
diff --git a/001courseLogistics/libraries/.DS_Store b/001courseLogistics/libraries/.DS_Store
deleted file mode 100644
index e6a1bb3..0000000
Binary files a/001courseLogistics/libraries/.DS_Store and /dev/null differ
diff --git a/001courseLogistics/libraries/frameworks/.DS_Store b/001courseLogistics/libraries/frameworks/.DS_Store
deleted file mode 100644
index c188b1a..0000000
Binary files a/001courseLogistics/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/001courseLogistics/libraries/frameworks/io2012/.DS_Store b/001courseLogistics/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 64b69ab..0000000
Binary files a/001courseLogistics/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/001courseLogistics/libraries/frameworks/io2012/default/.DS_Store b/001courseLogistics/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 9c98ef2..0000000
Binary files a/001courseLogistics/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/.DS_Store b/002gettingHelp/.DS_Store
deleted file mode 100644
index e71ca07..0000000
Binary files a/002gettingHelp/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/.Rhistory b/002gettingHelp/.Rhistory
deleted file mode 100644
index 7955cdc..0000000
--- a/002gettingHelp/.Rhistory
+++ /dev/null
@@ -1,437 +0,0 @@
-text(5.5,5.5,teamName1,col ="red", family = 'Helvetica', cex = cx/1.5)
-}else{
-text(5.5,5.5,teamName2,col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1,"Accuracy"))
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2,"Accuracy"))
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-makeVideo(teamName1="GregColin",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"GregColin"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-makeVideo(teamName1="GregColin",teamName2="JoelDan",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"GregColin"],
-team2Pred=nonPCA[battleSample,"JoelDan"],testImages=as.matrix(battleData[battleSample,-1]))
-names(PCA)
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="GregColinPCA",teamName2="JonPhoebe",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"GregColinPCA"],
-team2Pred=PCA[battleSample,"JonPhoebe"],testImages=as.matrix(battleData[battleSample,-1]))
-head(PCA)
-names(PCA)
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="WesJoeEm",teamName2="CalebChey",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"WesJoeEm"],
-team2Pred=PCA[battleSample,"CalebChey"],testImages=as.matrix(battleData[battleSample,-1]))
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="JonPhoebe",teamName2="GregColin",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"JonPhoebe"],
-team2Pred=nonPCA[battleSample,"GregColin"],testImages=as.matrix(battleData[battleSample,-1]))
-displayTeams <- function(teamName1="The Jets",teamName2="The Sharks",cx=5,nFrames=10){
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(1,1,1,2,2,2),byrow=T,nrow=2))
-colRampWhite = colorRampPalette(c("black","white"))(nFrames)
-colRampRed= colorRampPalette(c("black","red"))(nFrames)
-colRampBlue= colorRampPalette(c("black","blue"))(nFrames)
-for(i in 1:nFrames){
-Team1
-plot(1:10,1:10,type="n")
-text(5.5,5.5,teamName1,col = colRampRed[i], family = 'Helvetica', cex = cx)
-Team2
-plot(1:10,1:10,type="n",main="Versus",cex.main=3)
-text(5.5,5.5,teamName2,col = colRampBlue[i], family = 'Helvetica', cex = cx)
-Sys.sleep(2/nFrames)
-}
-predictionMatch <- function(teamName1,teamName2,trueLabels,testImages,team1Pred,team2Pred,cx=8){
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(2,1,4,3,0,5),byrow=T,nrow=2))
-for(i in 1:dim(testImages)[1]){
-zz = matrix(testImages[i,],nrow=28)
-image(zz[,ncol(zz):1],main="True Image",xaxt="n",yaxt="n",col=colRampWhite,cex.main=3)
-Sys.sleep(0.2)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1),cex.main=3)
-text(5.5,5.5,team1Pred[i],col ="red", family = 'Helvetica', cex = cx)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste("Accuracy"),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-Sys.sleep(0.2)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2),cex.main=3)
-text(5.5,5.5,team2Pred[i],col ="blue", family = 'Helvetica', cex = cx)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste("Accuracy"),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-Sys.sleep(0.4)
-}
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(1,1,1,2,0,3),byrow=T,nrow=2))
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main="Winner",cex.main=3)
-team1winner = cumMean(trueLabels ==team1Pred) > cumMean(trueLabels==team2Pred)
-if(team1winner){
-text(5.5,5.5,teamName1,col ="red", family = 'Helvetica', cex = cx/1.5)
-}else{
-text(5.5,5.5,teamName2,col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-cumMean = function(x){
-return(round(mean(x)*100,1))
-}
-makeVideo <- function(teamName1,teamName2,trueLabels,team1Pred,team2Pred,testImages){
-displayTeams(teamName1=teamName1,teamName2=teamName2)
-predictionMatch(teamName1=teamName1,teamName2=teamName2,
-trueLabels=trueLabels,team1Pred=team1Pred,
-team2Pred=team2Pred,testImages=testImages)
-}
-nonPCA = read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/nonPCAbattle.csv",header=T)
-PCA = read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/PCAbattle.csv",header=T)
-battleData= read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/battleData.csv",header=T)
-battleSample = sample(1:3000,size=5,replace=FALSE)
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-windowsFonts()
-?par
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4
-dim(pvalueDAta)
-dim(pvalueData)
-pvalueData2 = pvalueData
-load("~/Downloads/pvalueData00-10.rda")
-ls()
-dim(pvalueData)
-pvalueData[1,]
-pvalueData2[1,]
-names(pvalueDAta)
-names(pvalueData)
-names(pvalueData2)
-dim(pvalueData)
-dim(pvalueData2)
-pvalueData2[1,]
-pvalueData2[2,]
-pvalueData2[1,]
-pvalueData[1,]
-oo = match(pvalueData$pubmedID,pvalueData2$pubmedID)
-colnames(pvalueData)
-colnames(pvalueData2)
-oo = match(pvalueData[,3],pvalueData2[,3])
-length(oo)
-oo[1]
-sum(is.na(oo))
-tmp1 = pvalueData[,3]
-tmp2 = pvalueData2[,3]
-tmp1[1]
-tmp2[1]
-tmp2 = as.numeric(tmp2)
-tmp1 = tmp1[order(tmp1)]
-tmp2 = tmp2[order(tmp2)]
-tmp1[1]
-tmp2[1]
-length(tmp1)
-length(tmp2)
-sum(tmp1[1:15653] == tmp2[1:15653])
-tmp1[13427:13428]
-tmp1[13427:13429]
-tmp2[13427:13429]
-tmp1[13425:13429]
-tmp2[13425:13429]
-pvalueData[1,]
-pvalueData[pvalueData[,3]==19549972, ]
-pvalueData2[pvalueData2[,3]=="19549972", ]
-pvalueData2[pvalueData2[,3]=="19549973", ]
-tmp2[13425:13429]
-tmp2[13424:13429]
-tmp1[13424:13429]
-sum(tmp1[1:13424] == tmp2[1:13424])
-sum(tmp1[1:11940] == tmp2[1:11940])
-plot(tmp1,tmp2)
-length(tmp2)
-plot(tmp1,tmp2[1:15653])
-t1 = table(tmp1)
-t2 = table(tmp2)
-t1[1]
-t2[1]
-sum(t1 == t2)
-length(t2)
-length(t1)
-setdiff(names(t1),names(t2))
-sum(t1 == t2[1:5323])
-oo = match(names(t1),names(t2))
-length(oo)
-oo[1]
-oo = match(names(t2),names(t1))
-length(oo)
-sum(is.na(oo))
-which(is.na(oo))
-length(names(t2))
-t2[3097]
-sum(t2)
-dim(pvalueData)
-dim(pvalueData2)
-pvalueData2[pvalueData2[,3]=="16421237",]
-pvalueData3 = pvalueData2[-which(pvalueData2[,3]=="16421237"),]
-dim(pvalueData3)
-dim(pvalueData)
-tmp1 = pvalueData3[,3]
-tmp2 = pvalueData[,3]
-length(tmp1)
-length(tmp2)
-tmp1[1]
-tmp2[1]
-tmp1 = as.numeric(tmp1)
-tmp1 = tmp1[order(tmp1)]
-tmp2 = tmp2[order(tmp2)]
-tmp1[1]
-tmp2[1]
-plot(tmp1,tmp2)
-sum(tmp1==tmp2)
-mean(tmp1==tmp2)
-tmp1 = pvalueData3[,3]#
-tmp2 = pvalueData[,3]
-tmp1[1]
-tmp1 = as.numeric(tmp1)
-colnames(pvalueData3)
-pvals1 = as.numeric(pvalueData3[,1])
-pvals2 = as.numeric(pvalueData[,1])
-pvals1[1]
-pvals2[1]
-pvals1 = pvals1[order(tmp1)]
-pvals2 = pvals1[order(tmp2)]
-sum(pvals1==pvals2)
-length(pvals1)
-ne = which(pvals1!=pvals2)
-ne[1]
-pvals1 = as.numeric(pvalueData3[,1])
-pvals2 = as.numeric(pvalueData[,1])
-pvals1 = pvals1[order(tmp1)]
-pvals2 = pvals2[order(tmp2)]
-sum(pvals1==pvals2)
-length(pvals1)
-mean(pvals1==pvals2)
-mean((pvals1 - pvals2) < 1e-3)
-mean((pvals1 - pvals2) < 1e-5)
-mean(abs(pvals1 - pvals2) < 1e-5 )
-dim(pvalueData)
-dim(pvalueData3)
-rm(list=ls())
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-dim(pvalueData)
-rm(list=ls())
-pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueData.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueData.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-tmpData
-i
-j
-tmpData = getAbstractsPmids(journals[i],years[j])
-while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-barplot(c(1,1,-3))
-?barplot
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12[1,]
-pres08 = read.csv("~/Desktop/2008pres.csv")
-pres08[1,]
-sum(pres12$FIPS == 0)
-table(pres12$X[pres12$FIPS==0,])
-table(pres12$X[pres12$FIPS==0])
-pres12[pres12$X=="OK",]
-pres12 = pres12[pres12$FIPS==0,]
-dim(pres12)
-pres12[1,]
-pres12[2,]
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12[1:10,]
-pres12[21:30,]
-pres12[50:100,]
-pres12 = pres12[pres12$FIPS==0,]
-length(unique(pres12$X))
-which.max(pres12$X == "OK")
-which(pres12$X == "OK")
-pres12[c(36,37)]
-pres12[c(36,37),]
-pres12[1,]
-pres12[1,5]
-pres12[1,4]
-as.numeric(pres12[1,4])
-as.numeric(as.character(pres12[1,4])
-)
-as.numeric(as.character(pres12[1,4]))
-pres08[1,]
-sum(pres08$LAST.NAME == "McCain")
-sum(pres08$LAST.NAME == "McCain" & pres08$STATE=="Alabama")
-pres08[pres08$LAST.NAME == "McCain",]
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-pres12[1,]
-table(unique(pres12))
-table(unique(pres12$x))
-table(unique(pres12$X))
-substr
-gsub
-gsub(pres12[1,3])
-pres12[1,]
-pres12$Obama.vote[1]
-dem12 = as.character(pres12$Obama.vote)
-dem12[1]
-dem12 = sapply(dem12,function(x){gsub(x,",","")})
-dem12[1]
-dem12 = as.character(pres12$Obama.vote)
-gsub(dem12[1],",","")
-?gsub
-gsub(",","",dem12[1])
-dem12 = as.character(pres12$Obama.vote)
-dem12 = as.numeric(sapply(dem12,function(x){gsub(",","",x)}))
-dem12[1]
-hist(dem12)
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-dem12 = as.character(pres12$Obama.vote)
-dem12 = as.numeric(sapply(dem12,function(x){gsub(",","",x)}))
-rep12 = as.character(pres12$Romney.vote)
-rep12 = as.numeric(sapply(rep12,function(x){gsub(",","",x)}))
-plot(rep12,dem12)
-rep12[1]
-pres12[1,]
-table(pres12[,2])
-res12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-table(pres12[,2])
-table(pres12[,1])
-library(XML)
-theurl <- "http://uselectionatlas.org/RESULTS/data.php?year=2008&datatype=national&def=1&f=0&off=0&elect=0"
-tables <- readHTMLTable(theurl)
-tables[1,]
-dim(tables)
-tables[1]
-tables
-n.rows <- unlist(lapply(tables, function(t) dim(t)[1]))
-n.rows
-library(slidify)
-?author
-setwd("~/Documents/Work/teaching/2013/coursera/")
-ls()
-list.files()
-author("gettingStarted")
-slidify("gettingStarted")
-ls()
-list.files()
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("~/Documents/Work/teaching/2013/coursera/")
-setwd("week1/gettingHelp/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
diff --git a/002gettingHelp/assets/.DS_Store b/002gettingHelp/assets/.DS_Store
deleted file mode 100644
index a5027ca..0000000
Binary files a/002gettingHelp/assets/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/.DS_Store b/002gettingHelp/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/002gettingHelp/libraries/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/frameworks/.DS_Store b/002gettingHelp/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/002gettingHelp/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/frameworks/io2012/.DS_Store b/002gettingHelp/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/002gettingHelp/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/frameworks/io2012/default/.DS_Store b/002gettingHelp/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/002gettingHelp/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/frameworks/io2012/default/js/.DS_Store b/002gettingHelp/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/002gettingHelp/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/highlighters/.DS_Store b/002gettingHelp/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/002gettingHelp/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/002gettingHelp/libraries/highlighters/highlight.js/.DS_Store b/002gettingHelp/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/002gettingHelp/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ
diff --git a/003whatIsData/.DS_Store b/003whatIsData/.DS_Store
deleted file mode 100644
index e9c0ed7..0000000
Binary files a/003whatIsData/.DS_Store and /dev/null differ
diff --git a/003whatIsData/.Rhistory b/003whatIsData/.Rhistory
deleted file mode 100644
index 95c1638..0000000
--- a/003whatIsData/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-?symbols
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1),nrow=1),col="gold")
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1),nrow=1),col="gold",add=T)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1,1),nrow=1),col="gold",add=T)
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold")
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-?rect
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runi(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runif(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-rect(xPres-0.5,rep(0,10),xPres+0.5,runif(10,0,1),col=sample(c("blue","red"),size=10,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],rep(0,10),xPres[i]+xWidth[i],runif(10,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],runif(1,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.1*xWidth[i],0,xPres[i]+0.1*xWidth[i],xHeight[i],col="gold")
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample("gold","silver"))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1)
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-?png
-png("xmas.png",height=2*480,width=480)
-<script src="https://gist.github.com/4369771.js"></script>
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-dev.off()
-pvals = runif(10000)
-pvals05 = pvals[pvals < 0.05]
-hist(pvals05)
-data()
-?network
-install.packages("ergm")
-library(ergm)
-?network
-m <- matrix(rbinom(25,1,.4),5,5)
-diag(m) <- 0
-g <- network(m, directed=FALSE)
-summary(g)
-m
-ss = svd(M)
-ss = svd(m)
-plot(ss$v[,1])
-ss$u[,1] %*% t(ss$v[,1])
-ss$d[1]*ss$u[,1] %*% t(ss$v[,1])
-x = 3 asdfa
-setwd("~/Documents/Work/teaching/2013/coursera/")
-setwd("week1/gettingHelp/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("../whatIsData/")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
diff --git a/003whatIsData/assets/.DS_Store b/003whatIsData/assets/.DS_Store
deleted file mode 100644
index a48555f..0000000
Binary files a/003whatIsData/assets/.DS_Store and /dev/null differ
diff --git a/003whatIsData/assets/img/.DS_Store b/003whatIsData/assets/img/.DS_Store
deleted file mode 100644
index 5008ddf..0000000
Binary files a/003whatIsData/assets/img/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/.DS_Store b/003whatIsData/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/003whatIsData/libraries/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/frameworks/.DS_Store b/003whatIsData/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/003whatIsData/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/frameworks/io2012/.DS_Store b/003whatIsData/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/003whatIsData/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/frameworks/io2012/default/.DS_Store b/003whatIsData/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/003whatIsData/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/frameworks/io2012/default/js/.DS_Store b/003whatIsData/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/003whatIsData/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/highlighters/.DS_Store b/003whatIsData/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/003whatIsData/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/003whatIsData/libraries/highlighters/highlight.js/.DS_Store b/003whatIsData/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/003whatIsData/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ
diff --git a/004representingData/.DS_Store b/004representingData/.DS_Store
deleted file mode 100644
index b53cbeb..0000000
Binary files a/004representingData/.DS_Store and /dev/null differ
diff --git a/004representingData/.Rhistory b/004representingData/.Rhistory
deleted file mode 100644
index 95c1638..0000000
--- a/004representingData/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-?symbols
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1),nrow=1),col="gold")
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1),nrow=1),col="gold",add=T)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1,1),nrow=1),col="gold",add=T)
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold")
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-?rect
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runi(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runif(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-rect(xPres-0.5,rep(0,10),xPres+0.5,runif(10,0,1),col=sample(c("blue","red"),size=10,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],rep(0,10),xPres[i]+xWidth[i],runif(10,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],runif(1,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.1*xWidth[i],0,xPres[i]+0.1*xWidth[i],xHeight[i],col="gold")
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample("gold","silver"))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1)
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-?png
-png("xmas.png",height=2*480,width=480)
-<script src="https://gist.github.com/4369771.js"></script>
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-dev.off()
-pvals = runif(10000)
-pvals05 = pvals[pvals < 0.05]
-hist(pvals05)
-data()
-?network
-install.packages("ergm")
-library(ergm)
-?network
-m <- matrix(rbinom(25,1,.4),5,5)
-diag(m) <- 0
-g <- network(m, directed=FALSE)
-summary(g)
-m
-ss = svd(M)
-ss = svd(m)
-plot(ss$v[,1])
-ss$u[,1] %*% t(ss$v[,1])
-ss$d[1]*ss$u[,1] %*% t(ss$v[,1])
-x = 3 asdfa
-setwd("~/Documents/Work/teaching/2013/coursera/")
-setwd("week1/gettingHelp/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("../whatIsData/")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
diff --git a/004representingData/assets/.DS_Store b/004representingData/assets/.DS_Store
deleted file mode 100644
index 734fb8d..0000000
Binary files a/004representingData/assets/.DS_Store and /dev/null differ
diff --git a/004representingData/assets/img/.DS_Store b/004representingData/assets/img/.DS_Store
deleted file mode 100644
index 5008ddf..0000000
Binary files a/004representingData/assets/img/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/.DS_Store b/004representingData/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/004representingData/libraries/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/frameworks/.DS_Store b/004representingData/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/004representingData/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/frameworks/io2012/.DS_Store b/004representingData/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/004representingData/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/frameworks/io2012/default/.DS_Store b/004representingData/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/004representingData/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/frameworks/io2012/default/js/.DS_Store b/004representingData/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/004representingData/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/highlighters/.DS_Store b/004representingData/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/004representingData/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/004representingData/libraries/highlighters/highlight.js/.DS_Store b/004representingData/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/004representingData/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ
diff --git a/005representingDataR/.DS_Store b/005representingDataR/.DS_Store
deleted file mode 100644
index f117ad8..0000000
Binary files a/005representingDataR/.DS_Store and /dev/null differ
diff --git a/005representingDataR/.Rhistory b/005representingDataR/.Rhistory
deleted file mode 100644
index 7955cdc..0000000
--- a/005representingDataR/.Rhistory
+++ /dev/null
@@ -1,437 +0,0 @@
-text(5.5,5.5,teamName1,col ="red", family = 'Helvetica', cex = cx/1.5)
-}else{
-text(5.5,5.5,teamName2,col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1,"Accuracy"))
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2,"Accuracy"))
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-makeVideo(teamName1="GregColin",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"GregColin"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-makeVideo(teamName1="GregColin",teamName2="JoelDan",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"GregColin"],
-team2Pred=nonPCA[battleSample,"JoelDan"],testImages=as.matrix(battleData[battleSample,-1]))
-names(PCA)
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="GregColinPCA",teamName2="JonPhoebe",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"GregColinPCA"],
-team2Pred=PCA[battleSample,"JonPhoebe"],testImages=as.matrix(battleData[battleSample,-1]))
-head(PCA)
-names(PCA)
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="WesJoeEm",teamName2="CalebChey",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"WesJoeEm"],
-team2Pred=PCA[battleSample,"CalebChey"],testImages=as.matrix(battleData[battleSample,-1]))
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="JonPhoebe",teamName2="GregColin",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"JonPhoebe"],
-team2Pred=nonPCA[battleSample,"GregColin"],testImages=as.matrix(battleData[battleSample,-1]))
-displayTeams <- function(teamName1="The Jets",teamName2="The Sharks",cx=5,nFrames=10){
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(1,1,1,2,2,2),byrow=T,nrow=2))
-colRampWhite = colorRampPalette(c("black","white"))(nFrames)
-colRampRed= colorRampPalette(c("black","red"))(nFrames)
-colRampBlue= colorRampPalette(c("black","blue"))(nFrames)
-for(i in 1:nFrames){
-Team1
-plot(1:10,1:10,type="n")
-text(5.5,5.5,teamName1,col = colRampRed[i], family = 'Helvetica', cex = cx)
-Team2
-plot(1:10,1:10,type="n",main="Versus",cex.main=3)
-text(5.5,5.5,teamName2,col = colRampBlue[i], family = 'Helvetica', cex = cx)
-Sys.sleep(2/nFrames)
-}
-predictionMatch <- function(teamName1,teamName2,trueLabels,testImages,team1Pred,team2Pred,cx=8){
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(2,1,4,3,0,5),byrow=T,nrow=2))
-for(i in 1:dim(testImages)[1]){
-zz = matrix(testImages[i,],nrow=28)
-image(zz[,ncol(zz):1],main="True Image",xaxt="n",yaxt="n",col=colRampWhite,cex.main=3)
-Sys.sleep(0.2)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1),cex.main=3)
-text(5.5,5.5,team1Pred[i],col ="red", family = 'Helvetica', cex = cx)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste("Accuracy"),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-Sys.sleep(0.2)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2),cex.main=3)
-text(5.5,5.5,team2Pred[i],col ="blue", family = 'Helvetica', cex = cx)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste("Accuracy"),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-Sys.sleep(0.4)
-}
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(1,1,1,2,0,3),byrow=T,nrow=2))
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main="Winner",cex.main=3)
-team1winner = cumMean(trueLabels ==team1Pred) > cumMean(trueLabels==team2Pred)
-if(team1winner){
-text(5.5,5.5,teamName1,col ="red", family = 'Helvetica', cex = cx/1.5)
-}else{
-text(5.5,5.5,teamName2,col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-cumMean = function(x){
-return(round(mean(x)*100,1))
-}
-makeVideo <- function(teamName1,teamName2,trueLabels,team1Pred,team2Pred,testImages){
-displayTeams(teamName1=teamName1,teamName2=teamName2)
-predictionMatch(teamName1=teamName1,teamName2=teamName2,
-trueLabels=trueLabels,team1Pred=team1Pred,
-team2Pred=team2Pred,testImages=testImages)
-}
-nonPCA = read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/nonPCAbattle.csv",header=T)
-PCA = read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/PCAbattle.csv",header=T)
-battleData= read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/battleData.csv",header=T)
-battleSample = sample(1:3000,size=5,replace=FALSE)
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-windowsFonts()
-?par
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4
-dim(pvalueDAta)
-dim(pvalueData)
-pvalueData2 = pvalueData
-load("~/Downloads/pvalueData00-10.rda")
-ls()
-dim(pvalueData)
-pvalueData[1,]
-pvalueData2[1,]
-names(pvalueDAta)
-names(pvalueData)
-names(pvalueData2)
-dim(pvalueData)
-dim(pvalueData2)
-pvalueData2[1,]
-pvalueData2[2,]
-pvalueData2[1,]
-pvalueData[1,]
-oo = match(pvalueData$pubmedID,pvalueData2$pubmedID)
-colnames(pvalueData)
-colnames(pvalueData2)
-oo = match(pvalueData[,3],pvalueData2[,3])
-length(oo)
-oo[1]
-sum(is.na(oo))
-tmp1 = pvalueData[,3]
-tmp2 = pvalueData2[,3]
-tmp1[1]
-tmp2[1]
-tmp2 = as.numeric(tmp2)
-tmp1 = tmp1[order(tmp1)]
-tmp2 = tmp2[order(tmp2)]
-tmp1[1]
-tmp2[1]
-length(tmp1)
-length(tmp2)
-sum(tmp1[1:15653] == tmp2[1:15653])
-tmp1[13427:13428]
-tmp1[13427:13429]
-tmp2[13427:13429]
-tmp1[13425:13429]
-tmp2[13425:13429]
-pvalueData[1,]
-pvalueData[pvalueData[,3]==19549972, ]
-pvalueData2[pvalueData2[,3]=="19549972", ]
-pvalueData2[pvalueData2[,3]=="19549973", ]
-tmp2[13425:13429]
-tmp2[13424:13429]
-tmp1[13424:13429]
-sum(tmp1[1:13424] == tmp2[1:13424])
-sum(tmp1[1:11940] == tmp2[1:11940])
-plot(tmp1,tmp2)
-length(tmp2)
-plot(tmp1,tmp2[1:15653])
-t1 = table(tmp1)
-t2 = table(tmp2)
-t1[1]
-t2[1]
-sum(t1 == t2)
-length(t2)
-length(t1)
-setdiff(names(t1),names(t2))
-sum(t1 == t2[1:5323])
-oo = match(names(t1),names(t2))
-length(oo)
-oo[1]
-oo = match(names(t2),names(t1))
-length(oo)
-sum(is.na(oo))
-which(is.na(oo))
-length(names(t2))
-t2[3097]
-sum(t2)
-dim(pvalueData)
-dim(pvalueData2)
-pvalueData2[pvalueData2[,3]=="16421237",]
-pvalueData3 = pvalueData2[-which(pvalueData2[,3]=="16421237"),]
-dim(pvalueData3)
-dim(pvalueData)
-tmp1 = pvalueData3[,3]
-tmp2 = pvalueData[,3]
-length(tmp1)
-length(tmp2)
-tmp1[1]
-tmp2[1]
-tmp1 = as.numeric(tmp1)
-tmp1 = tmp1[order(tmp1)]
-tmp2 = tmp2[order(tmp2)]
-tmp1[1]
-tmp2[1]
-plot(tmp1,tmp2)
-sum(tmp1==tmp2)
-mean(tmp1==tmp2)
-tmp1 = pvalueData3[,3]#
-tmp2 = pvalueData[,3]
-tmp1[1]
-tmp1 = as.numeric(tmp1)
-colnames(pvalueData3)
-pvals1 = as.numeric(pvalueData3[,1])
-pvals2 = as.numeric(pvalueData[,1])
-pvals1[1]
-pvals2[1]
-pvals1 = pvals1[order(tmp1)]
-pvals2 = pvals1[order(tmp2)]
-sum(pvals1==pvals2)
-length(pvals1)
-ne = which(pvals1!=pvals2)
-ne[1]
-pvals1 = as.numeric(pvalueData3[,1])
-pvals2 = as.numeric(pvalueData[,1])
-pvals1 = pvals1[order(tmp1)]
-pvals2 = pvals2[order(tmp2)]
-sum(pvals1==pvals2)
-length(pvals1)
-mean(pvals1==pvals2)
-mean((pvals1 - pvals2) < 1e-3)
-mean((pvals1 - pvals2) < 1e-5)
-mean(abs(pvals1 - pvals2) < 1e-5 )
-dim(pvalueData)
-dim(pvalueData3)
-rm(list=ls())
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-dim(pvalueData)
-rm(list=ls())
-pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueData.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueData.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-tmpData
-i
-j
-tmpData = getAbstractsPmids(journals[i],years[j])
-while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-barplot(c(1,1,-3))
-?barplot
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12[1,]
-pres08 = read.csv("~/Desktop/2008pres.csv")
-pres08[1,]
-sum(pres12$FIPS == 0)
-table(pres12$X[pres12$FIPS==0,])
-table(pres12$X[pres12$FIPS==0])
-pres12[pres12$X=="OK",]
-pres12 = pres12[pres12$FIPS==0,]
-dim(pres12)
-pres12[1,]
-pres12[2,]
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12[1:10,]
-pres12[21:30,]
-pres12[50:100,]
-pres12 = pres12[pres12$FIPS==0,]
-length(unique(pres12$X))
-which.max(pres12$X == "OK")
-which(pres12$X == "OK")
-pres12[c(36,37)]
-pres12[c(36,37),]
-pres12[1,]
-pres12[1,5]
-pres12[1,4]
-as.numeric(pres12[1,4])
-as.numeric(as.character(pres12[1,4])
-)
-as.numeric(as.character(pres12[1,4]))
-pres08[1,]
-sum(pres08$LAST.NAME == "McCain")
-sum(pres08$LAST.NAME == "McCain" & pres08$STATE=="Alabama")
-pres08[pres08$LAST.NAME == "McCain",]
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-pres12[1,]
-table(unique(pres12))
-table(unique(pres12$x))
-table(unique(pres12$X))
-substr
-gsub
-gsub(pres12[1,3])
-pres12[1,]
-pres12$Obama.vote[1]
-dem12 = as.character(pres12$Obama.vote)
-dem12[1]
-dem12 = sapply(dem12,function(x){gsub(x,",","")})
-dem12[1]
-dem12 = as.character(pres12$Obama.vote)
-gsub(dem12[1],",","")
-?gsub
-gsub(",","",dem12[1])
-dem12 = as.character(pres12$Obama.vote)
-dem12 = as.numeric(sapply(dem12,function(x){gsub(",","",x)}))
-dem12[1]
-hist(dem12)
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-dem12 = as.character(pres12$Obama.vote)
-dem12 = as.numeric(sapply(dem12,function(x){gsub(",","",x)}))
-rep12 = as.character(pres12$Romney.vote)
-rep12 = as.numeric(sapply(rep12,function(x){gsub(",","",x)}))
-plot(rep12,dem12)
-rep12[1]
-pres12[1,]
-table(pres12[,2])
-res12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-table(pres12[,2])
-table(pres12[,1])
-library(XML)
-theurl <- "http://uselectionatlas.org/RESULTS/data.php?year=2008&datatype=national&def=1&f=0&off=0&elect=0"
-tables <- readHTMLTable(theurl)
-tables[1,]
-dim(tables)
-tables[1]
-tables
-n.rows <- unlist(lapply(tables, function(t) dim(t)[1]))
-n.rows
-library(slidify)
-?author
-setwd("~/Documents/Work/teaching/2013/coursera/")
-ls()
-list.files()
-author("gettingStarted")
-slidify("gettingStarted")
-ls()
-list.files()
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("~/Documents/Work/teaching/2013/coursera/")
-setwd("week1/gettingHelp/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
diff --git a/005representingDataR/assets/.DS_Store b/005representingDataR/assets/.DS_Store
deleted file mode 100644
index b312975..0000000
Binary files a/005representingDataR/assets/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/.DS_Store b/005representingDataR/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/005representingDataR/libraries/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/frameworks/.DS_Store b/005representingDataR/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/005representingDataR/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/frameworks/io2012/.DS_Store b/005representingDataR/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/005representingDataR/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/frameworks/io2012/default/.DS_Store b/005representingDataR/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/005representingDataR/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/frameworks/io2012/default/js/.DS_Store b/005representingDataR/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/005representingDataR/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/highlighters/.DS_Store b/005representingDataR/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/005representingDataR/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/005representingDataR/libraries/highlighters/highlight.js/.DS_Store b/005representingDataR/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/005representingDataR/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/.DS_Store b/006simulationBasics/.DS_Store
deleted file mode 100644
index e71ca07..0000000
Binary files a/006simulationBasics/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/.Rhistory b/006simulationBasics/.Rhistory
deleted file mode 100644
index 7955cdc..0000000
--- a/006simulationBasics/.Rhistory
+++ /dev/null
@@ -1,437 +0,0 @@
-text(5.5,5.5,teamName1,col ="red", family = 'Helvetica', cex = cx/1.5)
-}else{
-text(5.5,5.5,teamName2,col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1,"Accuracy"))
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2,"Accuracy"))
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-makeVideo(teamName1="GregColin",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"GregColin"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-makeVideo(teamName1="GregColin",teamName2="JoelDan",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"GregColin"],
-team2Pred=nonPCA[battleSample,"JoelDan"],testImages=as.matrix(battleData[battleSample,-1]))
-names(PCA)
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="GregColinPCA",teamName2="JonPhoebe",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"GregColinPCA"],
-team2Pred=PCA[battleSample,"JonPhoebe"],testImages=as.matrix(battleData[battleSample,-1]))
-head(PCA)
-names(PCA)
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="WesJoeEm",teamName2="CalebChey",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"WesJoeEm"],
-team2Pred=PCA[battleSample,"CalebChey"],testImages=as.matrix(battleData[battleSample,-1]))
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="JonPhoebe",teamName2="GregColin",
-trueLabels=battleData[battleSample,1],team1Pred=PCA[battleSample,"JonPhoebe"],
-team2Pred=nonPCA[battleSample,"GregColin"],testImages=as.matrix(battleData[battleSample,-1]))
-displayTeams <- function(teamName1="The Jets",teamName2="The Sharks",cx=5,nFrames=10){
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(1,1,1,2,2,2),byrow=T,nrow=2))
-colRampWhite = colorRampPalette(c("black","white"))(nFrames)
-colRampRed= colorRampPalette(c("black","red"))(nFrames)
-colRampBlue= colorRampPalette(c("black","blue"))(nFrames)
-for(i in 1:nFrames){
-Team1
-plot(1:10,1:10,type="n")
-text(5.5,5.5,teamName1,col = colRampRed[i], family = 'Helvetica', cex = cx)
-Team2
-plot(1:10,1:10,type="n",main="Versus",cex.main=3)
-text(5.5,5.5,teamName2,col = colRampBlue[i], family = 'Helvetica', cex = cx)
-Sys.sleep(2/nFrames)
-}
-predictionMatch <- function(teamName1,teamName2,trueLabels,testImages,team1Pred,team2Pred,cx=8){
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(2,1,4,3,0,5),byrow=T,nrow=2))
-for(i in 1:dim(testImages)[1]){
-zz = matrix(testImages[i,],nrow=28)
-image(zz[,ncol(zz):1],main="True Image",xaxt="n",yaxt="n",col=colRampWhite,cex.main=3)
-Sys.sleep(0.2)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1),cex.main=3)
-text(5.5,5.5,team1Pred[i],col ="red", family = 'Helvetica', cex = cx)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste("Accuracy"),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-Sys.sleep(0.2)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2),cex.main=3)
-text(5.5,5.5,team2Pred[i],col ="blue", family = 'Helvetica', cex = cx)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste("Accuracy"),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-Sys.sleep(0.4)
-}
-par(mar=c(0,0,4,0),bg="black",col.main="white")
-layout(matrix(c(1,1,1,2,0,3),byrow=T,nrow=2))
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main="Winner",cex.main=3)
-team1winner = cumMean(trueLabels ==team1Pred) > cumMean(trueLabels==team2Pred)
-if(team1winner){
-text(5.5,5.5,teamName1,col ="red", family = 'Helvetica', cex = cx/1.5)
-}else{
-text(5.5,5.5,teamName2,col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName1),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team1Pred[1:i]),"%"),col ="red", family = 'Helvetica', cex = cx/1.5)
-plot(1:10,1:10,type="n",xaxt="n",yaxt="n",main=paste(teamName2),cex.main=3)
-text(5.5,5.5,paste(cumMean(trueLabels[1:i] == team2Pred[1:i]),"%"),col ="blue", family = 'Helvetica', cex = cx/1.5)
-}
-cumMean = function(x){
-return(round(mean(x)*100,1))
-}
-makeVideo <- function(teamName1,teamName2,trueLabels,team1Pred,team2Pred,testImages){
-displayTeams(teamName1=teamName1,teamName2=teamName2)
-predictionMatch(teamName1=teamName1,teamName2=teamName2,
-trueLabels=trueLabels,team1Pred=team1Pred,
-team2Pred=team2Pred,testImages=testImages)
-}
-nonPCA = read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/nonPCAbattle.csv",header=T)
-PCA = read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/PCAbattle.csv",header=T)
-battleData= read.csv("~/Dropbox/Leah/Teaching/SM439/SM439/Project2/battleData.csv",header=T)
-battleSample = sample(1:3000,size=5,replace=FALSE)
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-battleSample = sample(1:3000,size=100,replace=FALSE)
-makeVideo(teamName1="JoelDan",teamName2="SarahMax",
-trueLabels=battleData[battleSample,1],team1Pred=nonPCA[battleSample,"JoelDan"],
-team2Pred=nonPCA[battleSample,"SarahMax"],testImages=as.matrix(battleData[battleSample,-1]))
-windowsFonts()
-?par
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4
-dim(pvalueDAta)
-dim(pvalueData)
-pvalueData2 = pvalueData
-load("~/Downloads/pvalueData00-10.rda")
-ls()
-dim(pvalueData)
-pvalueData[1,]
-pvalueData2[1,]
-names(pvalueDAta)
-names(pvalueData)
-names(pvalueData2)
-dim(pvalueData)
-dim(pvalueData2)
-pvalueData2[1,]
-pvalueData2[2,]
-pvalueData2[1,]
-pvalueData[1,]
-oo = match(pvalueData$pubmedID,pvalueData2$pubmedID)
-colnames(pvalueData)
-colnames(pvalueData2)
-oo = match(pvalueData[,3],pvalueData2[,3])
-length(oo)
-oo[1]
-sum(is.na(oo))
-tmp1 = pvalueData[,3]
-tmp2 = pvalueData2[,3]
-tmp1[1]
-tmp2[1]
-tmp2 = as.numeric(tmp2)
-tmp1 = tmp1[order(tmp1)]
-tmp2 = tmp2[order(tmp2)]
-tmp1[1]
-tmp2[1]
-length(tmp1)
-length(tmp2)
-sum(tmp1[1:15653] == tmp2[1:15653])
-tmp1[13427:13428]
-tmp1[13427:13429]
-tmp2[13427:13429]
-tmp1[13425:13429]
-tmp2[13425:13429]
-pvalueData[1,]
-pvalueData[pvalueData[,3]==19549972, ]
-pvalueData2[pvalueData2[,3]=="19549972", ]
-pvalueData2[pvalueData2[,3]=="19549973", ]
-tmp2[13425:13429]
-tmp2[13424:13429]
-tmp1[13424:13429]
-sum(tmp1[1:13424] == tmp2[1:13424])
-sum(tmp1[1:11940] == tmp2[1:11940])
-plot(tmp1,tmp2)
-length(tmp2)
-plot(tmp1,tmp2[1:15653])
-t1 = table(tmp1)
-t2 = table(tmp2)
-t1[1]
-t2[1]
-sum(t1 == t2)
-length(t2)
-length(t1)
-setdiff(names(t1),names(t2))
-sum(t1 == t2[1:5323])
-oo = match(names(t1),names(t2))
-length(oo)
-oo[1]
-oo = match(names(t2),names(t1))
-length(oo)
-sum(is.na(oo))
-which(is.na(oo))
-length(names(t2))
-t2[3097]
-sum(t2)
-dim(pvalueData)
-dim(pvalueData2)
-pvalueData2[pvalueData2[,3]=="16421237",]
-pvalueData3 = pvalueData2[-which(pvalueData2[,3]=="16421237"),]
-dim(pvalueData3)
-dim(pvalueData)
-tmp1 = pvalueData3[,3]
-tmp2 = pvalueData[,3]
-length(tmp1)
-length(tmp2)
-tmp1[1]
-tmp2[1]
-tmp1 = as.numeric(tmp1)
-tmp1 = tmp1[order(tmp1)]
-tmp2 = tmp2[order(tmp2)]
-tmp1[1]
-tmp2[1]
-plot(tmp1,tmp2)
-sum(tmp1==tmp2)
-mean(tmp1==tmp2)
-tmp1 = pvalueData3[,3]#
-tmp2 = pvalueData[,3]
-tmp1[1]
-tmp1 = as.numeric(tmp1)
-colnames(pvalueData3)
-pvals1 = as.numeric(pvalueData3[,1])
-pvals2 = as.numeric(pvalueData[,1])
-pvals1[1]
-pvals2[1]
-pvals1 = pvals1[order(tmp1)]
-pvals2 = pvals1[order(tmp2)]
-sum(pvals1==pvals2)
-length(pvals1)
-ne = which(pvals1!=pvals2)
-ne[1]
-pvals1 = as.numeric(pvalueData3[,1])
-pvals2 = as.numeric(pvalueData[,1])
-pvals1 = pvals1[order(tmp1)]
-pvals2 = pvals2[order(tmp2)]
-sum(pvals1==pvals2)
-length(pvals1)
-mean(pvals1==pvals2)
-mean((pvals1 - pvals2) < 1e-3)
-mean((pvals1 - pvals2) < 1e-5)
-mean(abs(pvals1 - pvals2) < 1e-5 )
-dim(pvalueData)
-dim(pvalueData3)
-rm(list=ls())
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-dim(pvalueData)
-rm(list=ls())
-pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueDataTest.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueData.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}#
-## These come from the paper Pubmed ID = 20876667 and are reports from
## a GWAS. Update some P-values that are incorrectly scraped because of
## variation in scientific notation.

pvalueData[pvalueData[,1] == 10,1] = 10e-7
pvalueData = pvalueData[-1,]

## These come from the Lancet, with missed periods in the P-values

pvalueData[13392,1] = 0.003
pvalueData[13413,1] = 0.014
pvalueData[13414,1] = 0.004

## This one comes from the Lancet too, where an incorrect P-value is grabbed.

pvalueData = pvalueData[-14674,]#
-# Remove rows with P-values that are 
pvalueData = pvalueData[!is.na(pvalueData[,1]),]

# This one for some reason replaced a period with "small middle dot"

pvalueData[which(pvalueData[,3] == 11943262),1] = 1e-4

# This one has a <<< in the P-value definition
pvalueData = pvalueData[-which(pvalueData[,3]=="16421237"),] #
-save(pvalueData,npapers,file="pvalueData.rda")
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1
-]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]
-?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}#
-## Run the above functions over a specified set of journals and years
## to obtain P-values#
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-Functions to scrape P-values from Pubmed abstracts
# Date: 7-1-12
# Copyright (C) 2011 Jeffrey T. Leek (http://www.biostat.jhsph.edu/~jleek/contact.html) and Leah R. Jager
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details, see <http://www.gnu.org/licenses/>.
#
#
#    Note: These functions were written on a Mac and may have difficulties when
#          read on windows machines. 
#
#########################################################################################
-library(RCurl)
library(XML)
library(tm)#
-# A function to get all abstracts and pubmed ids for papers from the journal "journaltitle" in the year "year"
# by scraping the Pubmed API.

getAbstractsPmids = function(journaltitle,year){
# esearch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
q = paste("db=pubmed&term=",gsub(" ","+",journaltitle),"[ta]+AND+",year,"[dp]&usehistory=y",sep="")
esearch <- xmlTreeParse(getURL(paste(url, q, sep="")), useInternal = T)
webenv  <- xmlValue(getNodeSet(esearch, "//WebEnv")[[1]])
key     <- xmlValue(getNodeSet(esearch, "//QueryKey")[[1]])

# efetch
url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
q   <- "db=pubmed&retmode=xml&rettype=abstract"
efetch <- xmlTreeParse(getURL(paste(url, q, "&WebEnv=", webenv, "&query_key=", key, sep="")), useInternal = T)
r = xmlRoot(efetch)

n = xmlSize(r)
abstracts = pmid = titles = rep(NA,n)
for(i in 1:n){abstracts[i] =  xmlValue(r[[i]][[1]][["Article"]][["Abstract"]]); pmid[i] = xmlValue(r[[i]][[1]][["PMID"]]); titles[i] = xmlValue(r[[i]][[1]][["Article"]][["ArticleTitle"]]) }
return(list(abstracts=abstracts,pmid=pmid,titles=titles))
}#
-#A function to remove trailing zeros from the P-value strings
removeTrailing = function(string){
  while(length(grep("[0-9]",strsplit(string,"")[[1]][nchar(string)])) == 0){
    string = substr(string,1,(nchar(string)-1))
  }
  return(string)
}#
-# A function to convert the scientific notation used by journals into
# numeric values that can be analyzed. 
convertScientific = function(string){
  if(length(grep("[[:punct:]][[:space:]]",string))>0){
    string = strsplit(string,"[[:punct:]][[:space:]]")[[1]][1]
    string = removeTrailing(string)
  }
  if(length(grep("[×x]",string))>0){
    string = gsub("[:space:]","",string)
    tmp1 = as.numeric(strsplit(string,"[×x]")[[1]][1])
    tmp2 = as.numeric(strsplit(strsplit(string,"[×x]")[[1]][2],"[−-]")[[1]][2])
    return(tmp1*10^(-tmp2))
  }else{
    return(as.numeric(string))
  }
}#
-# A function to scrape the P-values from a vector of abstracts with corresponding
# pubmed ids

getPvalues = function(abstract,pmid){
  pvalues = numeric(0)
  trunc = numeric(0)
  ids = numeric(0)

  # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?[<≤]",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?[<≤]")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,1)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }

   # Get the truncated p-values
  ind = grep("[Pp][[:space:]]?=",abstract)
  for(i in 1:length(ind)){
    tmp = strsplit(abstract[ind[i]],"[[:space:](][Pp][[:space:]]?=")[[1]]
    n = length(tmp)
    for(j in 1:n){
      if(length(grep("[.0123456789]",substr(tmp[j],1,2))) > 0){
        if(length(grep("[A-Z]",substr(tmp[j],1,1)))>0){next;}
        tmp2 = strsplit(tmp[j],"[^[:punct:][:space:][:digit:]x[:space:]]")[[1]][1]
        tmp2 = removeTrailing(tmp2)
        tmp2 = gsub(" ","",tmp2)
        tmp2 = convertScientific(tmp2)
        pvalues = c(pvalues,as.numeric(tmp2))
        trunc = c(trunc,0)
        ids = c(ids,pmid[ind[i]])
      }
    }
  }
  return(list(pvalues=pvalues,ids=ids,trunc=trunc))
}
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-tmpData
-i
-j
-tmpData = getAbstractsPmids(journals[i],years[j])
-while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
-journals = c("JAMA","New England Journal of Medicine","BMJ","American Journal of Epidemiology","Lancet")
years = 2000:2010

pvalueData = matrix(NA,nrow=1,ncol=6)
colnames(pvalueData) = c("pvalue","pvalueTruncated","pubmedID","year","abstract","title")

npapers = matrix(NA,nrow=length(journals),ncol=length(years))

for(i in 1:length(journals)){
  for(j in 1:length(years)){
    cat(journals[i]); cat(" "); cat(years[j]); cat(" "); 
    tmpData = getAbstractsPmids(journals[i],years[j])
    while(length(tmpData$abstracts) ==1 & is.na(tmpData$abstracts[1])){tmpData = getAbstractsPmids(journals[i],years[j])}
    cat("Downloaded"); cat(" ");
    npapers[i,j] = length(tmpData$abstracts)
    tmpOut = getPvalues(tmpData$abstracts,tmpData$pmid)#
-nPvalues = length(tmpOut$pvalues)
    aa = match(tmpOut$ids,tmpData$pmid)#
-tmpMatrix = cbind(tmpOut$pvalues,tmpOut$trunc,as.numeric(tmpOut$ids),rep(years[j],nPvalues),tmpData$abstracts[aa],tmpData$titles[aa])
    rownames(tmpMatrix) = rep(journals[i],nPvalues)
    pvalueData = rbind(pvalueData,tmpMatrix)
    cat("Done\n")
  }
}
-barplot(c(1,1,-3))
-?barplot
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12[1,]
-pres08 = read.csv("~/Desktop/2008pres.csv")
-pres08[1,]
-sum(pres12$FIPS == 0)
-table(pres12$X[pres12$FIPS==0,])
-table(pres12$X[pres12$FIPS==0])
-pres12[pres12$X=="OK",]
-pres12 = pres12[pres12$FIPS==0,]
-dim(pres12)
-pres12[1,]
-pres12[2,]
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12[1:10,]
-pres12[21:30,]
-pres12[50:100,]
-pres12 = pres12[pres12$FIPS==0,]
-length(unique(pres12$X))
-which.max(pres12$X == "OK")
-which(pres12$X == "OK")
-pres12[c(36,37)]
-pres12[c(36,37),]
-pres12[1,]
-pres12[1,5]
-pres12[1,4]
-as.numeric(pres12[1,4])
-as.numeric(as.character(pres12[1,4])
-)
-as.numeric(as.character(pres12[1,4]))
-pres08[1,]
-sum(pres08$LAST.NAME == "McCain")
-sum(pres08$LAST.NAME == "McCain" & pres08$STATE=="Alabama")
-pres08[pres08$LAST.NAME == "McCain",]
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-pres12[1,]
-table(unique(pres12))
-table(unique(pres12$x))
-table(unique(pres12$X))
-substr
-gsub
-gsub(pres12[1,3])
-pres12[1,]
-pres12$Obama.vote[1]
-dem12 = as.character(pres12$Obama.vote)
-dem12[1]
-dem12 = sapply(dem12,function(x){gsub(x,",","")})
-dem12[1]
-dem12 = as.character(pres12$Obama.vote)
-gsub(dem12[1],",","")
-?gsub
-gsub(",","",dem12[1])
-dem12 = as.character(pres12$Obama.vote)
-dem12 = as.numeric(sapply(dem12,function(x){gsub(",","",x)}))
-dem12[1]
-hist(dem12)
-pres12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-dem12 = as.character(pres12$Obama.vote)
-dem12 = as.numeric(sapply(dem12,function(x){gsub(",","",x)}))
-rep12 = as.character(pres12$Romney.vote)
-rep12 = as.numeric(sapply(rep12,function(x){gsub(",","",x)}))
-plot(rep12,dem12)
-rep12[1]
-pres12[1,]
-table(pres12[,2])
-res12 = read.csv("~/Desktop/2012-pres.csv")
-pres12 = pres12[pres12$FIPS==0,]
-table(pres12[,2])
-table(pres12[,1])
-library(XML)
-theurl <- "http://uselectionatlas.org/RESULTS/data.php?year=2008&datatype=national&def=1&f=0&off=0&elect=0"
-tables <- readHTMLTable(theurl)
-tables[1,]
-dim(tables)
-tables[1]
-tables
-n.rows <- unlist(lapply(tables, function(t) dim(t)[1]))
-n.rows
-library(slidify)
-?author
-setwd("~/Documents/Work/teaching/2013/coursera/")
-ls()
-list.files()
-author("gettingStarted")
-slidify("gettingStarted")
-ls()
-list.files()
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("~/Documents/Work/teaching/2013/coursera/")
-setwd("week1/gettingHelp/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
diff --git a/006simulationBasics/assets/.DS_Store b/006simulationBasics/assets/.DS_Store
deleted file mode 100644
index a5027ca..0000000
Binary files a/006simulationBasics/assets/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/.DS_Store b/006simulationBasics/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/006simulationBasics/libraries/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/frameworks/.DS_Store b/006simulationBasics/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/006simulationBasics/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/frameworks/io2012/.DS_Store b/006simulationBasics/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/006simulationBasics/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/frameworks/io2012/default/.DS_Store b/006simulationBasics/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/006simulationBasics/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/frameworks/io2012/default/js/.DS_Store b/006simulationBasics/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/006simulationBasics/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/highlighters/.DS_Store b/006simulationBasics/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/006simulationBasics/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/006simulationBasics/libraries/highlighters/highlight.js/.DS_Store b/006simulationBasics/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/006simulationBasics/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/.DS_Store b/007typesOfQuestions/.DS_Store
deleted file mode 100644
index 29cf3af..0000000
Binary files a/007typesOfQuestions/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/.Rhistory b/007typesOfQuestions/.Rhistory
deleted file mode 100644
index 95c1638..0000000
--- a/007typesOfQuestions/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-?symbols
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1),nrow=1),col="gold")
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1),nrow=1),col="gold",add=T)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1,1),nrow=1),col="gold",add=T)
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold")
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-?rect
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runi(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runif(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-rect(xPres-0.5,rep(0,10),xPres+0.5,runif(10,0,1),col=sample(c("blue","red"),size=10,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],rep(0,10),xPres[i]+xWidth[i],runif(10,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],runif(1,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.1*xWidth[i],0,xPres[i]+0.1*xWidth[i],xHeight[i],col="gold")
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample("gold","silver"))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1)
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-?png
-png("xmas.png",height=2*480,width=480)
-<script src="https://gist.github.com/4369771.js"></script>
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-dev.off()
-pvals = runif(10000)
-pvals05 = pvals[pvals < 0.05]
-hist(pvals05)
-data()
-?network
-install.packages("ergm")
-library(ergm)
-?network
-m <- matrix(rbinom(25,1,.4),5,5)
-diag(m) <- 0
-g <- network(m, directed=FALSE)
-summary(g)
-m
-ss = svd(M)
-ss = svd(m)
-plot(ss$v[,1])
-ss$u[,1] %*% t(ss$v[,1])
-ss$d[1]*ss$u[,1] %*% t(ss$v[,1])
-x = 3 asdfa
-setwd("~/Documents/Work/teaching/2013/coursera/")
-setwd("week1/gettingHelp/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("../whatIsData/")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-slidify("index.Rmd")
diff --git a/007typesOfQuestions/assets/.DS_Store b/007typesOfQuestions/assets/.DS_Store
deleted file mode 100644
index 856b1ab..0000000
Binary files a/007typesOfQuestions/assets/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/assets/img/.DS_Store b/007typesOfQuestions/assets/img/.DS_Store
deleted file mode 100644
index 5008ddf..0000000
Binary files a/007typesOfQuestions/assets/img/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/.DS_Store b/007typesOfQuestions/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/007typesOfQuestions/libraries/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/frameworks/.DS_Store b/007typesOfQuestions/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/007typesOfQuestions/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/frameworks/io2012/.DS_Store b/007typesOfQuestions/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/007typesOfQuestions/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/frameworks/io2012/default/.DS_Store b/007typesOfQuestions/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/007typesOfQuestions/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/frameworks/io2012/default/js/.DS_Store b/007typesOfQuestions/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/007typesOfQuestions/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/highlighters/.DS_Store b/007typesOfQuestions/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/007typesOfQuestions/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/007typesOfQuestions/libraries/highlighters/highlight.js/.DS_Store b/007typesOfQuestions/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/007typesOfQuestions/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/.DS_Store b/008sourcesOfDataSets/.DS_Store
deleted file mode 100644
index c5900c1..0000000
Binary files a/008sourcesOfDataSets/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/.Rhistory b/008sourcesOfDataSets/.Rhistory
deleted file mode 100644
index 4eda0f2..0000000
--- a/008sourcesOfDataSets/.Rhistory
+++ /dev/null
@@ -1,512 +0,0 @@
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-symbols(runif(4,-4,4),rep(2,4),circles=rep(0.1,4),fg=sample(c("blue","red"),size=4,replace=T),add=T)
-?symbols
-symbols(x=runif(4,-4,4),y=rep(2,4),circles=rep(0.01,4),bg=sample(c("blue","red"),size=4,replace=T),add=T)
-rep(0.01,4)
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-4,4),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-?symbols
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1),nrow=1),col="gold")
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1),nrow=1),col="gold",add=T)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-symbols(0,7.5,stars=matrix(c(1,1,1,1,1,1),nrow=1),col="gold",add=T)
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold")
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-?rect
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runi(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Add some presents
-xPres = runif(3,-4.5,4.5)
-rect(xPres-0.5,rep(0,3),xPres+0.5,runif(3,0,1),col=sample(c("blue","red"),size=3,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-rect(xPres-0.5,rep(0,10),xPres+0.5,runif(10,0,1),col=sample(c("blue","red"),size=10,replace=T))
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],rep(0,10),xPres[i]+xWidth[i],runif(10,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],runif(1,0,1),col=sample(c("blue","red"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.1*xWidth[i],0,xPres[i]+0.1*xWidth[i],xHeight[i],col="gold")
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample("gold","silver"))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1)
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","silver"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-?png
-png("xmas.png",height=2*480,width=480)
-<script src="https://gist.github.com/4369771.js"></script>
-# Make the canvas
-plot(1:10,1:10,xlim=c(-5,5),ylim=c(0,10),type="n",xlab="",ylab="",xaxt="n",yaxt="n")
-# Make the branches
-rect(-1,0,1,2,col="tan3",border="tan4",lwd=3)
-polygon(c(-5,0,5),c(2,4,2),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-4,0,4),c(3.5,5.5,3.5),col="palegreen4",border="palegreen3",lwd=3)
-polygon(c(-3,0,3),c(5,6.5,5),col="palegreen3",border="palegreen4",lwd=3)
-polygon(c(-2,0,2),c(6.25,7.5,6.25),col="palegreen4",border="palegreen3",lwd=3)
-#Add some ornaments
-points(x=runif(4,-5,5),y=rep(2,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-4,4),y=rep(3.5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-3,3),y=rep(5,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(x=runif(4,-2,2),y=rep(6.25,4),col=sample(c("blue","red"),size=4,replace=T),cex=3,pch=19)
-points(0,7.5,pch=8,cex=5,col="gold",lwd=3)
-# Add some presents
-xPres = runif(10,-4.5,4.5)
-xWidth = runif(10,0.1,0.5)
-xHeight=runif(10,0,1)
-for(i in 1:10){
-rect(xPres[i]-xWidth[i],0,xPres[i]+xWidth[i],xHeight[i],col=sample(c("blue","red"),size=1))
-rect(xPres[i]-0.2*xWidth[i],0,xPres[i]+0.2*xWidth[i],xHeight[i],col=sample(c("gold","grey87"),size=1))
-}
-dev.off()
-pvals = runif(10000)
-pvals05 = pvals[pvals < 0.05]
-hist(pvals05)
-data()
-?network
-install.packages("ergm")
-library(ergm)
-?network
-m <- matrix(rbinom(25,1,.4),5,5)
-diag(m) <- 0
-g <- network(m, directed=FALSE)
-summary(g)
-m
-ss = svd(M)
-ss = svd(m)
-plot(ss$v[,1])
-ss$u[,1] %*% t(ss$v[,1])
-ss$d[1]*ss$u[,1] %*% t(ss$v[,1])
-setwd("~/Dropbox/Jeff/teaching/2013/coursera/")
-setwd("week1/001courseLogistics/")
-slidify("index.Rmd")
-library(slidify)
-slidify("index.Rmd")
-browseURL("index.html")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-setwd("../002gettingHelp/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-setwd("../003whatIsData/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-setwd("../004representingData/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-setwd("../005representingDataR/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-setwd("../006simulationBasics/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-x = seq(0,5,length=6)
-x
-slidify("index.Rmd")
-?dnorm
-x = seq(0,10,by=1)
-x
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("../007structureOfADataAnalysis/")
-setwd("../")
-slidify("index.Rmd")
-setwd("007structureOfADataAnalysis1/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-slidify("index.Rmd")
-setwd("../008structureOfADataAnalysis2/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-browseURL("index.html")
-getwd()
-setwd("~/Dropbox/Jeff/teaching/2013/coursera/week1/008structureOfADataAnalysis2/")
-slidify("index.Rmd")
-browseURL("index.html")
-setwd("../007structureOfADataAnalysis1/")
-slidify("index.Rmd")
-browseURL("index.html")
-setwd("../007typesOfQuestions/")
-slidify("index.Rmd")
-browseURL("index.html")
-slidify("index.Rmd")
-setwd("../008structureOfADataAnalysis1/")
-slidify("index.Rmd")
-browseURL("index.html")
-setwd("../008sourcesOfDataSets/")
-slidify("index.Rmd")
-browseURL("index.Rmd")
-browseURL("index.html")
diff --git a/008sourcesOfDataSets/assets/.DS_Store b/008sourcesOfDataSets/assets/.DS_Store
deleted file mode 100644
index ab559cc..0000000
Binary files a/008sourcesOfDataSets/assets/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/assets/img/.DS_Store b/008sourcesOfDataSets/assets/img/.DS_Store
deleted file mode 100644
index b9dba98..0000000
Binary files a/008sourcesOfDataSets/assets/img/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/.DS_Store b/008sourcesOfDataSets/libraries/.DS_Store
deleted file mode 100644
index 2b852ca..0000000
Binary files a/008sourcesOfDataSets/libraries/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/frameworks/.DS_Store b/008sourcesOfDataSets/libraries/frameworks/.DS_Store
deleted file mode 100644
index 1616e9a..0000000
Binary files a/008sourcesOfDataSets/libraries/frameworks/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/frameworks/io2012/.DS_Store b/008sourcesOfDataSets/libraries/frameworks/io2012/.DS_Store
deleted file mode 100644
index 397ac06..0000000
Binary files a/008sourcesOfDataSets/libraries/frameworks/io2012/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/frameworks/io2012/default/.DS_Store b/008sourcesOfDataSets/libraries/frameworks/io2012/default/.DS_Store
deleted file mode 100644
index 7f3dbc0..0000000
Binary files a/008sourcesOfDataSets/libraries/frameworks/io2012/default/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/frameworks/io2012/default/js/.DS_Store b/008sourcesOfDataSets/libraries/frameworks/io2012/default/js/.DS_Store
deleted file mode 100644
index 49e525c..0000000
Binary files a/008sourcesOfDataSets/libraries/frameworks/io2012/default/js/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/highlighters/.DS_Store b/008sourcesOfDataSets/libraries/highlighters/.DS_Store
deleted file mode 100644
index 78059f8..0000000
Binary files a/008sourcesOfDataSets/libraries/highlighters/.DS_Store and /dev/null differ
diff --git a/008sourcesOfDataSets/libraries/highlighters/highlight.js/.DS_Store b/008sourcesOfDataSets/libraries/highlighters/highlight.js/.DS_Store
deleted file mode 100644
index 132bdd4..0000000
Binary files a/008sourcesOfDataSets/libraries/highlighters/highlight.js/.DS_Store and /dev/null differ