Merge pull request #72 from rpact-com/dev/4.1.1

README updated
rpact-com · Jan 31, 2025 · dd4318f · dd4318f
2 parents a6516fa + 863a6c0
commit dd4318f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rpact
 Title: Confirmatory Adaptive Clinical Trial Design and Analysis
-Version: 4.1.1.9279
-Date: 2025-01-27
+Version: 4.1.1.9280
+Date: 2025-01-28
 Authors@R: c(
 	person(
 		given = "Gernot", 

diff --git a/R/class_summary.R b/R/class_summary.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8508 $
-## |  Last changed: $Date: 2025-01-24 09:01:34 +0100 (Fr, 24 Jan 2025) $
+## |  File version: $Revision: 8518 $
+## |  Last changed: $Date: 2025-01-29 15:42:08 +0100 (Mi, 29 Jan 2025) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -1008,7 +1008,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         }
     }
 
-    if (any(is.nan(formattedValue)) || any(trimws(formattedValue) == "NaN")) {
+    if (any(is.nan(formattedValue), na.rm = TRUE) || any(trimws(formattedValue) == "NaN", na.rm = TRUE)) {
         formattedValue[is.nan(formattedValue) | trimws(formattedValue) == "NaN"] <- NA_real_
         showNA <- TRUE
     }
@@ -1922,7 +1922,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         if (!.isDelayedInformationEnabled(design = design) &&
                 ((.isTrialDesignInverseNormalOrGroupSequential(design) &&
                     any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) ||
-                    (.isTrialDesignFisher(design) && any(design$alpha0Vec < 1)))) {
+                    (.isTrialDesignFisher(design) && any(design$alpha0Vec < 1, na.rm = TRUE)))) {
             header <- .concatenateSummaryText(
                 header,
                 paste0(ifelse(design$bindingFutility, "binding", "non-binding"), " futility")
@@ -3224,7 +3224,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
     )
 
     if (.isTrialDesignFisher(design)) {
-        if (any(design$alpha0Vec < 1)) {
+        if (any(design$alpha0Vec < 1, na.rm = TRUE)) {
             summaryFactory$addParameter(design,
                 parameterName = "alpha0Vec",
                 parameterCaption = "Futility boundary (separate p-value scale)",
@@ -3233,7 +3233,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
             )
         }
     } else {
-        if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT)) {
+        if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) {
             summaryFactory$addParameter(design,
                 parameterName = "futilityBounds",
                 parameterCaption = .getSummaryParameterCaptionFutilityBounds(design),
@@ -3892,7 +3892,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
                 probsH1$rejectPerStage <- probsH1$rejectPerStage[1:(design$kMax - 1)]
             }
 
-            if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT)) {
+            if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) {
                 if (is.matrix(probsH1$earlyStop)) {
                     probsH1$earlyStop <- matrix(probsH1$earlyStop[1:(design$kMax - 1), ],
                         ncol = ncol(probsH1$earlyStop)
@@ -3983,7 +3983,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE) &&
                 !is.null(designPlan[["futilityPerStage"]]) &&
                 !any(is.na(designPlan[["futilityPerStage"]])) &&
-                any(designPlan$futilityPerStage != 0) && any(designPlan$futilityPerStage > 1e-08)) {
+                any(designPlan$futilityPerStage != 0) && 
+                any(designPlan$futilityPerStage > 1e-08)) {
             summaryFactory$addParameter(designPlan,
                 parameterName = "futilityPerStage",
                 parameterCaption = "Exit probability for futility", # under H1

diff --git a/R/f_core_utilities.R b/R/f_core_utilities.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8473 $
-## |  Last changed: $Date: 2025-01-13 18:47:32 +0100 (Mo, 13 Jan 2025) $
+## |  File version: $Revision: 8518 $
+## |  Last changed: $Date: 2025-01-29 15:42:08 +0100 (Mi, 29 Jan 2025) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 

diff --git a/R/f_design_group_sequential.R b/R/f_design_group_sequential.R
@@ -1038,13 +1038,34 @@ getDesignInverseNormal <- function(...,
         sided = 1L, # C_SIDED_DEFAULT
         informationRates = NA_real_,
         futilityBounds = NA_real_,
-        typeOfDesign = c("OF", "P", "WT", "PT", "HP", "WToptimum", "asP", "asOF", "asKD", "asHSD", "asUser", "noEarlyEfficacy"), # C_DEFAULT_TYPE_OF_DESIGN,
+        typeOfDesign = c(
+            "OF", 
+            "P", 
+            "WT", 
+            "PT", 
+            "HP", 
+            "WToptimum", 
+            "asP", 
+            "asOF", 
+            "asKD", 
+            "asHSD", 
+            "asUser", 
+            "noEarlyEfficacy"), # C_DEFAULT_TYPE_OF_DESIGN,
         deltaWT = NA_real_,
         deltaPT1 = NA_real_,
         deltaPT0 = NA_real_,
-        optimizationCriterion = c("ASNH1", "ASNIFH1", "ASNsum"), # C_OPTIMIZATION_CRITERION_DEFAULT
+        optimizationCriterion = c(
+            "ASNH1", 
+            "ASNIFH1", 
+            "ASNsum"), # C_OPTIMIZATION_CRITERION_DEFAULT
         gammaA = NA_real_,
-        typeBetaSpending = c("none", "bsP", "bsOF", "bsKD", "bsHSD", "bsUser"), # C_TYPE_OF_DESIGN_BS_NONE
+        typeBetaSpending = c(
+            "none", 
+            "bsP", 
+            "bsOF", 
+            "bsKD", 
+            "bsHSD", 
+            "bsUser"), # C_TYPE_OF_DESIGN_BS_NONE
         userAlphaSpending = NA_real_,
         userBetaSpending = NA_real_,
         gammaB = NA_real_,
@@ -1713,13 +1734,34 @@ getDesignGroupSequential <- function(
         sided = 1L, # C_SIDED_DEFAULT
         informationRates = NA_real_,
         futilityBounds = NA_real_,
-        typeOfDesign = c("OF", "P", "WT", "PT", "HP", "WToptimum", "asP", "asOF", "asKD", "asHSD", "asUser", "noEarlyEfficacy"), # C_DEFAULT_TYPE_OF_DESIGN,
+        typeOfDesign = c(
+            "OF", 
+            "P", 
+            "WT", 
+            "PT", 
+            "HP", 
+            "WToptimum", 
+            "asP", 
+            "asOF", 
+            "asKD", 
+            "asHSD", 
+            "asUser", 
+            "noEarlyEfficacy"), # C_DEFAULT_TYPE_OF_DESIGN,
         deltaWT = NA_real_,
         deltaPT1 = NA_real_,
         deltaPT0 = NA_real_,
-        optimizationCriterion = c("ASNH1", "ASNIFH1", "ASNsum"), # C_OPTIMIZATION_CRITERION_DEFAULT
+        optimizationCriterion = c(
+            "ASNH1", 
+            "ASNIFH1", 
+            "ASNsum"), # C_OPTIMIZATION_CRITERION_DEFAULT
         gammaA = NA_real_,
-        typeBetaSpending = c("none", "bsP", "bsOF", "bsKD", "bsHSD", "bsUser"), # C_TYPE_OF_DESIGN_BS_NONE
+        typeBetaSpending = c(
+            "none", 
+            "bsP", 
+            "bsOF", 
+            "bsKD", 
+            "bsHSD", 
+            "bsUser"), # C_TYPE_OF_DESIGN_BS_NONE
         userAlphaSpending = NA_real_,
         userBetaSpending = NA_real_,
         gammaB = NA_real_,

diff --git a/R/f_design_plan_survival.R b/R/f_design_plan_survival.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8416 $
-## |  Last changed: $Date: 2024-11-18 16:13:44 +0100 (Mo, 18 Nov 2024) $
+## |  File version: $Revision: 8518 $
+## |  Last changed: $Date: 2025-01-29 15:42:08 +0100 (Mi, 29 Jan 2025) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -1512,7 +1512,7 @@ NULL
     }
 
     if (!is.null(designCharacteristics$futilityProbabilities) &&
-            any(designPlan$.design$futilityBounds != C_FUTILITY_BOUNDS_DEFAULT)) {
+            any(designPlan$.design$futilityBounds != C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) {
         designPlan$futilityPerStage <- matrix(designCharacteristics$futilityProbabilities,
             nrow = designPlan$.design$kMax - 1
         )

diff --git a/R/f_design_plan_utilities.R b/R/f_design_plan_utilities.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8225 $
-## |  Last changed: $Date: 2024-09-18 09:38:40 +0200 (Mi, 18 Sep 2024) $
+## |  File version: $Revision: 8518 $
+## |  Last changed: $Date: 2025-01-29 15:42:08 +0100 (Mi, 29 Jan 2025) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -243,7 +243,7 @@ NULL
             designPlan$.setParameterType("earlyStop", C_PARAM_GENERATED)
         }
         if (!is.null(sampleSizeSequential$futilityPerStage) &&
-                any(designPlan$.design$futilityBounds != C_FUTILITY_BOUNDS_DEFAULT)) {
+                any(designPlan$.design$futilityBounds != C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) {
             designPlan$futilityPerStage <- matrix(sampleSizeSequential$futilityPerStage,
                 nrow = designPlan$.design$kMax - 1
             )

diff --git a/R/f_quality_assurance.R b/R/f_quality_assurance.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8482 $
-## |  Last changed: $Date: 2025-01-15 16:25:01 +0100 (Mi, 15 Jan 2025) $
+## |  File version: $Revision: 8518 $
+## |  Last changed: $Date: 2025-01-29 15:42:08 +0100 (Mi, 29 Jan 2025) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 

diff --git a/README.Rmd b/README.Rmd
@@ -77,6 +77,11 @@ The documentation is hosted at [www.rpact.org](https://www.rpact.org)
 The vignettes are hosted at
 [www.rpact.org/vignettes](https://www.rpact.org/vignettes/)
 
+## RPACT Connect 
+
+Connecting you to insights, downloads, and premium support:
+[connect.rpact.com](https://connect.rpact.com)
+
 ## The rpact user group
 
 The *rpact project* has an active user group consisting of decision-makers and

diff --git a/README.md b/README.md
@@ -65,6 +65,11 @@ The documentation is hosted at [www.rpact.org](https://www.rpact.org)
 The vignettes are hosted at
 [www.rpact.org/vignettes](https://www.rpact.org/vignettes/)
 
+## RPACT Connect 
+
+Connecting you to insights, downloads, and premium support:
+[connect.rpact.com](https://connect.rpact.com)
+
 ## The rpact user group
 
 The *rpact project* has an active user group consisting of

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,4 +1,19 @@
 url: https://rpact-com.github.io/rpact/
+
 template:
   bootstrap: 5
+  includes:
+    in_header: |
+      <meta name="keywords" content="rpact, adaptive designs, clinical trials, simulation, analysis, rstats, Shiny, r-project, R package"/>
+      <link href="reference/figures/favicon.ico" rel="icon"/>
+      <link href="reference/figures/favicon.ico" rel="apple-touch-icon"/>
+      <link href="reference/figures/favicon.ico" rel="shortcut icon" type="image/vnd.microsoft.icon"/>
 
+home:
+  links:
+  - text: RPACT Connect
+    href: https://connect.rpact.com
+  - text: RPACT Cloud
+    href: https://cloud.rpact.com
+  - text: rpact R package website
+    href: https://www.rpact.org
diff --git a/inst/doc/rpact_getting_started.html b/inst/doc/rpact_getting_started.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Friedrich Pahlke and Gernot Wassmer" />
 
-<meta name="date" content="2025-01-24" />
+<meta name="date" content="2025-01-28" />
 
 <title>Getting started with rpact</title>
 
@@ -239,7 +239,7 @@
 
 <h1 class="title toc-ignore">Getting started with rpact</h1>
 <h4 class="author">Friedrich Pahlke and Gernot Wassmer</h4>
-<h4 class="date">2025-01-24</h4>
+<h4 class="date">2025-01-28</h4>
 
 
 

diff --git a/man/figures/favicon.ico b/man/figures/favicon.ico