Merge pull request #185 from pepaaran/master

Last changes for CRAN submission
geco-bern · Oct 30, 2023 · 33d26a8 · 33d26a8
2 parents aae2737 + 9c1234b
commit 33d26a8
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 4.4
-Date: 2023-10-12 11:08:56 UTC
-SHA: 8c228455a5dd87a4cb749a9bf502d5b5238cfd0a
+Date: 2023-10-30 09:56:10 UTC
+SHA: 50aa48c8f7cb621dcd99b77ccd6ea6d8e8ca13ba
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,6 +20,18 @@ Authors@R: c(
                email = "[email protected]",
                comment = c(ORCID = "0009-0006-7176-2311"),
                role = c("aut")),
+            person(
+               family = "Marqués",
+               given = "Laura",
+               email = "[email protected]",
+               comment = c(ORCID = "0000-0002-3593-5557"),
+               role = c("ctb")),
+            person(
+               family = "Weng",
+               given = "Ensheng",
+               email = "[email protected]",
+               comment = c(ORCID = "0000-0002-1858-4847"),
+               role = c("ctb")),
             person(given = "Geocomputation and Earth Observation, University of Bern",
                 role = c("cph", "fnd"))
            )

diff --git a/R/calib_sofun.R b/R/calib_sofun.R
@@ -44,7 +44,6 @@
 #' @import GenSA BayesianTools
 #' 
 #' @examples
-#' \donttest{
 #' # Fix model parameters that won't be calibrated
 #' params_fix <- list(
 #'   kphio_par_a        = 0,
@@ -84,7 +83,6 @@
 #'    par_fixed = params_fix,
 #'    targets = c("gpp")
 #'  )
-#' }
 
 calib_sofun <- function(
     drivers,

diff --git a/R/cost_likelihood_pmodel.R b/R/cost_likelihood_pmodel.R
@@ -51,7 +51,6 @@
 #' @export
 #' 
 #' @examples
-#' \donttest{
 #' # Compute the likelihood for a set of 
 #' # model parameter values involved in the
 #' # temperature dependence of kphio 
@@ -71,7 +70,6 @@
 #'   kc_jmax            = 0.41
 #'  )
 #' )
-#' }
 
 cost_likelihood_pmodel <- function(
     par,   # model parameters & error terms for each target

diff --git a/R/cost_rmse_pmodel.R b/R/cost_rmse_pmodel.R
@@ -48,7 +48,6 @@
 #' @export
 #' 
 #' @examples
-#' \donttest{
 #' # Compute RMSE for a set
 #' # of model parameter values
 #' # and example data
@@ -66,7 +65,6 @@
 #'   kc_jmax            = 0.41
 #'  )
 #' )
-#' }
 
 cost_rmse_pmodel <- function(
     par,  # ordered vector of model parameters

diff --git a/R/init_dates_dataframe.R b/R/init_dates_dataframe.R
@@ -27,10 +27,8 @@
 #' @export
 #'
 #' @examples
-#' \donttest{
 #'  ddf <- init_dates_dataframe( 2000, 2003, startmoy=1, startdoy=1,
 #'   freq="days", endmoy=12, enddom=31, noleap=FALSE )
-#' }
 
 init_dates_dataframe <- function(
   yrstart,

diff --git a/R/run_pmodel_f_bysite.R b/R/run_pmodel_f_bysite.R
@@ -130,7 +130,6 @@
 #' @useDynLib rsofun
 #'
 #' @examples
-#' \donttest{
 #' # Define model parameter values from previous work
 #' params_modl <- list(
 #'   kphio              = 0.04998,    # setup ORG in Stocker et al. 2020 GMD
@@ -153,7 +152,6 @@
 #'   forcing = p_model_drivers$forcing[[1]],
 #'   params_modl = params_modl
 #'  )
-#' }
 
 run_pmodel_f_bysite <- function(
   sitename,

diff --git a/R/runread_biomee_f.R b/R/runread_biomee_f.R
@@ -22,7 +22,8 @@
 #' # Example BiomeE model run
 #' 
 #' mod_output <- runread_biomee_f(
-#'   drivers = biomee_gs_leuning_drivers)
+#'   drivers = biomee_gs_leuning_drivers
+#' )
 #' }
 
 runread_biomee_f <- function(

diff --git a/R/runread_pmodel_f.R b/R/runread_pmodel_f.R
@@ -77,7 +77,6 @@
 #' exactly replicated.
 #' 
 #' @examples
-#' \donttest{
 #' # Define model parameter values from previous work
 #' params_modl <- list(
 #'   kphio              = 0.04998,    # setup ORG in Stocker et al. 2020 GMD
@@ -95,7 +94,6 @@
 #' output <- rsofun::runread_pmodel_f(
 #'   drivers = rsofun::p_model_drivers,
 #'   par = params_modl)
-#' }
 
 runread_pmodel_f <- function(
   drivers,

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,18 +1,10 @@
 Dear CRAN team,
 
 This is the re-submission of the {rsofun} package. We have addressed the following
-concerns voiced by Benjamin Altman:
-
-- Corrected the software naming in package title and description.
-- Added a \value field to all the exported functions, explaining the object returned
-  by each function.
-- Removed \dontrun statements in the documentation examples, now \donttest
-  is used for examples that have long runtimes.
-- Included license and copyright statements in a COPYING file. The original authors
-  of the software borrowed for this package were contacted and permissions to use
-  parts of their code were discussed, as well as the copyright and license that
-  accompany their code. The direct authors of this package are listed in the
-  DESCRIPTION file.
+concerns flagged by the automatic checks:
+
+- Wrapped examples running the BiomeE model in \donttest because they took 16 sec to run in the Windows pre-test. 
+- Reviewed DESCRIPTION file for misspelled words. The NOTE in the pre-tests is a false positive.
 
 ---
 

diff --git a/man/calib_sofun.Rd b/man/calib_sofun.Rd
diff --git a/man/cost_likelihood_pmodel.Rd b/man/cost_likelihood_pmodel.Rd
diff --git a/man/cost_rmse_pmodel.Rd b/man/cost_rmse_pmodel.Rd
diff --git a/man/init_dates_dataframe.Rd b/man/init_dates_dataframe.Rd
diff --git a/man/run_pmodel_f_bysite.Rd b/man/run_pmodel_f_bysite.Rd
diff --git a/man/runread_biomee_f.Rd b/man/runread_biomee_f.Rd
diff --git a/man/runread_pmodel_f.Rd b/man/runread_pmodel_f.Rd