Fix some issues to pass CRAN checks

/!\ WARNING: replaced complem_init_values that is not used by user_init_values, but I'm not sure it is what was meant.

.Rbuildignore

@@ -6,11 +6,14 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+CODE_OF_CONDUCT.md
+README.Rmd
 
 # temporary
 R/tests.txt
 Preliminary\ work
+tmp
 vignettes/JavaSTICS-1.41-stics-9.0
 vignettes/ApsimX_parameter_estimation_simple_case_files
 vignettes/Parameter_estimation_Specific_and_Varietal_files
-vignettes/Parameter_estimation_simple_case_files
+vignettes/Parameter_estimation_simple_case_files

R/get_params_bounds.R

@@ -21,8 +21,12 @@
 #'
 #' # A case with groups of situations per parameter
 #' prior_information=list()
-#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1", "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),lb=0.0005,ub=0.0025)
-#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"), c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),lb=c(50,50),ub=c(400,400))
+#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1",
+#'                                                "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),
+#'                                lb=0.0005,ub=0.0025)
+#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"),
+#'                                              c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),
+#'                                lb=c(50,50),ub=c(400,400))
 #' SticsOptimizR:::get_params_bounds(prior_information)
 #' }
 

R/get_params_init_values.R

@@ -20,16 +20,20 @@
 #'
 #' Cases with groups of situations per parameter
 #' prior_information=list()
-#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1", "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),
+#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1",
+#'                                                "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),
 #'                                init_values=0.001,lb=0.0001,ub=0.1)
-#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"), c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),
+#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"),
+#'                                              c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),
 #'                                init_values=c(200,300),lb=50,ub=400)
 #' get_params_init_values(prior_information)
 #'
 #' prior_information=list()
-#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1", "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),
+#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1",
+#'                                                "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),
 #'                                init_values=c(0.001,0.002),lb=0.0001,ub=0.1)
-#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"), c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),
+#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"),
+#'                                              c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),
 #'                                init_values=data.frame(c(200,300),c(250,350)),lb=50,ub=400)
 #' SticsOptimizR:::get_params_init_values(prior_information)
 #' }

R/get_params_names.R

@@ -22,8 +22,12 @@
 #'
 #' # A case with groups of situations per parameter
 #' prior_information=list()
-#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1", "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),lb=0.0005,ub=0.0025)
-#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"), c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),lb=c(50,50),ub=c(400,400))
+#' prior_information$dlaimax=list(sit_list=list(c("bou99t3", "bou00t3", "bou99t1", "bou00t1",
+#'                                                "bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+")),
+#'                                lb=0.0005,ub=0.0025)
+#' prior_information$durvieF=list(sit_list=list(c("bo96iN+", "lu96iN+", "lu96iN6", "lu97iN+"),
+#'                                              c("bou99t3", "bou00t3", "bou99t1", "bou00t1")),
+#'                                lb=c(50,50),ub=c(400,400))
 #' SticsOptimizR:::get_params_names(prior_information)
 #' }
 

R/get_params_per_sit.R

@@ -13,7 +13,8 @@
 #' active for the given situation
 #'
 #' @examples
-#' sg=list(p1=list(sit_list=list(c("sit1","sit2","sit3"),c("sit4","sit5","sit6"))),p2=list(sit_list=list(c("sit1","sit2","sit3","sit4","sit5","sit6"))))
+#' sg=list(p1=list(sit_list=list(c("sit1","sit2","sit3"),c("sit4","sit5","sit6"))),
+#'         p2=list(sit_list=list(c("sit1","sit2","sit3","sit4","sit5","sit6"))))
 #' vec=c(1,2,3)
 #' SticsOptimizR:::get_params_per_sit(sg,"sit2",vec)   # should give c(1,3)
 #' SticsOptimizR:::get_params_per_sit(sg,"sit4",vec)   # should give c(2,3)

R/optim_switch.R

@@ -85,7 +85,7 @@ optim_switch <- function(param_names,obs_list,crit_function,model_function,model
 
   sample_sz=nb_rep-NROW(init_values)
   if (sample_sz>0) {
-    init_values=rbind(init_values,complem_init_values)
+    init_values=rbind(init_values,user_init_values)
   }
 
   # Run nloptr for each repetition

vignettes/ApsimX_parameter_estimation_simple_case.Rmd

@@ -9,7 +9,7 @@ author:
 - name "Drew Holzworth"
 date: "`r Sys.Date()`"
 vignette: >
-  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteIndexEntry{Parameter estimation with ApsimX}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 params: