Switch argument name.

Author: Dongchen Zhang

modules/assim.sequential/R/sda.enkf_MultiSite.R

@@ -321,12 +321,12 @@ sda.enkf.multisite <- function(settings,
   if(restart_flag){
     new.params <- new.params
   } else {
-    gen.samples <- FALSE
+    generate_samples <- FALSE
     if (is.null(ensemble.samples)) {
       if (file.exists(file.path(settings$outdir, "samples.Rdata"))) {
         load(file.path(settings$outdir, "samples.Rdata"))
       } else {
-        gen.samples <- TRUE
+        generate_samples <- TRUE
       }
     }
     # get the joint input design.
@@ -347,7 +347,7 @@ sda.enkf.multisite <- function(settings,
       }
     }
     # if we generated new samples file within the `generate_joint_ensemble_design` function.
-    if (gen.samples) {
+    if (generate_samples) {
       load(file.path(settings$outdir, "samples.Rdata"))
     }
     new.params <- sda_matchparam(settings, ensemble.samples, site.ids, nens)

modules/assim.sequential/R/sda.enkf_parallel.R

@@ -195,12 +195,12 @@ sda.enkf_local <- function(settings,
   ###-------------------------------------------------------------------###----
   # Reading param samples------------------------------- 
   # create params object using samples generated from TRAITS functions
-  gen.samples <- FALSE
+  generate_samples <- FALSE
   if (is.null(ensemble.samples)) {
     if (file.exists(file.path(settings$outdir, "samples.Rdata"))) {
       load(file.path(settings$outdir, "samples.Rdata"))
     } else {
-      gen.samples <- TRUE
+      generate_samples <- TRUE
     }
   }
   # get the joint input design.
@@ -220,7 +220,7 @@ sda.enkf_local <- function(settings,
   }
   # reformatting params.
   # if we generated new samples file within the `generate_joint_ensemble_design` function.
-  if (gen.samples) {
+  if (generate_samples) {
     load(file.path(settings$outdir, "samples.Rdata"))
   }
   new.params <- sda_matchparam(settings, ensemble.samples, site.ids, nens)

modules/uncertainty/R/generate_joint_ensemble_design.R

@@ -5,7 +5,8 @@
 #'
 #' @param settings A PEcAn settings object containing ensemble configuration
 #' @param ensemble_size Integer specifying the number of ensemble members
-#' @param gen.samples Logical: logical variable determine if we want to generate the samples.
+#' @param generate_samples Logical: logical variable determine if we want to generate the samples.
+#' Default is TRUE.
 #' Since the `input_design` will only be generated once for the entire model run,
 #' the only situation, where we might want to recycle the existing `ensemble_samples`,
 #' is when we split and submit the larger SDA runs (e.g., 8,000 sites) into 
@@ -19,7 +20,7 @@
 
 generate_joint_ensemble_design <- function(settings,
                                            ensemble_size,
-                                           gen.samples = FALSE,
+                                           generate_samples = TRUE,
                                            sobol = FALSE) {
   if (sobol) {
     ensemble_size <- as.numeric(ensemble_size) * 2