Corrections

Fix in the case : tuning with just PAdataset et full.model

+ Fix modification ModelsTable

R/BIOMOD_Modeling.R

@@ -472,14 +472,18 @@ BIOMOD_Modeling <- function(bm.format,
             OPT.user@options[[mod]]@args.values[[ii]] <- val
           }
         } else if (all(grepl("_allRun", nam))){ #Check if the user create the options just for PA dataset
-          model.name <- unlist(strsplit(mod,split = '[.]'))[1]
-          cat("\n \t The options for",model.name, "for '_PAx_allRun' will be given to all runs with PAx (_PAx_RUN1, _PAx_RUN2,...) \n")
+          sep.name <- unlist(strsplit(mod,split = '[.]'))
+          cat("\n \n \t The options for",sep.name[1], "for '_PAx_allRun' will be given to all runs with PAx (_PAx_RUN1, _PAx_RUN2,...) \n")
           for (run in vals){
-            PA.set <- grep("PA", unlist(strsplit(run, "_")), value = T)
-            if (length(PA.set) == 0){
-              PA.set <- "allData"
+            PA.set <- grep("PA|allData", unlist(strsplit(run, "_")), value = T)
+            if (is.null(OPT.user@options[[mod]]@args.values[[paste0("_", PA.set, "_allRun")]])){
+              opt.default <- BIOMOD.options.dataset(mod = sep.name[1],typ = sep.name[2],pkg =sep.name[3], fun = sep.name[4], strategy = "default",
+                                                    bm.format = bm.format, calib.lines = calib.lines)
+              OPT.user@options[[mod]]@args.values[[run]] <- opt.default@args.values[["_allData_allRun"]]
+            } else {
+              OPT.user@options[[mod]]@args.values[[run]] <- OPT.user@options[[mod]]@args.values[[paste0("_", PA.set, "_allRun")]]
             }
-            OPT.user@options[[mod]]@args.values[[run]] <- OPT.user@options[[mod]]@args.values[[paste0("_", PA.set, "_allRun")]]
+
           }
         } else {
           stop(paste0("\n", "names(OPT.user@options[['", mod, "']]@args.values)", " must be '",

R/biomod2_classes_0.R

@@ -446,6 +446,8 @@ setMethod('BIOMOD.options.dataset', signature(strategy = 'character'),
               argstmp$type <- "classification"
             }
             if (mod == "XGBOOST") { argstmp$nrounds = 4 }
+
+            argstmp[["..."]] = NULL
             BOM@args.default <- argstmp
             ## SHOULD BE MOVED to place when testing values !! ??
 

R/biomod2_data.R

@@ -41,6 +41,7 @@
 #                            , train = c('avNNet', 'rpart', 'fda', 'gamLoess', 'bam', 'gam', 'gbm', 'glm'
 #                                        , 'earth', 'ENMevaluate', 'maxnet', 'rf', 'bm_SRE', 'xgbTree'))
 
+# usethis::use_data(ModelsTable, overwrite = TRUE)
 # usethis::use_data(ModelsTable, overwrite = TRUE, internal = TRUE)
 
 #' Bigboss pre-defined parameter values for single models