diff --git a/R/BIOMOD_Modeling.R b/R/BIOMOD_Modeling.R
index a8751734..c08cfd5a 100644
--- a/R/BIOMOD_Modeling.R
+++ b/R/BIOMOD_Modeling.R
@@ -471,14 +471,14 @@ BIOMOD_Modeling <- function(bm.format,
for (ii in vals) {
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
- 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|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)
+ } else if (all(grepl("_allRun", nam))) { #Check if the user create the options just for PA dataset
+ 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|allData", unlist(strsplit(run, "_")), value = TRUE)
+ 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")]]
diff --git a/README.md b/README.md
index 91285c98..2ff1e442 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,7 @@ devtools::install_github("biomodhub/biomod2", dependencies = TRUE)
### `biomod 4.2-5` - Modeling options & Tuning Update
-**! `biomod2 4.2-5` is now available on GitHub !**
+**! `biomod2 4.2-5` is now available on CRAN !**
`/!\` Please **feel free to indicate if you notice some strange new behaviors** !
@@ -70,7 +70,10 @@ devtools::install_github("biomodhub/biomod2", dependencies = TRUE)
#### What is new ?
- `ModelsTable` and `OptionsBigboss` datasets (*note that improvement of bigboss modeling options is planned in near future*)
-- [data preparation vignette](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) has been created (*questions you should ask yourself before modeling*)
+- 3 new vignettes have been created :
+ - [data preparation](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*questions you should ask yourself before modeling*)
+ - [cross-validation](https://biomodhub.github.io/biomod2/articles/vignette_crossValidation.html) (*to prepare your own calibration / validation datasets*)
+ - [modeling options](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*to help you navigate through the new way of parameterizing single models*)
diff --git a/docs/articles/news.html b/docs/articles/news.html
index 7e8c7ef7..e3ff383e 100644
--- a/docs/articles/news.html
+++ b/docs/articles/news.html
@@ -138,15 +138,84 @@
BIOMOD.options.dataset
and
+BIOMOD.models.options
classesGAM.binary.gam.gam
and
+GAM.binary.mgcv.bam
in OptionsBigboss
+datasetobs
and fit
parameters in
+bm_FindOptimStat
+bm_Tuning
function :
+MAXENT.algorithm
and MAXENT.parallel
+parametersXGBOOST
and SRE
+gamSpline
to gamLoess
method
+to tune GAM.gam.gam
model, and add GAM.span
+and GAM.degree
parametersBIOMOD_Modeling
+BIOMOD_PresenceOnly
function and add
@@ -189,7 +258,7 @@ wrap
applied to a
@@ -233,7 +302,7 @@ MAXENT.Phillips
predict method for large dataset
@@ -564,7 +633,7 @@ ProbDensFunc()
function to package to produce nice
@@ -1107,7 +1176,7 @@ biomod 4.2-5
- Modeling options & Tuning Update
! biomod2 4.2-5
is now available on GitHub !
! biomod2 4.2-5
is now available on CRAN !
/!\
Please feel free to indicate if you notice some strange new behaviors !
ModelsTable
and OptionsBigboss
datasets (note that improvement of bigboss modeling options is planned in near future)