Update documentation (R and Rd files)

Author: MayaGueguen

NAMESPACE

@@ -127,20 +127,16 @@ exportMethods(plot)
 exportMethods(predict)
 exportMethods(show)
 exportMethods(summary)
-importFrom(MASS,stepAIC)
 importFrom(PresenceAbsence,optimal.thresholds)
 importFrom(PresenceAbsence,presence.absence.accuracy)
 importFrom(abind,abind)
 importFrom(abind,asub)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,mutate_at)
-importFrom(dplyr,select_at)
-importFrom(earth,earth)
 importFrom(foreach,"%:%")
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
-importFrom(gbm,gbm)
 importFrom(gbm,gbm.perf)
 importFrom(gbm,predict.gbm)
 importFrom(ggplot2,aes)
@@ -188,22 +184,14 @@ importFrom(graphics,plot.new)
 importFrom(graphics,points)
 importFrom(graphics,polygon)
 importFrom(graphics,text)
-importFrom(maxnet,maxnet)
-importFrom(mda,fda)
-importFrom(mda,mars)
-importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,new)
-importFrom(methods,validObject)
-importFrom(nnet,nnet)
 importFrom(pROC,auc)
 importFrom(pROC,coords)
 importFrom(pROC,roc)
-importFrom(randomForest,randomForest)
 importFrom(reshape,melt.array)
 importFrom(reshape2,melt)
 importFrom(rpart,prune)
-importFrom(rpart,rpart)
 importFrom(sp,read.asciigrid)
 importFrom(stats,aggregate)
 importFrom(stats,reshape)
@@ -251,5 +239,4 @@ importFrom(utils,setTxtProgressBar)
 importFrom(utils,tail)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
-importFrom(xgboost,xgboost)
 importMethodsFrom(methods,show)

R/BIOMOD_Modeling.R

@@ -56,12 +56,11 @@
 ##' @param data.split.table \emph{deprecated}, now called \code{CV.user.table}
 ##' @param do.full.models \emph{deprecated}, now called \code{CV.do.full.models}
 ##' 
-##' @param OPT.data.type a \code{character} corresponding to the data type to 
-##' be used, must be either \code{binary}, \code{binary.PA}, \code{abundance}, 
-##' \code{compositional}
-##' @param OPT.strategy a \code{character} corresponding to the method to 
-##' select models' parameters values, must be either \code{default}, 
-##' \code{bigboss}, \code{user.defined}, \code{tuned}
+##' @param OPT.data.type a \code{character} corresponding to the data type to be used, must be 
+##' either \code{binary}, \code{binary.PA}, \code{abundance}, \code{compositional}
+##' @param OPT.strategy a \code{character} corresponding to the method to select models' 
+##' parameters values, must be either \code{default}, \code{bigboss}, \code{user.defined}, 
+##' \code{tuned}
 ##' @param OPT.val.list (\emph{optional, default} \code{NULL}) \cr
 ##' A \code{list} containing parameters values for some (all) models
 ##' @param OPT.user (\emph{optional, default} \code{TRUE}) \cr  
@@ -120,24 +119,24 @@
 ##'   \code{\link{BIOMOD_FormatingData}}), \cr \code{PA.nb.rep *(nb.rep + 1)} models will be 
 ##'   created.}
 ##'   
-##'   \item{models}{The set of models to be calibrated on the data. 10 modeling techniques 
+##'   \item{models}{The set of models to be calibrated on the data. 12 modeling techniques 
 ##'   are currently available :
 ##'   \itemize{
-##'     \item \code{GLM} : Generalized Linear Model (\code{\link[stats]{glm}})
+##'     \item \code{ANN} : Artificial Neural Network (\code{\link[nnet]{nnet}})
+##'     \item \code{CTA} : Classification Tree Analysis (\code{\link[rpart]{rpart}})
+##'     \item \code{FDA} : Flexible Discriminant Analysis (\code{\link[mda]{fda}})
 ##'     \item \code{GAM} : Generalized Additive Model (\code{\link[gam]{gam}}, \code{\link[mgcv]{gam}} 
 ##'     or \code{\link[mgcv]{bam}}) \cr 
 ##'     (see \code{\link{bm_ModelingOptions} for details on algorithm selection})
 ##'     \item \code{GBM} : Generalized Boosting Model, or usually called Boosted Regression Trees 
 ##'     (\code{\link[gbm]{gbm}})
-##'     \item \code{CTA} : Classification Tree Analysis (\code{\link[rpart]{rpart}})
-##'     \item \code{ANN} : Artificial Neural Network (\code{\link[nnet]{nnet}})
-##'     \item \code{SRE} : Surface Range Envelop or usually called BIOCLIM
-##'     \item \code{FDA} : Flexible Discriminant Analysis (\code{\link[mda]{fda}})
+##'     \item \code{GLM} : Generalized Linear Model (\code{\link[stats]{glm}})
 ##'     \item \code{MARS} : Multiple Adaptive Regression Splines (\code{\link[earth]{earth}})
-##'     \item \code{RF} : Random Forest (\code{\link[randomForest]{randomForest}})
 ##'     \item \code{MAXENT} : Maximum Entropy 
 ##'     (\url{https://biodiversityinformatics.amnh.org/open_source/maxent/})
 ##'     \item \code{MAXNET} : Maximum Entropy (\code{\link[maxnet]{maxnet}})
+##'     \item \code{RF} : Random Forest (\code{\link[randomForest]{randomForest}})
+##'     \item \code{SRE} : Surface Range Envelop or usually called BIOCLIM
 ##'     \item \code{XGBOOST} : eXtreme Gradient Boosting Training (\code{\link[xgboost]{xgboost}})
 ##'   }}
 ##'   

R/biomod2_data.R

@@ -3,14 +3,31 @@
 #' A \code{data.frame} containing for each single model available in \pkg{biomod2} 
 #' the package and functions to be called.
 #'
-#' @format A data frame with 12 rows and 5 variables:
+#' @format A \code{data.frame} object with 12 rows and 5 variables:
 #' \describe{
 #'   \item{model}{all single models that can be computed in \pkg{biomod2}}
 #'   \item{type}{data type associated to the models}
-#'   \item{package}{R package used}
-#'   \item{func}{function used in the R package}
+#'   \item{package}{\code{R} package used}
+#'   \item{func}{function used in the \code{R} package}
 #'   \item{train}{function called by \pkg{caret} for the tuning}
 #' }
+#' 
+#' All single models available are the following : 
+#' 
+#' \itemize{
+#'   \item ANN (\code{\link[nnet]{nnet}})
+#'   \item CTA (\code{\link[rpart]{rpart}})
+#'   \item FDA (\code{\link[mda]{fda}})
+#'   \item GAM (\code{\link[gam]{gam}}, \code{\link[mgcv]{gam}} or \code{\link[mgcv]{bam}})
+#'   \item GBM (\code{\link[gbm]{gbm}})
+#'   \item GLM (\code{\link[stats]{glm}})
+#'   \item MARS (\code{\link[earth]{earth}})
+#'   \item MAXENT (\url{https://biodiversityinformatics.amnh.org/open_source/maxent/})
+#'   \item MAXNET (\code{\link[maxnet]{maxnet}})
+#'   \item RF (\code{\link[randomForest]{randomForest}})
+#'   \item SRE (\code{\link{bm_SRE}})
+#'   \item XGBOOST (\code{\link[xgboost]{xgboost}})
+#' }
 
 "ModelsTable"
 
@@ -90,7 +107,7 @@
 #' species. Presence/absence were derived from range maps downloaded at 
 #' \href{https://www.iucnredlist.org/}{IUCN}.
 #'
-#' @format A data frame with 2488 rows and 10 variables:
+#' @format A \code{data.frame} object with 2488 rows and 10 variables:
 #' \describe{
 #'   \item{X_WGS84}{Longitude}
 #'   \item{Y_WGS84}{Latitude}