Mino corrections to pass checks

DESCRIPTION

@@ -2,7 +2,7 @@ Package: biomod2
 Type: Package
 Title: Ensemble Platform for Species Distribution Modeling
 Version: 4.2-5
-Date: 2023-09-12
+Date: 2024-04-04
 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut")
                     , email = "[email protected]"),
              person("Damien", "Georges", role = c("aut")),

R/BIOMOD_EnsembleForecasting.R

@@ -218,6 +218,7 @@
 ##' plot(myBiomodEMProj)
 ##' 
 ##' 
+##' @importFrom foreach foreach %dopar%
 ##' @importFrom terra rast `add<-` wrap writeRaster mask
 ##' 
 ##' 

R/BIOMOD_EnsembleModeling.R

@@ -359,6 +359,7 @@
 ##' #                       do.bivariate = TRUE)
 ##' 
 ##' 
+##' @importFrom foreach foreach %do% %dopar%
 ##' @importFrom terra rast  
 ##' 
 ##' 

R/BIOMOD_FormatingData.R

@@ -99,9 +99,10 @@
 ##' 
 ##' A \code{\link{BIOMOD.formated.data}} object that can be used to build species distribution 
 ##' model(s) with the \code{\link{BIOMOD_Modeling}} function. \cr
-##' \href{BIOMOD.formated.data.html}{\code{print/show}}, \href{plot.html}{\code{plot}} and 
-##' \href{summary.html}{\code{summary}} functions are available to have a summary of the 
-##' created object. 
+##' \href{https://biomodhub.github.io/biomod2/reference/BIOMOD.formated.data.html}{\code{print/show}}, 
+##' \href{https://biomodhub.github.io/biomod2/reference/plot.html}{\code{plot}} and 
+##' \href{https://biomodhub.github.io/biomod2/reference/summary.html}{\code{summary}} functions 
+##' are available to have a summary of the created object. 
 ##' 
 ##' 
 ##' @details  

R/BIOMOD_Modeling.R

@@ -339,6 +339,8 @@
 ##' #                       do.bivariate = TRUE)
 ##' 
 ##' 
+##' @importFrom foreach foreach %do%
+##' 
 ##' @export
 ##' 
 ##' 

R/BIOMOD_Projection.R

@@ -183,7 +183,6 @@
 ##' 
 ##' 
 ##' @importFrom foreach foreach %dopar% 
-## @importFrom doParallel registerDoParallel
 ##' @importFrom terra rast subset nlyr writeRaster terraOptions wrap unwrap
 ##'  mem_info app is.factor mask
 ##' @importFrom utils capture.output

R/BIOMOD_RangeSize.R

@@ -173,6 +173,7 @@
 ##' bm_PlotRangeSize(bm.range = myBiomodRangeSize)
 ##' 
 ##' 
+##' @importFrom foreach foreach %do%
 ##' @importFrom terra rast nlyr `add<-` values
 ##' 
 ##' @export

R/biomod2_classes_5.R

@@ -154,9 +154,6 @@ setMethod('show', signature('biomod2_ensemble_model'),
 ##' \code{boolean} describing whether \code{newdata} is given as raw environmental 
 ##' data (\code{FALSE}) or as formal predictions of the individual models 
 ##' used to build the ensemble model (\code{TRUE}).
-##' @param na.rm (\emph{optional, default} \code{TRUE}) \cr
-##' A boolean defining whether Ensemble Model projection should ignore \code{NA}
-##' in Individual Model projection. Argument ignored by EWmean ensemble algorithm.
 ##' 
 ##' @param \ldots (\emph{optional}) 
 ##' @inheritParams predict2.bm

R/biomod2_globalVariables.R

@@ -78,6 +78,9 @@ utils::globalVariables(names = c("i.abs"))
 ## bm_Tuning ------------
 utils::globalVariables(names = c("dataset.i", "PA.i", "tuned.mod", "train.params", "tuning.grid", "criteria.AIC"))
 
+## bm_ModelingOptions ------------
+utils::globalVariables(names = c("ModelsTable"))
+
 ## bm_CrossValidation ------------
 utils::globalVariables(names = c("pa", "env", "this.colnames"))
 

R/bm_CrossValidation.R

@@ -217,6 +217,8 @@
 ##' apply(cv.e, 2, table)
 ##' 
 ##' 
+##' @importFrom foreach foreach %do%
+##' 
 ##' @export
 ##' 
 ##' 

R/bm_PlotResponseCurves.R

@@ -163,7 +163,7 @@
 ##'                                       
 ##'                                       
 ##' @importFrom terra rast cats global is.factor nlyr                                    
-##' @importFrom foreach foreach %:%
+##' @importFrom foreach foreach %do% %:%
 ##' @importFrom reshape2 melt
 ##' @importFrom ggplot2 ggplot aes_string geom_line geom_rug geom_raster facet_wrap xlab ylab labs 
 ##' theme element_blank element_rect element_text scale_fill_viridis_c

R/bm_PseudoAbsences.R

@@ -187,6 +187,7 @@
 ##' apply(PA.r_mult$pa.tab, 2, table)
 ##'
 ##' 
+##' @importFrom foreach foreach %do%
 ##' @importFrom terra rast vect freq spatSample values extract
 ##' @importFrom utils packageVersion
 ##'

R/bm_RunModelsLoop.R

@@ -94,7 +94,7 @@
 ##' @family Secundary functions
 ##' 
 ##' 
-##' @importFrom foreach foreach %dopar% 
+##' @importFrom foreach foreach %do% %dopar% 
 ##' @importFrom rpart prune
 ##' @importFrom gbm gbm.perf
 ##' @importFrom dplyr mutate_at %>%

R/bm_Tuning.R

@@ -176,7 +176,7 @@
 ##' 
 ##' 
 ##' 
-##' @importFrom foreach foreach %do%
+##' @importFrom foreach foreach %do% %:%
 ##' @importFrom stats aggregate  
 ##' @importFrom PresenceAbsence optimal.thresholds presence.absence.accuracy
 ##' 

R/bm_VariablesImportance.R

@@ -84,8 +84,7 @@
 ##'                        nb.rep = 3)
 ##' 
 ##' 
-##' @importFrom foreach foreach %:% %dopar%
-## @importFrom doParallel registerDoParallel
+##' @importFrom foreach foreach %do% %:% 
 ##' @importFrom stats cor
 ##' 
 ##' 
@@ -99,7 +98,6 @@ bm_VariablesImportance <- function(bm.model,
                                    variables = NULL,
                                    method = "full_rand", 
                                    nb.rep = 1,
-                                   # nb.cpu = 1,
                                    seed.val = NULL,
                                    do.progress = TRUE,
                                    temp.workdir = NULL)
@@ -122,14 +120,6 @@ bm_VariablesImportance <- function(bm.model,
     PROGRESS = txtProgressBar(min = 0, max = nb.rep * length(variables), style = 3)
     i.iter = 0
   }
-  # if (nb.cpu > 1) {
-  #   if (.getOS() != "windows") {
-  #     if (!isNamespaceLoaded("doParallel")) { requireNamespace("doParallel", quietly = TRUE) }
-  #     doParallel::registerDoParallel(cores = nb.cpu)
-  #   } else {
-  #     warning("Parallelisation with `foreach` is not available for Windows. Sorry.")
-  #   }
-  # }
   out = foreach (r = 1:nb.rep, .combine = "rbind") %:%
     foreach (v = variables, .combine = "rbind") %do%
     {