Merge v2.2.1 changes

.Rbuildignore

@@ -1,8 +1,7 @@
 ^.*\.Rproj$         # Automatically added by RStudio,
 ^\.Rproj\.user$     # used for temporary files.
 ^README\.Rmd$       # An Rmarkdown file used to generate README.md
-^cran-comments\.md$ # Comments for CRAN submission
-^NEWS\.md$          # A news file written in Markdown
+^cran-comments\.md$ # Comments for CRAN submissionS
 \.DS_Store$	    # for macs
 cmip5*    # worldclim files
 ^wallace.Rproj
@@ -13,3 +12,4 @@ cmip5*    # worldclim files
 ^docs$
 ^pkgdown$
 ^LICENSE$
+^CRAN-SUBMISSION$

.gitignore

@@ -18,6 +18,7 @@ cmip5
 # r proj files
 .Rproj.user
 .RData
+.Rproj
 # .rmd files
 temp*
 #

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2.2.0
-Date: 2025-03-06
+Version: 2.2.1
+Date: 2026-05-05
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 
@@ -12,8 +12,8 @@ Description: The 'shiny' application Wallace is a modular platform for
     most package functionality can be found on the package's GitHub Pages 
     website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
 Authors@R: 
-    c(person("Bethany A.", "Johnson", email = "bjohnso005@citymail.cuny.edu", role = "aut"),
-    person("Daniel F.", "Lopez-Lozano", email = "dlopezlozano@amnh.org", role = "aut"),
+    c(person("Daniel F.", "Lopez-Lozano", email = "dlopezlozano@amnh.org", role = "aut"),
+    person("Bethany A.", "Johnson", email = "bjohnso005@citymail.cuny.edu", role = "aut"),
     person("Jamie M.", "Kass", email = "jamie.m.kass@gmail.com", role = "aut"),
     person("Gonzalo E.", "Pinilla-Buitrago", email = "gepinillab@gmail.com", role = "aut"),
     person("Andrea", "Paz", email = "paz.andreita@gmail.com", role = "aut"),
@@ -41,12 +41,11 @@ Imports:
     ecospat (>= 4.0.0),
     ENMeval (>= 2.0.5),
     geodata,
+    htmltools,
     knitcitations,
     leafem,
-    leaflet.extras (>= 1.0.0),
     magrittr,
     markdown,
-    methods,
     RColorBrewer,
     rJava,
     rlang,
@@ -73,10 +72,10 @@ Suggests:
     raster,
     rgbif (>= 3.3.0),
     sp,
-    terra, 
+    terra (>= 1.9-11), 
     testthat,
     tools
 License: GPL-3
-URL: http://wallaceecomod.github.io/wallace/,
+URL: https://wallaceecomod.github.io/wallace/
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+export(addDrawToolbar)
 export(clearAll)
 export(create_module)
 export(ecoClimate_getdata)
 export(ecoClimate_select)
 export(ecospat.plot.nicheDEV)
+export(editToolbarOptions)
 export(envs_ecoClimate)
 export(envs_userEnvs)
 export(envs_worldclim)
@@ -34,6 +36,7 @@ export(predictMaxnet)
 export(printVecAsis)
 export(register_module)
 export(remEnvsValsNA)
+export(removeDrawToolbar)
 export(reverseLabel)
 export(run_wallace)
 export(smartProgress)

NEWS.md

@@ -1,3 +1,14 @@
+wallace 2.2.1
+=============
+- Fixed image paths in the Team section.
+- Enabled support for models with categorical variables when using ENMeval > 2.0.5.
+- Fixed an issue occurring during model transfer to new areas or time periods when using BIOCLIM or Maxent.jar.
+- Fixed a loading error triggered by selecting multiple species in Environmental Space.
+- Integrated the drawing functionality of leaflet.extras directly into wallace to streamline dependencies.
+- Fixed an issue with session code generation when visualizing map predictions and transferring to a new time period.
+- Fixed UI rendering issue where the power-off icon was hidden on macOS.
+- Fixed an issue affecting Maxent models when using terra > '1.9.11'.
+
 wallace 2.2.0
 =============
 - updated for ENMeval v2.0.5 functionality

R/helper_functions.R

@@ -65,7 +65,6 @@ spurious <- function(x) {
   DT::renderDataTable(x)
   RColorBrewer::brewer.pal(x)
   leafem::addMouseCoordinates(x)
-  leaflet.extras::removeDrawToolbar(x)
   markdown::html_format()
   rmarkdown::github_document(x)
   shinyWidgets::pickerInput(x)

R/model_bioclim.R

@@ -35,8 +35,8 @@
 #' @param bg  coordinates of background points to be used for modeling.
 #' @param user.grp  a list of two vectors containing group assignments for
 #'   occurrences (occs.grp) and background points (bg.grp).
-#' @param bgMsk a RasterStack or a RasterBrick of environmental layers cropped
-#'   and masked to match the provided background extent.
+#' @param bgMsk a SpatRaster of environmental layers cropped and masked to 
+#'   match the provided background extent.
 #' @param logger Stores all notification messages to be displayed in the Log
 #'   Window of Wallace GUI. Insert the logger reactive list here for running
 #'   in shiny, otherwise leave the default NULL.
@@ -55,7 +55,7 @@
 #' bg <- read.csv(system.file("extdata/Bassaricyon_alleni_bgPoints.csv",
 #'                package = "wallace"))
 #' partblock <- part_partitionOccs(occs, bg, method = 'block')
-#' m <- model_bioclim(occs, bg, partblock, envs)
+#' m <- model_bioclim(occs, bg, partblock, terra::rast(envs))
 #' }
 #'
 #' @return Function returns an ENMevaluate object with all the evaluated models
@@ -80,7 +80,7 @@ model_bioclim <- function(occs, bg, user.grp, bgMsk, logger = NULL,
   smartProgress(logger,
                        message = paste0("Building/Evaluating BIOCLIM model for ",
                                  spName(spN), "..."), {
-     e <- ENMeval::ENMevaluate(occs = occs.xy, envs = terra::rast(bgMsk), bg = bg.xy,
+     e <- ENMeval::ENMevaluate(occs = occs.xy, envs = bgMsk, bg = bg.xy,
                                algorithm = "bioclim", partitions = "user",
                                user.grp = user.grp)
   })

R/model_maxent.R

@@ -36,8 +36,8 @@
 #' @param bg  coordinates of background points to be used for modeling.
 #' @param user.grp  a list of two vectors containing group assignments for
 #'   occurrences (occs.grp) and background points (bg.grp).
-#' @param bgMsk a RasterStack or a RasterBrick of environmental layers cropped
-#'   and masked to match the provided background extent.
+#' @param bgMsk a SpatRaster of environmental layers cropped and masked to
+#'   match the provided background extent.
 #' @param rms vector of range of regularization multipliers to be used in the
 #'   ENMeval run.
 #' @param rmsStep step to be used when defining regularization multipliers to
@@ -76,7 +76,7 @@
 #' rmsStep <- 1
 #' fcs <- c('L', 'LQ')
 #' m <- model_maxent(occs = occs, bg = bg, user.grp = partblock,
-#'                   bgMsk = envs, rms = rms, rmsStep, fcs,
+#'                   bgMsk = terra::rast(envs), rms = rms, rmsStep, fcs,
 #'                   clampSel = TRUE, algMaxent = "maxnet",
 #'                   parallel = FALSE)
 #' }
@@ -86,6 +86,7 @@
 #' @author Jamie M. Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 #' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
+#' @author Daniel Lopez-Lozano <dlopezlozano@@amnh.org.co>
 # @note
 
 #' @seealso \code{\link[ENMeval]{ENMevaluate}}
@@ -192,12 +193,18 @@ model_maxent <- function(occs, bg, user.grp, bgMsk, rms, rmsStep, fcs,
   # get just coordinates
   occs.xy <- occs %>% dplyr::select("longitude", "latitude")
   bg.xy <- bg %>% dplyr::select("longitude", "latitude")
+
+  # convert the categorical variables to factors
+  if (!is.null(catEnvs)) {
+    bgMsk[[catEnvs]] <- terra::as.factor(bgMsk[[catEnvs]])
+  }
+
   # run ENMeval
   e <- ENMeval::ENMevaluate(occs = as.data.frame(occs.xy),
                             bg = as.data.frame(bg.xy),
                             partitions = 'user',
                             user.grp = user.grp,
-                            envs = terra::rast(bgMsk),
+                            envs = bgMsk,
                             tune.args = tune.args,
                             doClamp = clampSel,
                             algorithm = algMaxent,
@@ -219,7 +226,11 @@ model_maxent <- function(occs, bg, user.grp, bgMsk, rms, rmsStep, fcs,
                             updateProgress = updateProgress,
                             quiet = FALSE)
 
-  occPredVals <- raster::extract(e@predictions, occs.xy)
+  # Make sure e@predictions has an assigned CRS
+  if(terra::crs(e@predictions) == ""){
+    terra::crs(e@predictions) <- terra::crs(bgMsk)
+  }
+  occPredVals <- terra::extract(e@predictions, occs.xy)
 
   endTxt <- paste("]), using", algMaxent, "with clamping",
                   ifelse(clampSel, "on.", "off."))

R/penvs_bgMask.R

@@ -31,8 +31,8 @@
 #'    environmental layers to be used in the modeling are cropped and masked
 #'    to the provided background area. The background area is determined in
 #'    the function penvs_bgExtent from the same component. The function returns
-#'    the provided environmental layers cropped and masked in the provided
-#'    format (either a rasterBrick or a rasterStack).
+#'    the provided environmental layers cropped and masked in the SpatRaster
+#'    format.
 #'
 #' @param occs data frame of cleaned or processed occurrences obtained from
 #'   components occs: Obtain occurrence data or, poccs: Process occurrence data.
@@ -59,10 +59,11 @@
 #' bgMask <- penvs_bgMask(occs, envs, bgExt)
 #' }
 #'
-#' @return A RasterStack or a RasterBrick of environmental layers cropped and
+#' @return A SpatRaster of environmental layers cropped and
 #'   masked to match the provided background extent.
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
+#' @author Daniel Lopez-Lozano <dlopezlozano@@amnh.org.co>
 #' @seealso   \code{\link{penvs_userBgExtent}},
 #'   \code{\link{penvs_drawBgExtent}}, \code{\link{penvs_bgExtent}},
 #'   \code{\link{penvs_bgSample}}
@@ -81,18 +82,17 @@ penvs_bgMask <- function(occs, envs, bgExt, logger = NULL, spN = NULL) {
                        message = paste0("Masking rasters for ",
                                         spName(spN), "..."), {
 
-    bgCrop <- raster::crop(envs, bgExt)
-    bgMask <- raster::mask(bgCrop, bgExt)
+    envs <- terra::rast(envs)
+    bgCrop <- terra::crop(envs, bgExt)
+    bgMask <- terra::mask(bgCrop, terra::vect(bgExt))
     # GEPB: Workaround when raster alignment is changed after crop, which makes appears
     # new duplicated occs in the same grid cells.
-    occsEnvsVals <- as.data.frame(raster::extract(bgMask,
+    occsEnvsVals <- as.data.frame(terra::extract(bgMask,
                                                   occs[, c('longitude', 'latitude')],
                                                   cellnumbers = TRUE))
     occs.dups <- duplicated(occsEnvsVals[, 1])
     if (sum(occs.dups) > 0) {
-      bgMask <- terra::project(terra::rast(bgMask),
-                               terra::rast(envs), method = 'near')
-      bgMask <- methods::as(bgMask, "Raster")
+      bgMask <- terra::project(bgMask, envs, method = 'near')
     }
   })
 

R/penvs_bgSample.R

@@ -58,7 +58,7 @@
 #'                        doBrick = TRUE)
 #' bgExt <- penvs_bgExtent(occs, bgSel = 'bounding box', bgBuf = 0.5)
 #' bgMask <- penvs_bgMask(occs, envs, bgExt)
-#' bgsample <- penvs_bgSample(occs, bgMask, bgPtsNum = 1000)
+#' bgsample <- penvs_bgSample(occs, raster::stack(bgMask), bgPtsNum = 1000)
 #' }
 #'
 #' @return a dataframe containing point coordinates (longitude and latitude).