merge v2.1.3 into biomodelos

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2024.02.23
-Date: 2024-02-23
+Version: 2024.08.02
+Date: 2024-08-02
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 
@@ -12,24 +12,24 @@ 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("Jamie M.", "Kass", email = "[email protected]", role = "aut"),
+    c(person("Bethany A.", "Johnson", email = "[email protected]", role = "aut"),
+    person("Jamie M.", "Kass", email = "[email protected]", role = "aut"),
     person("Gonzalo E.", "Pinilla-Buitrago", email = "[email protected]", role = "aut"),
-	 	person("Andrea", "Paz", email = "[email protected]", role = "aut"),
-	 	person("Bethany A.", "Johnson", email = "[email protected]", role = "aut"),
-	 	person("Valentina", "Grisales-Betancur", email = "[email protected]", role = "aut"),
-	  person("Dean", "Attali", email = "[email protected]", role = "aut"),
-	  person("Matthew E.", "Aiello-Lammens", email = "[email protected]", role = "aut"),
-	  person("Cory", "Merow", email = "[email protected]", role = "aut"),
-	  person("Mary E.", "Blair", email = "[email protected]", role = c("aut", "cre")),
-	  person("Robert P.", "Anderson", email = "[email protected]", role = "aut"),
-	  person("Sarah I.", "Meenan", email = "[email protected]", role = "ctb"),
-	  person("Olivier", "Broennimann", email = "[email protected]", role = "ctb"),
-	  person("Peter J.", "Galante", email = "[email protected]", role = "ctb"),
-	  person("Brian S.", "Maitner", email = "[email protected]", role = "ctb"),
-	  person("Hannah L.", "Owens", email = "[email protected]", role = "ctb"),
-	  person("Sara", "Varela", email = "[email protected]", role = "ctb"),
-	  person("Bruno", "Vilela", email = "[email protected]", role = "ctb"),
-	  person("Robert", "Muscarella", email = "[email protected]", role = "ctb"))
+    person("Andrea", "Paz", email = "[email protected]", role = "aut"),
+    person("Valentina", "Grisales-Betancur", email = "[email protected]", role = "aut"),
+    person("Dean", "Attali", email = "[email protected]", role = "aut"),
+    person("Matthew E.", "Aiello-Lammens", email = "[email protected]", role = "aut"),
+    person("Cory", "Merow", email = "[email protected]", role = "aut"),
+    person("Mary E.", "Blair", email = "[email protected]", role = c("aut", "cre")),
+    person("Robert P.", "Anderson", email = "[email protected]", role = "aut"),
+    person("Sarah I.", "Meenan", email = "[email protected]", role = "ctb"),
+    person("Olivier", "Broennimann", email = "[email protected]", role = "ctb"),
+    person("Peter J.", "Galante", email = "[email protected]", role = "ctb"),
+    person("Brian S.", "Maitner", email = "[email protected]", role = "ctb"),
+    person("Hannah L.", "Owens", email = "[email protected]", role = "ctb"),
+    person("Sara", "Varela", email = "[email protected]", role = "ctb"),
+    person("Bruno", "Vilela", email = "[email protected]", role = "ctb"),
+    person("Robert", "Muscarella", email = "[email protected]", role = "ctb"))
 Depends:
     R (>= 3.5.0),
     shiny (>= 1.6.0),
@@ -40,11 +40,14 @@ Imports:
     DT (>= 0.5),
     ecospat (>= 4.0.0),
     ENMeval (>= 2.0.3),
+    geodata,
     knitcitations,
     leafem,
     leaflet.extras (>= 1.0.0),
     magrittr,
     maskRangeR,
+    markdown,
+    methods,
     RColorBrewer,
     rJava,
     rlang,

NEWS.md

@@ -1,3 +1,24 @@
+wallace 2.1.3
+=============
+- Fixed NULL error in poccs_selectOccs Rmd code
+- Updated JK's email
+- Added model name (FC + RM) to file name when prediction downloaded
+- Fixed vis_responsePlot knitting to Rmd
+- Fixed predictor variable bug in vis_responsePlot Rmd
+- Fixed NA value warning in userEnvs
+- Fixed broken function to disable `xfer_time` when using `envs_userEnvs`
+- Replaced `raster::getdata` with `geodata` functions
+- WorldClim v2.1 bioclimatic variables now available for Envs & Xfer_time!
+- Added tryCatch for querying worldclim data (envs_wc & xfer_time)
+
+wallace 2.1.2
+=============
+- Fixed FAIL in test_occs_queryDB
+- Fixed bug in error msgs for xfer_time
+- Fixed broken link in v1 vignette
+- Added `markdown` to imports
+- Updated team members
+
 wallace 2.1.1
 =============
 - Fixed bug in occ density grid & niche overlap

R/envs_worldclim.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # envs_worldclim.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -53,8 +53,9 @@
 #'
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 #'
-#' @seealso \code{\link[raster]{getData}}
+#' @seealso \code{\link[geodata]{worldclim_global}}, \code{\link[geodata]{worldclim_tile}}
 #'
 #' @export
 
@@ -66,20 +67,42 @@ envs_worldclim <- function(bcRes, bcSel, mapCntr, doBrick = FALSE,
   }
 
   smartProgress(logger, message = "Retrieving WorldClim data...", {
-      wcbc <- raster::getData(name = "worldclim", var = "bio", res = bcRes,
-                              lon = mapCntr[1], lat = mapCntr[2])
-      # change names if bio01 is bio1, and so forth
-      if (bcRes == 0.5) {
-        names(wcbc) <- gsub("_.*", "", names(wcbc))
-      }
+    if (bcRes == 0.5) {
+      wcbc <- tryCatch(expr = geodata::worldclim_tile(var = "bio",
+                                                      lon = mapCntr[1], lat = mapCntr[2],
+                                                      path = tempdir(),
+                                                      version="2.1"),
+                       error = function(e) NULL)
+    } else {
+      wcbc <- tryCatch(expr = geodata::worldclim_global(var = "bio",
+                                                        res = bcRes,
+                                                        path = tempdir(),
+                                                        version = "2.1"),
+                       error= function(e) NULL)
+    }
+    #trycatch error
+    if (is.null(wcbc)) {
+      logger %>% writeLog(
+        type = "error",
+        paste0("Unable to retrieve data from WorldClim.
+               Server may be down.
+               Please use User-Specified module instead."))
+      return()
+    } else {
+    # change names to bioXX
+    names(wcbc) <- gsub(".*_", "bio", names(wcbc))
+    # change names if bio01 is bio1, and so forth
       i <- grep('bio[0-9]$', names(wcbc))
       editNames <- paste('bio', sapply(strsplit(names(wcbc)[i], 'bio'),
                                        function(x) x[2]), sep = '0')
       names(wcbc)[i] <- editNames
-
       wcbc <- wcbc[[bcSel]]
+    }
   })
 
+  # convert from spatraster to raster
+  wcbc <- raster::stack(wcbc)
+
   # convert to brick for faster processing
   if(doBrick == TRUE) {
     smartProgress(logger,

R/helper_functions.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # helper_functions.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -74,6 +74,7 @@ spurious <- function(x) {
   RColorBrewer::brewer.pal(x)
   leafem::addMouseCoordinates(x)
   leaflet.extras::removeDrawToolbar(x)
+  markdown::html_format()
   rmarkdown::github_document(x)
   shinyWidgets::pickerInput(x)
   shinyjs::disable(x)

R/model_bioclim.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # model_bioclim.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -61,7 +61,7 @@
 #' @return Function returns an ENMevaluate object with all the evaluated models
 #'   and a selection of appropriate fields.
 
-#' @author Jamie M. Kass <jkass@@gradcenter.cuny.edu>
+#' @author Jamie M. Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 # @note
 
@@ -73,8 +73,8 @@ model_bioclim <- function(occs, bg, user.grp, bgMsk, logger = NULL,
                           spN = NULL) {
 
   # get just coordinates
-  occs.xy <- occs %>% dplyr::select(.data$longitude, .data$latitude)
-  bg.xy <- bg %>% dplyr::select(.data$longitude, .data$latitude)
+  occs.xy <- occs %>% dplyr::select("longitude", "latitude")
+  bg.xy <- bg %>% dplyr::select("longitude", "latitude")
 
   smartProgress(logger,
                        message = paste0("Building/Evaluating BIOCLIM model for ",

R/model_maxent.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # model_maxent.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -83,7 +83,7 @@
 #'
 #' @return Function returns an ENMevaluate object with all the evaluated models
 #'   and a selection of appropriate fields.
-#' @author Jamie M. Kass <jkass@@gradcenter.cuny.edu>
+#' @author Jamie M. Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 # @note
 
@@ -189,8 +189,8 @@ model_maxent <- function(occs, bg, user.grp, bgMsk, rms, rmsStep, fcs,
   }
 
   # get just coordinates
-  occs.xy <- occs %>% dplyr::select(.data$longitude, .data$latitude)
-  bg.xy <- bg %>% dplyr::select(.data$longitude, .data$latitude)
+  occs.xy <- occs %>% dplyr::select("longitude", "latitude")
+  bg.xy <- bg %>% dplyr::select("longitude", "latitude")
   # run ENMeval
   e <- ENMeval::ENMevaluate(occs = as.data.frame(occs.xy),
                             bg = as.data.frame(bg.xy),

R/occs_queryDb.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # occs_queryDb.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -259,12 +259,12 @@ occs_queryDb <- function(spNames, occDb, occNum = NULL, doCitations = FALSE,
                   "institutionCode", "elevation", "coordinateUncertaintyInMeters")
       for (i in fields) if (!(i %in% names(occs))) occs[i] <- NA
       occs <- occs %>%
-        dplyr::rename(scientific_name = .data$name,
-                      state_province = .data$stateProvince,
-                      record_type = .data$basisOfRecord,
-                      institution_code = .data$institutionCode,
-                      catalog_number = .data$catalogNumber,
-                      uncertainty = .data$coordinateUncertaintyInMeters)
+        dplyr::rename(scientific_name = "name",
+                      state_province = "stateProvince",
+                      record_type = "basisOfRecord",
+                      institution_code = "institutionCode",
+                      catalog_number = "catalogNumber",
+                      uncertainty = "coordinateUncertaintyInMeters")
 
     } else if (occDb == 'vertnet') { # standardize VertNet column names
       fields <- c("name", "longitude", "latitude", "country", "stateprovince",
@@ -273,13 +273,13 @@ occs_queryDb <- function(spNames, occDb, occNum = NULL, doCitations = FALSE,
                   "coordinateuncertaintyinmeters")
       for (i in fields) if (!(i %in% names(occs))) occs[i] <- NA
       occs <- occs %>%
-        dplyr::rename(scientific_name = .data$name,
-                      state_province = .data$stateprovince,
-                      record_type = .data$basisofrecord,
-                      institution_code = .data$institutioncode,
-                      catalog_number = .data$catalognumber,
-                      elevation = .data$maximumelevationinmeters,
-                      uncertainty = .data$coordinateuncertaintyinmeters)
+        dplyr::rename(scientific_name = "name",
+                      state_province = "stateprovince",
+                      record_type = "basisofrecord",
+                      institution_code = "institutioncode",
+                      catalog_number = "catalognumber",
+                      elevation = "maximumelevationinmeters",
+                      uncertainty = "coordinateuncertaintyinmeters")
     # } else if (occDb == 'bison') { # standardize BISON column names
     #   fields <- c("providedScientificName", "longitude", "latitude", "countryCode",
     #               "stateProvince", "verbatimLocality", "year", "basisOfRecord",

R/part_partitionOccs.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # part_partitionOccs.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -96,8 +96,8 @@ part_partitionOccs <- function(occs, bg, method, kfolds = NULL, bgMask = NULL,
     return()
   }
 
-  occs.xy <- occs %>% dplyr::select(.data$longitude, .data$latitude)
-  bg.xy <- bg %>% dplyr::select(.data$longitude, .data$latitude)
+  occs.xy <- occs %>% dplyr::select("longitude", "latitude")
+  bg.xy <- bg %>% dplyr::select("longitude", "latitude")
 
   if (method == 'jack') {
     group.data <- ENMeval::get.jackknife(occs.xy, bg.xy)

R/penvs_bgSample.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # penvs_bgSample.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -78,7 +78,7 @@ penvs_bgSample <- function(occs, bgMask, bgPtsNum, logger = NULL, spN = NULL) {
   smartProgress(logger, message = "Generating background points...", {
     bgXY <- dismo::randomPoints(bgMask, bgPtsNum)
     bgXY <- bgXY %>% as.data.frame() %>%
-      dplyr::select(longitude = .data$x, latitude = .data$y)
+      dplyr::select(longitude = "x", latitude = "y")
     bgNonNA <- raster::ncell(bgMask) - raster::freq(bgMask, value = NA)[[1]]
   })
   bg.prop <- round(nrow(bgXY)/bgPtsNum, digits = 2)

R/poccs_selectOccs.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # poccs_selectOccs.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -98,7 +98,7 @@ poccs_selectOccs <- function(occs, polySelXY, polySelID = 1, logger = NULL,
         hlSpp(spN),
         "Your polygon is selecting all occurrences. None will be removed.")
       occs.sel <- occs
-      return()
+      return(occs.sel)
     }
     occs.sel <- occs[-ptRemIndex,]
 

R/run_wallace.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # run_wallace.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -36,7 +36,7 @@
 #' if(interactive()) {
 #' run_wallace()
 #' }
-#' @author Jamie Kass <jkass@@gradcenter.cuny.edu>
+#' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 #' @export
 run_wallace <- function(launch.browser = TRUE, port = getOption("shiny.port"),

R/vis_bioclimPlot.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # vis_bioclimPlot.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -66,7 +66,7 @@
 #'   that are inside the envelope for all layers (included those not plotted)
 #'   are shown as green circles and those outside of the envelope for one ore
 #'   more variables are plotted as orange triangles.
-#' @author Jamie Kass <jkass@@gradcenter.cuny.edu>
+#' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 # @note
 #' @seealso

R/xfer_area.R

@@ -1,6 +1,6 @@
 # Wallace EcoMod: a flexible platform for reproducible modeling of
 # species niches and distributions.
-# 
+#
 # xfer_area.R
 # File author: Wallace EcoMod Dev Team. 2023.
 # --------------------------------------------------------------------------
@@ -81,9 +81,10 @@
 #'   RasterBrick or a RasterStack of the environmental variables cropped to the
 #'   area of transfer. The second element is a raster of the transferred model with
 #'   the specified output type.
-#' @author Jamie Kass <jkass@@gradcenter.cuny.edu>
+#' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Andrea Paz <paz.andreita@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 # @note
 #' @seealso \code{\link[dismo]{predict}}, \code{\link{xfer_time}}
 #' \code{\link{xfer_userEnvs}}