Merging dev v2.2.0 into master

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2.1.3
-Date: 2024-07-18
+Version: 2.2.0
+Date: 2025-03-06
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 
@@ -13,6 +13,7 @@ Description: The 'shiny' application Wallace is a modular platform for
     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"),
     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"),
@@ -38,7 +39,7 @@ Imports:
     dplyr (>= 1.0.2),
     DT (>= 0.5),
     ecospat (>= 4.0.0),
-    ENMeval (>= 2.0.3),
+    ENMeval (>= 2.0.5),
     geodata,
     knitcitations,
     leafem,
@@ -67,6 +68,7 @@ Suggests:
     mapview,
     maxnet,
     occCite,
+    predicts,
     rangeModelMetadata,
     raster,
     rgbif (>= 3.3.0),

NEWS.md

@@ -1,3 +1,9 @@
+wallace 2.2.0
+=============
+- updated for ENMeval v2.0.5 functionality
+- updated module skeleton & module addition vignette to include `knitcitations` for References
+- RPA edits to guidance texts
+
 wallace 2.1.3
 =============
 - Fixed NULL error in poccs_selectOccs Rmd code

R/model_bioclim.R

@@ -63,6 +63,7 @@
 
 #' @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>
 # @note
 
 #' @seealso \code{\link[ENMeval]{ENMevaluate}}
@@ -79,7 +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 = bgMsk, bg = bg.xy,
+     e <- ENMeval::ENMevaluate(occs = occs.xy, envs = terra::rast(bgMsk), bg = bg.xy,
                                algorithm = "bioclim", partitions = "user",
                                user.grp = user.grp)
   })

R/model_maxent.R

@@ -85,6 +85,7 @@
 #'   and a selection of appropriate fields.
 #' @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>
 # @note
 
 #' @seealso \code{\link[ENMeval]{ENMevaluate}}
@@ -196,14 +197,14 @@ model_maxent <- function(occs, bg, user.grp, bgMsk, rms, rmsStep, fcs,
                             bg = as.data.frame(bg.xy),
                             partitions = 'user',
                             user.grp = user.grp,
-                            envs = bgMsk,
+                            envs = terra::rast(bgMsk),
                             tune.args = tune.args,
                             doClamp = clampSel,
                             algorithm = algMaxent,
                             categoricals = catEnvs,
                             parallel = parallel,
                             numCores = numCores,
-                            parallelType = "doSNOW",
+                           # parallelType = "doSNOW",
                             # taxon.name = NULL,
                             # user.enm = NULL,
                             # occs.ind = NULL,

R/part_partitionOccs.R

@@ -40,8 +40,8 @@
 #'  (1) 'jack' Non-spatial Partition - jackknife  \cr
 #'  (2) 'rand' Non-spatial Partition - random k-fold  \cr
 #'  (3) 'block' spatial Partition - block  \cr
-#'  (4) 'cb1' spatial Partition - checkerboard 1 (K=2)  \cr
-#'  (5) 'cb2' spatial Partition - checkerboard 2 (K=4)  \cr
+#'  (4) 'cb1' spatial Partition - checkerboard (k=2)  \cr
+#'  (5) 'cb2' spatial Partition - hierarchical checkerboard (k=4)  \cr
 #' @param kfolds numeric. Number of partitions to create if selected method is
 #'   random k-fold (must be >=2). If other method then keep default of NULL.
 #' @param bgMask a RasterStack or a RasterBrick of environmental layers cropped
@@ -75,6 +75,7 @@
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 #' @author Andrea Paz <paz.andreita@@gmail.com>
+#' @author Bethany A Johnson <bjohnso005@@citymail.cuny.edu>
 # @note
 #' @seealso \code{\link[ENMeval]{partitions}}
 # @references
@@ -163,22 +164,23 @@ part_partitionOccs <- function(occs, bg, method, kfolds = NULL, bgMask = NULL,
 
   if(method == 'cb1') {
     smartProgress(logger, message = "Aggregating rasters...", {
-      group.data <- ENMeval::get.checkerboard1(occs.xy, bgMask, bg.xy, aggFact)
+      group.data <- ENMeval::get.checkerboard(occs.xy, terra::rast(bgMask), bg.xy, aggFact)
     })
 
     logger %>% writeLog(hlSpp(spN),
-                        "Occurrences partitioned by checkerboard 1 method with ",
-                        "aggregation factor ", aggFact, ".")
+                        "Occurrences partitioned by checkerboard method with ",
+                        "aggregation factor of ", aggFact, ".")
   }
 
   if(method == 'cb2') {
     smartProgress(logger, message = "Aggregating rasters...", {
-      group.data <- ENMeval::get.checkerboard2(occs.xy, bgMask, bg.xy, aggFact)
+      group.data <- ENMeval::get.checkerboard(occs.xy, terra::rast(bgMask),
+                                               bg.xy, c(aggFact, aggFact))
     })
 
     logger %>% writeLog(hlSpp(spN),
-                        "Occurrences partitioned by checkerboard 2 method with ",
-                        "aggregation factor ", aggFact, ".")
+                        "Occurrences partitioned by hierarchical checkerboard method with ",
+                        "aggregation factor of ", aggFact, ".")
   }
   return(group.data)
 }

R/vis_bioclimPlot.R

@@ -68,6 +68,7 @@
 #'   more variables are plotted as orange triangles.
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 # @note
 #' @seealso
 #'\code{\link{model_bioclim}} \code{\link[ENMeval]{ENMevaluate}}

R/xfer_area.R

@@ -69,11 +69,22 @@
 #' polyExt <-
 #'   sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(selCoords)),
 #'                       ID = 1)))
-#' # load model
-#' m <- readRDS(system.file("extdata/model.RDS",
-#'                          package = "wallace"))
+#' # build model
+#' occs <- read.csv(system.file("extdata/Bassaricyon_alleni.csv",
+#'   package = "wallace"))
+#' bg <- read.csv(system.file("extdata/Bassaricyon_alleni_bgPoints.csv",
+#'   package = "wallace"))
+#' partblock <- part_partitionOccs(occs, bg, method = 'block')
+#' m <- model_maxent(occs, bg,
+#'   user.grp = partblock,
+#'   bgMsk = envs, rms = c(1:2),
+#'   rmsStep = 1, fcs = c('L', 'LQ'),
+#'   clampSel = TRUE,
+#'   algMaxent = "maxnet",
+#'   parallel = FALSE)
+#' ### run function
 #' modXfer <- xfer_area(evalOut = m, curModel = 1, envs,
-#'                      outputType = 'cloglog', alg = 'maxent.jar',
+#'                      outputType = 'cloglog', alg = 'maxnet',
 #'                      clamp = TRUE, xfExt = polyExt)
 #' }
 #'
@@ -117,18 +128,16 @@ xfer_area <- function(evalOut, curModel, envs, xfExt, alg, outputType = NULL,
 
   smartProgress(logger, message = 'Transferring model to new area...', {
     if (alg == 'BIOCLIM') {
-      modXferArea <- dismo::predict(evalOut@models[[curModel]], xferMsk,
-                                    useC = FALSE)
+      modXferArea <- dismo::predict(evalOut@models[[curModel]], terra::rast(xferMsk))
     } else if (alg == 'maxnet') {
       if (outputType == "raw") outputType <- "exponential"
       modXferArea <- predictMaxnet(evalOut@models[[curModel]], xferMsk,
                                           type = outputType, clamp = clamp)
     } else if (alg == 'maxent.jar') {
       modXferArea <- dismo::predict(
-        evalOut@models[[curModel]], xferMsk,
+        evalOut@models[[curModel]], terra::rast(xferMsk),
         args = c(paste0("outputformat=", outputType),
-                 paste0("doclamp=", tolower(as.character(clamp)))),
-        na.rm = TRUE)
+                 paste0("doclamp=", tolower(as.character(clamp)))))
     }
   })
 

R/xfer_time.R

@@ -74,17 +74,21 @@
 #' selCoords <- matrix(c(longitude, latitude), byrow = FALSE, ncol = 2)
 #' polyExt <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(selCoords)),
 #'                                                  ID = 1)))
-#' # load model
-#' m <- readRDS(system.file("extdata/model.RDS",
-#'                          package = "wallace"))
+#' # build model
+#' occs <- read.csv(system.file("extdata/Bassaricyon_alleni.csv",package = "wallace"))
+#' bg <- read.csv(system.file("extdata/Bassaricyon_alleni_bgPoints.csv", package = "wallace"))
+#' partblock <- part_partitionOccs(occs, bg, method = 'block')
+#' m <- model_maxent(occs, bg, user.grp = partblock, bgMsk = envs, rms = c(1:2),
+#' rmsStep = 1, fcs = c('L', 'LQ'),
+#' clampSel = TRUE, algMaxent = "maxnet", parallel = FALSE)
 #' occsEnvs <- m@@occs
 #' bgEnvs <- m@@bg
 #' envsFut <- list.files(path = system.file('extdata/wc/future',
 #'                                          package = "wallace"),
 #'                       full.names = TRUE)
 #' envsFut <- raster::stack(envsFut)
 #' modXfer <- xfer_time(evalOut = m, curModel = 1,
-#'                      envs = envsFut, alg = 'maxent.jar',
+#'                      envs = envsFut, alg = 'maxnet',
 #'                      xfExt = polyExt, clamp = FALSE, outputType = 'cloglog')
 #' }
 
@@ -129,18 +133,16 @@ xfer_time <- function(evalOut, curModel, envs, xfExt, alg, outputType = NULL,
     logger,
     message = ("Transferring to new time..."), {
     if (alg == 'BIOCLIM') {
-      modXferTime <- dismo::predict(evalOut@models[[curModel]], xftMsk,
-                                    useC = FALSE)
+      modXferTime <- dismo::predict(evalOut@models[[curModel]], terra::rast(xftMsk))
     } else if (alg == 'maxnet') {
       if (outputType == "raw") outputType <- "exponential"
       modXferTime <- predictMaxnet(evalOut@models[[curModel]], xftMsk,
                                           type = outputType, clamp = clamp)
     } else if (alg == 'maxent.jar') {
       modXferTime <- dismo::predict(
-        evalOut@models[[curModel]], xftMsk,
+        evalOut@models[[curModel]], terra::rast(xftMsk),
         args = c(paste0("outputformat=", outputType),
-                 paste0("doclamp=", tolower(as.character(clamp)))),
-        na.rm = TRUE)
+                 paste0("doclamp=", tolower(as.character(clamp)))))
     }
   })
   return(list(xferExt = xftMsk, xferTime = modXferTime))

R/xfer_userEnvs.R

@@ -63,16 +63,24 @@
 #' selCoords <- matrix(c(longitude, latitude), byrow = FALSE, ncol = 2)
 #' polyExt <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(selCoords)),
 #'                                                  ID = 1)))
-#' # load model
-#' m <- readRDS(system.file("extdata/model.RDS",
-#'                          package = "wallace"))
+#' # build model
+#' occs <- read.csv(system.file("extdata/Bassaricyon_alleni.csv",package = "wallace"))
+#' bg <- read.csv(system.file("extdata/Bassaricyon_alleni_bgPoints.csv",
+#' package = "wallace"))
+#' envs <- envs_userEnvs(rasPath = list.files(system.file("extdata/wc",
+#' package = "wallace"), pattern = ".tif$", full.names = TRUE),
+#' rasName = list.files(system.file("extdata/wc",package = "wallace"),
+#' pattern = ".tif$", full.names = FALSE))
+#' partblock <- part_partitionOccs(occs, bg, method = 'block')
+#' m <- model_maxent(occs, bg, user.grp = partblock, bgMsk = envs, rms = c(1:2),
+#' rmsStep = 1, fcs = c('L', 'LQ'), clampSel = TRUE, algMaxent = "maxnet", parallel = FALSE)
 #' envsFut <- list.files(path = system.file('extdata/wc/future',
 #'                                          package = "wallace"),
 #'                       full.names = TRUE)
 #' envsFut <- raster::stack(envsFut)
 #' ### run function
 #' modXfer <- xfer_userEnvs(evalOut = m, curModel = 1, envs = envsFut,
-#'                          outputType = "cloglog", alg = "maxent.jar",
+#'                          outputType = "cloglog", alg = "maxnet",
 #'                          clamp = FALSE, xfExt = polyExt)
 #' }
 #'
@@ -114,18 +122,16 @@ xfer_userEnvs <- function(evalOut, curModel, envs, xfExt, alg, outputType = NULL
     logger,
     message = 'Transferring model to user uploaded environmental variables & area', {
     if (alg == 'BIOCLIM') {
-      modXferUser <- dismo::predict(evalOut@models[[curModel]], xferMsk,
-                                    useC = FALSE)
+      modXferUser <- dismo::predict(evalOut@models[[curModel]], terra::rast(xferMsk))
     } else if (alg == 'maxnet') {
       if (outputType == "raw") outputType <- "exponential"
       modXferUser <- predictMaxnet(evalOut@models[[curModel]], xferMsk,
                                           type = outputType, clamp = clamp)
     } else if (alg == 'maxent.jar') {
       modXferUser <- dismo::predict(
-        evalOut@models[[curModel]], xferMsk,
+        evalOut@models[[curModel]], terra::rast(xferMsk),
         args = c(paste0("outputformat=", outputType),
-                 paste0("doclamp=", tolower(as.character(clamp)))),
-        na.rm = TRUE)
+                 paste0("doclamp=", tolower(as.character(clamp)))))
     }
   })
 

README.md

@@ -1,6 +1,6 @@
 [![R-CMD-check](https://github.com/wallaceEcoMod/wallace/workflows/R-CMD-check/badge.svg)](https://github.com/wallaceEcoMod/wallace/actions) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![CRAN version](http://www.r-pkg.org/badges/version/wallace)](https://CRAN.R-project.org/package=wallace) [![downloads](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)
 
-# Wallace (v2.1.3)
+# Wallace (v2.2.0)
 
 *Wallace* is a modular platform for reproducible modeling of species niches and distributions, written in R. The application guides users through a complete analysis, from the acquisition of data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
 
@@ -27,7 +27,7 @@ run_wallace()
 Please make sure you have installed the latest versions of both R (<a href= "https://cran.r-project.org/bin/macosx/" target="_blank">Mac OS</a>, <a href= "https://cran.r-project.org/bin/windows/base/" target="_blank">Windows</a>) and RStudio (<a href= "https://posit.co/download/rstudio-desktop/" target="_blank">Mac OS /  Windows</a>: choose the free version).
 
 #### How to run Maxent with maxent.jar
-*Wallace* v2.1.3 includes two options to run Maxent models: maxnet and maxent.jar. The former, which is an R implementation and fits the model with the package `glmnet`, is now the default and does not require the package `rJava` (see Phillips et al. 2017). The latter, which is the Java implementation, runs the `maxent()` function in the package `dismo`. This function requires the user to place the `maxent.jar` file in the `/java` directory of the `dismo` package root folder. You can download Maxent <a href="https://biodiversityinformatics.amnh.org/open_source/maxent/" target="_blank">here</a>, and locate `maxent.jar`, which is the Maxent program itself, in the downloaded folder. You can find the directory path to `dismo/java` by running `system.file('java', package="dismo")` at the R console. Simply copy `maxent.jar` and paste it into this folder. If you try to run Maxent in *Wallace* without the file in place, you will get a warning message in the log window and Maxent will not run.
+*Wallace* v2.2.0 includes two options to run Maxent models: maxnet and maxent.jar. The former, which is an R implementation and fits the model with the package `glmnet`, is now the default and does not require the package `rJava` (see Phillips et al. 2017). The latter, which is the Java implementation, runs the `maxent()` function in the package `dismo`. This function requires the user to place the `maxent.jar` file in the `/java` directory of the `dismo` package root folder. You can download Maxent <a href="https://biodiversityinformatics.amnh.org/open_source/maxent/" target="_blank">here</a>, and locate `maxent.jar`, which is the Maxent program itself, in the downloaded folder. You can find the directory path to `dismo/java` by running `system.file('java', package="dismo")` at the R console. Simply copy `maxent.jar` and paste it into this folder. If you try to run Maxent in *Wallace* without the file in place, you will get a warning message in the log window and Maxent will not run.
 
 ### Potential Issues
 

inst/module_skeleton/skeleton.R

@@ -15,6 +15,8 @@
 
     # LOAD INTO SPP ####
 
+    # REFERENCES ####
+
     # METADATA ####
   })
 

inst/shiny/Rmd/text_about.Rmd

@@ -7,7 +7,7 @@ output: html_document
 
 <img src="logo.png" alt="logo" style="width: 150px; float:right; padding:10px;"/>
 
-Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v2.1.3) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results.
+Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v2.2.0) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results.
 
 The application is written in `R` with the web app development package `shiny`. Please find the stable version of *Wallace* on <a href="https://CRAN.R-project.org/package=wallace" target="_blank">CRAN</a>, and the development version on <a href="https://github.com/wallaceEcoMod/wallace" target="_blank">Github</a>. We also maintain a *Wallace* <a href="https://wallaceecomod.github.io/" target="_blank">website</a> that has some basic info, links, and will be updated with tutorial materials in the near future.
 

inst/shiny/Rmd/text_intro_tab.Rmd

@@ -5,7 +5,7 @@ output: html_document
 
 #### WORKFLOW
 
-*Wallace* (v2.1.3) currently includes ten components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step.  
+*Wallace* (v2.2.0) currently includes ten components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step.  
 
 **Components:**  
 

inst/shiny/Rmd/userReport_intro.Rmd

@@ -10,7 +10,7 @@ knit_engines$set(asis = function(options) {
 knitr::opts_chunk$set(message = FALSE, warning = FALSE, eval = FALSE)
 ```
 
-Please find below the R code history from your *Wallace* v2.1.3 session. 
+Please find below the R code history from your *Wallace* v2.2.0 session. 
 
 You can reproduce your session results by running this R Markdown file in RStudio. 
 

inst/shiny/modules/envs_userEnvs.md

@@ -26,6 +26,6 @@ Users will need to know what the original CRS of their rasters is, then look up
 
 *NOTE: A reminder that some file types like .asc cannot embed CRS information in the file, so please avoid these types -- instead use types such as .tif that retain the CRS.*
 
-A warning message will appear if your layers have NA values falling in pixels that are not consistent among each layer.  You can continue using them, but some downstream steps of analyses may not be functional. Alternatively, you can assign values in a GIS program or mask the layers to have matching NA values outside of Wallace in R.  
+A warning message will appear if your layers have NA values for pixels that are not consistent among all of the layers.  You can continue using them, but some downstream analyses may not be functional. Alternatively, before uploading rasters to Wallace, you can assign values in a GIS program or mask the rasters in R to have matching NA values.  
 
-Using your own environmental data will disable the Module: *Transfer to New Time*, as this module requires WorldClim bioclimatic variables. The Module: *Transfer to User Environments* is still available. 
+Using your own environmental data here will disable the later *Transfer to New Time* module, as it requires WorldClim bioclimatic variables. The later Module: *Transfer to User Environments* is still available.