Merge pull request #415 from bjohnso005/biomodelos_DEV

Updates from v2 on biomodelos branch

.Rbuildignore

@@ -12,3 +12,4 @@ cmip5*    # worldclim files
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^LICENSE$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2023.03.16
-Date: 2023-03-16
+Version: 2024.02.23
+Date: 2024-02-23
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 
@@ -13,14 +13,14 @@ Description: The 'shiny' application Wallace is a modular platform for
     website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
 Authors@R: 
     c(person("Jamie M.", "Kass", email = "[email protected]", role = "aut"),
-    person("Gonzalo E.", "Pinilla-Buitrago", email = "[email protected]", role = c("aut", "cre")),
+    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 = "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"),
@@ -35,22 +35,26 @@ Depends:
     shiny (>= 1.6.0),
     leaflet (>= 2.0.2)
 Imports:
-    dplyr (>= 1.0.2),
     changeRangeR,
+    dplyr (>= 1.0.2),
     DT (>= 0.5),
-    ecospat,
+    ecospat (>= 4.0.0),
     ENMeval (>= 2.0.3),
     knitcitations,
     leafem,
     leaflet.extras (>= 1.0.0),
     magrittr,
     maskRangeR,
     RColorBrewer,
+    rJava,
     rlang,
     rmarkdown,
+    sf,
     shinyalert,
     shinyjs,
     shinyWidgets (>= 0.6.0),
+    spocc (>= 1.2.0),
+    spThin,
     terra (>= 1.6-7),
     zip
 Suggests: 
@@ -60,27 +64,23 @@ Suggests:
     geojsonsf,
     glue,
     httr,
+    glue,
     jsonlite,
     knitr,
     lubridate,
     mapview,
     maxnet,
     methods,
     occCite,
-    paleobioDB,
     rangeModelMetadata,
     raster,
     rgbif (>= 3.3.0),
-    rgdal,
-    rgeos,
-    rJava,
     sf,
     sp,
-    spThin,
-    spocc (>= 1.2.0),
     stars,
     testthat,
-    tidyselect
+    tidyselect,
+    tools
 Remotes: cmerow/changeRangeR
 License: GPL-3
 URL: http://wallaceecomod.github.io/wallace/,

NAMESPACE

@@ -4,6 +4,7 @@ export(clearAll)
 export(create_module)
 export(ecoClimate_getdata)
 export(ecoClimate_select)
+export(ecospat.plot.nicheDEV)
 export(envs_ecoClimate)
 export(envs_userEnvs)
 export(envs_worldclim)
@@ -32,7 +33,6 @@ export(model_bioclim)
 export(model_maxent)
 export(mxNonzeroCoefs)
 export(occs_biomodelos)
-export(occs_paleoDb)
 export(occs_queryDb)
 export(occs_userOccs)
 export(part_partitionOccs)

NEWS.md

@@ -1,3 +1,28 @@
+wallace 2.1.1
+=============
+- Fixed bug in occ density grid & niche overlap
+- Updated licensing
+- Updated developers & pkg maintainer
+
+wallace 2.1.0
+=============
+- Removed `rgeos` (package expiring)
+- Updated team bios
+- Added clarification to occs_queryDb guidance text
+- Added error msgs to xfer_time
+
+wallace 2.0.6
+=============
+- Removed `paleobioDB` (package off CRAN)
+- Removed `rgdal` (package expiring)
+- Changed Maintainer e-mail
+
+wallace 2.0.5
+=============
+- added try() to test_envs_worldclim.R
+- fixed broken links in guidance texts refs
+- fixed typo in thinOccs documentation
+
 wallace 2.0.4
 =============
 - Added Spanish translation of vignette

R/custom_modules.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# custom_modules.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 #' Register a Wallace module
 #'
 #' Before running the Wallace application with \code{run_wallace()}, you can

R/envs_ecoClimate.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# envs_ecoClimate.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title envs_ecoClimate Obtain ecoClimate variables
 #' @description download ecoClimate variables. See www.ecoclimate.org.
@@ -32,7 +55,7 @@
 #'
 #' @author Sara Varela <sara_varela@@yahoo.com>
 #' @author Jamie M. Kass <jamie.m.kass@@gmail.com>
-#' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
+#' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 #'
 #' @export
 #'

R/envs_userEnvs.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# envs_userEnvs.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 #'
 #' @title  envs_userEnvs
 #' @description Load user provided rasters
@@ -30,7 +53,7 @@
 #'   provided rasters
 #'
 #' @author Jamie Kass <jamie.m.kass@@gmail.com >
-#' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
+#' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 #' @export
 #'
 #'

R/envs_worldclim.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# envs_worldclim.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 #' @title envs_worldclim Obtain WorldClim variables
 #' @description download WorldClim variables. See www.worldclim.com.
 #'
@@ -29,7 +52,7 @@
 #'  worldclim rasters at the requested resolution.
 #'
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
-#' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
+#' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
 #'
 #' @seealso \code{\link[raster]{getData}}
 #'

R/espace_nicheOv.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# espace_nicheOv.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 #' @title espace_nicheOv Niche Overlap
 #' @description Function evaluates niche overlap between the two species for
 #'   which the occurrence density grid was computed
@@ -54,7 +77,7 @@
 #' }
 #'
 #' @return A list of 4 elements if all is set to TRUE. Elements are overlap
-#'   (Schoener's D), USE (ecopstat.niche.dyn.index), equiv and simil.
+#'   (Schoener's D), USE (ecospat.niche.dyn.index), equiv and simil.
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Olivier Broennimann <olivier.broennimann@@unil.ch>
 #' @seealso  \code{\link{espace_pca}} \code{\link{espace_occDens}}
@@ -80,15 +103,15 @@ espace_nicheOv <- function(z1, z2, iter = 100, equivalency = FALSE,
   if (equivalency == TRUE) {
     smartProgress(logger, message = "Calculating niche equivalency...", {
       nicheOv$equiv <- ecospat::ecospat.niche.equivalency.test(
-        z1, z2, iter, overlap.alternative = "higher"
+        z1, z2, rep = 100, overlap.alternative = "higher"
       )
     })
   }
 
   if (similarity == TRUE) {
     smartProgress(logger, message = "Calculating niche similarity", {
       nicheOv$simil <- ecospat::ecospat.niche.similarity.test(
-        z1, z2, iter, overlap.alternative = "higher", rand.type = 1
+        z1, z2, rep = 100, overlap.alternative = "higher", rand.type = 1
       )
     })
   }

R/espace_occDens.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# espace_occDens.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 
 #' @title Occurrence density grid
 #' @description calculates the part of environmental space more densely
@@ -48,7 +71,7 @@
 #' }
 #'
 #' @return Returns a list of 2 lists (one for each species). Each list is an
-#'   ecospat noche object that contains 10 species specific slots with
+#'   ecospat niche object that contains 10 species specific slots with
 #'   information outputed by ecospat::grid.clim.dyn. z.uncor is the density of
 #'   occurrence of the species and z.cor the occupancy of the environment by
 #'   the species. It has the input parameters as individual slots.

R/espace_pca.R

@@ -1,3 +1,26 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+# 
+# espace_pca.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 #' @title espace_pca Principal component analysis
 #' @description Principal component analysis to reduce dimensionality of
 #'   environmental space