Merge pull request #410 from bjohnso005/BAJdev

[v2.1.1] bug fix + license & maintainer edits
wallaceEcoMod · Dec 5, 2023 · 22ed5d6 · 22ed5d6
2 parents 17b0a4b + 9e08e2c
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@ cmip5*    # worldclim files
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^LICENSE$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2.1.0
-Date: 2023-09-25
+Version: 2.1.1
+Date: 2023-12-05
 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 = "jamie.kass@oist.jp", role = "aut"),
-    person("Gonzalo E.", "Pinilla-Buitrago", email = "gepinillab@gmail.com", role = c("aut", "cre")),
+    person("Gonzalo E.", "Pinilla-Buitrago", email = "gepinillab@gmail.com", role = "aut"),
 	 	person("Andrea", "Paz", email = "paz.andreita@gmail.com", role = "aut"),
 	 	person("Bethany A.", "Johnson", email = "bjohnso005@citymail.cuny.edu", role = "aut"),
 	 	person("Valentina", "Grisales-Betancur", email = "vgrisale@eafit.edu.co", role = "aut"),
 	  person("Dean", "Attali", email = "daattali@gmail.com", role = "aut"),
 	  person("Matthew E.", "Aiello-Lammens", email = "matt.lammens@gmail.com", role = "aut"),
 	  person("Cory", "Merow", email = "corymerow@gmail.com", role = "aut"),
-	  person("Mary E.", "Blair", email = "mblair1@amnh.org", role = "aut"),
+	  person("Mary E.", "Blair", email = "mblair1@amnh.org", role = c("aut", "cre")),
 	  person("Robert P.", "Anderson", email = "randerson@ccny.cuny.edu", role = "aut"),
 	  person("Sarah I.", "Meenan", email = "sarah.meenan@gmail.com", role = "ctb"),
 	  person("Olivier", "Broennimann", email = "olivier.broennimann@unil.ch", role = "ctb"),

diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/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)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+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)

diff --git a/R/espace_nicheOv.R b/R/espace_nicheOv.R
@@ -54,7 +54,7 @@
 #' }
 #'
 #' @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 +80,15 @@ 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
       )
     })
   }

diff --git a/R/espace_occDens.R b/R/espace_occDens.R
@@ -48,7 +48,7 @@
 #' }
 #'
 #' @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.

diff --git a/R/helper_functions.R b/R/helper_functions.R
@@ -311,6 +311,50 @@ remEnvsValsNA <- function(occs, occsEnvsVals, spN, logger) {
   })
 }
 
+####################### #
+# ESPACE #
+####################### #
+#' @title ecospat.plot.nicheDEV
+#' @description For internal use. Plot occ density
+#' @param z A gridclim object for the species distribution created by ecospat.grid.clim.dyn()/espace_occDens().
+#' @param title A title for the plot.
+#' @param name.axis1 A label for the first axis.
+#' @param name.axis2 A label for the second axis.
+#' @param cor Correct the occurrence densities of the species by the prevalence of the environments in its range (TRUE = yes, FALSE = no).
+#' @keywords internal
+#' @export
+ecospat.plot.nicheDEV <- function(z, title = "", name.axis1 = "Axis 1", name.axis2 = "Axis 2", cor = FALSE) {
+  if (is.null(z$y)) {
+    R <- length(z$x)
+    x <- z$x
+    xx <- sort(rep(1:length(x), 2))
+    if (cor == FALSE)
+      y1 <- z$z.uncor/max(z$z.uncor)
+    if (cor == TRUE)
+      y1 <- z$z.cor/max(z$z.cor)
+    Y1 <- z$Z/max(z$Z)
+    yy1 <- sort(rep(1:length(y1), 2))[-c(1:2, length(y1) * 2)]
+    YY1 <- sort(rep(1:length(Y1), 2))[-c(1:2, length(Y1) * 2)]
+    plot(x, y1, type = "n", xlab = name.axis1, ylab = "density of occurrence")
+    graphics::polygon(x[xx], c(0, y1[yy1], 0, 0), col = "grey")
+    graphics::lines(x[xx], c(0, Y1[YY1], 0, 0))
+  }
+  if (!is.null(z$y)) {
+    if (cor == FALSE)
+      terra::plot(z$z.uncor,col=grDevices::gray(100:0 / 100),legend=FALSE, xlab = name.axis1,
+                  ylab = name.axis2,mar = c(3.1,3.1,2.1,3.1))
+    if (cor == TRUE)
+      terra::plot(z$z.cor,col=grDevices::gray(100:0 / 100),legend=FALSE, xlab = name.axis1,
+                  ylab = name.axis2,mar = c(3.1,3.1,2.1,3.1))
+    terra::contour(
+      z$Z, add = TRUE, levels = stats::quantile(z$Z[z$Z > 0], c(0, 0.5)),
+      drawlabels = FALSE, lty = c(1, 2)
+    )
+  }
+  title(title)
+}
+# end of espace. BAJ added 10/31/2023 after ecospat.plot.niche() from ecospat 4.0.0 wasn't working
+
 ####################### #
 # VISUALIZE & TRANSFER #
 ####################### #

diff --git a/R/penvs_bgExtent.R b/R/penvs_bgExtent.R
@@ -29,6 +29,7 @@
 #' @return A SpatialPolygons object that contains all occurrences from occs
 #' @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{penvs_userBgExtent}}, \code{\link{penvs_drawBgExtent}},

diff --git a/R/penvs_drawBgExtent.R b/R/penvs_drawBgExtent.R
@@ -42,6 +42,7 @@
 
 #' @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{penvs_userBgExtent}}, \code{\link{penvs_bgExtent}},
 #' \code{\link{penvs_bgMask}} , \code{\link{penvs_bgSample}}

diff --git a/R/penvs_userBgExtent.R b/R/penvs_userBgExtent.R
@@ -39,6 +39,7 @@
 #' @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{penvs_drawBgExtent}}, \code{\link{penvs_bgExtent}},

diff --git a/R/xfer_draw.R b/R/xfer_draw.R
@@ -34,6 +34,7 @@
 #'   larger than specified if drawBgBuf > 0.
 
 #' @author Gonzalo Pinilla <gepinillab@@gmail.com>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 # @note
 #' @seealso  \code{\link{xfer_userEnvs}}
 #' @export

diff --git a/R/xfer_userExtent.R b/R/xfer_userExtent.R
@@ -33,6 +33,7 @@
 #' @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>
 #' @seealso \code{\link{penvs_drawBgExtent}}, \code{\link{penvs_bgExtent}},
 #'   \code{\link{penvs_bgMask}} , \code{\link{penvs_bgSample}}
 #' @export

diff --git a/README.md b/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 (v2.1.0)
+# Wallace (v2.1.1)
 
 *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* v2.1.0 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.
+*Wallace* v2.1.1 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
 

diff --git a/inst/shiny/Rmd/text_about.Rmd b/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* (v2.1.0) 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* (v2.1.1) 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.
 
@@ -47,15 +47,17 @@ For more information and relevant links see our <a href="https://wallaceecomod.g
 
 *The following webinar was part of "ENM 2020", a free online course on ecological niche modeling, organized by Town Peterson. The full series can be found on YouTube: <a href="https://www.youtube.com/playlist?list=PLhEJuWmv8Jf67qSdifDvgOk5DOJsNNiam" target="_blank">ENM 2020</a>.*
 
-Kass, J.M. and G.E. Pinilla-Buitrago. 18 May 2020. “Wallace Ecological Modeling Application: flexible and reproducible modeling of species’ niches and distributions built for community expansion.” ENM 2020: Online course in ecological niche modeling (Peterson, A. T. editor), Week 19, Talk 2. <a href="https://youtu.be/kWNyNd2X1uo" target="_blank">Watch on YouTube</a>.  
+Kass, J.M. and G.E. Pinilla-Buitrago. 18 May 2020. “Wallace Ecological Modeling Application: flexible and reproducible modeling of species’ niches and distributions built for community expansion.” ENM 2020: Online course in ecological niche modeling (Peterson, A. T. editor), <a href="https://youtu.be/kWNyNd2X1uo" target="_blank">Week 19, Talk 2</a>.  
 
 *The following webinar was the "37th Global Online Biodiversity Informatics Seminar" in the Biodiversity Informatics Training Curriculum organized by Town Peterson.*
 
-Kass, J. M. 9 May 2018. "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. <a href="https://www.youtube.com/watch?v=00CSd9vx2CE&feature=youtu.be" target="_blank">Watch on YouTube</a>.
+Kass, J. M. 9 May 2018. "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. <a href="https://www.youtube.com/watch?v=00CSd9vx2CE&feature=youtu.be" target="_blank">Global Online Seminar #37 - Wallace</a>.
 
-*The following webinar was part of the "Modelado de Distribuciones Potenciales" series, organized by Angela Cuervo.*
+*Para seminarios en español, los siguientes seminarios fueron organizados por Angela Cuervo como parte de la serie Modelado de Distribuciones Potenciales y Analisis Espaciales.*
 
-Anderson, R. P. 21 May 2018. "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. <a href="https://www.youtube.com/watch?v=0652g9PDKp4" target="_blank">Watch on YouTube</a>.  
+Paz, A. 3 October 2023. "Wallace EcoMod: Nuevas funcionalidades para aplicaciones en conservación". <a href="https://www.youtube.com/live/_X5fXqRJ_EY?si=xHbQSw9dnvQemqAJ" target="_blank">Seminarios 2023 - Wallace EcoMod</a>  
+
+Anderson, R. P. 21 May 2018. "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. <a href="https://www.youtube.com/watch?v=0652g9PDKp4" target="_blank">Analisis espaciales: 2017 - El software Wallace</a>.  
 
 *For more videos, check out the <a href="https://www.youtube.com/channel/UCDSLCE5bmw12B7oqmlKk7rg" target="_blank">Wallace EcoMod YouTube channel</a>.*
 

diff --git a/inst/shiny/Rmd/text_intro_tab.Rmd b/inst/shiny/Rmd/text_intro_tab.Rmd
@@ -5,7 +5,7 @@ output: html_document
 
 #### WORKFLOW
 
-*Wallace* (v2.1.0) currently includes ten components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step.  
+*Wallace* (v2.1.1) 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:**  
 

diff --git a/inst/shiny/Rmd/userReport_intro.Rmd b/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* v2.1.0 session. 
+Please find below the R code history from your *Wallace* v2.1.1 session. 
 
 You can reproduce your session results by running this R Markdown file in RStudio. 
 

diff --git a/inst/shiny/modules/espace_occDens.R b/inst/shiny/modules/espace_occDens.R
@@ -66,8 +66,8 @@ espace_occDens_module_server <- function(input, output, session, common) {
       mSp <- curSp()
     }
     req(spp[[mSp]]$occDens)
-    ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp1]], title = spName(sp1))
-    ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp2]], title = spName(sp2))
+    ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp1]], title = spName(sp1))
+    ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp2]], title = spName(sp2))
   })
 }
 

diff --git a/inst/shiny/modules/espace_occDens.Rmd b/inst/shiny/modules/espace_occDens.Rmd
@@ -11,8 +11,8 @@ espace_occDens_{{multAbr}} <- espace_occDens(
   pca = espace_pca_{{multAbr}}) 
 # Plots
 graphics::par(mfrow = c(1,2))
-ecospat::ecospat.plot.niche(espace_occDens_{{multAbr}}[["{{spName1}}"]], 
+ecospat.plot.nicheDEV(espace_occDens_{{multAbr}}[["{{spName1}}"]], 
                             title = "{{spName1}}")
-ecospat::ecospat.plot.niche(espace_occDens_{{multAbr}}[["{{spName2}}"]], 
+ecospat.plot.nicheDEV(espace_occDens_{{multAbr}}[["{{spName2}}"]], 
                             title = "{{spName2}}")
 ```
diff --git a/inst/shiny/modules/penvs_bgExtent.yml b/inst/shiny/modules/penvs_bgExtent.yml
@@ -1,5 +1,5 @@
 component: "penvs"
 short_name: "Select Study Region"
 long_name: "Select Study Region by Extent"
-authors: "Jamie M. Kass, Bruno Vilela, Robert P. Anderson"
+authors: "Jamie M. Kass, Bruno Vilela, Bethany A. Johnson, Robert P. Anderson"
 package: [sp, sf]
diff --git a/inst/shiny/modules/penvs_drawBgExtent.yml b/inst/shiny/modules/penvs_drawBgExtent.yml
@@ -1,5 +1,5 @@
 component: "penvs"
 short_name: "Draw Study Region"
 long_name: "Draw Study Region"
-authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Bruno Vilela, Robert P. Anderson"
+authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Bruno Vilela, Bethany A. Johnson, Robert P. Anderson"
 package: []
diff --git a/inst/shiny/modules/penvs_userBgExtent.yml b/inst/shiny/modules/penvs_userBgExtent.yml
@@ -1,5 +1,5 @@
 component: "penvs"
 short_name: "User-specified Study Region"
 long_name: "User-specified Study Region"
-authors: "Jamie M. Kass, Bruno Vilela, Robert P. Anderson"
+authors: "Jamie M. Kass, Bruno Vilela, Bethany A. Johnson, Robert P. Anderson"
 package: []
diff --git a/inst/shiny/modules/xfer_area.yml b/inst/shiny/modules/xfer_area.yml
@@ -1,5 +1,5 @@
 component: "xfer"
 short_name: "Transfer to New Extent"
 long_name: "Transfer to New Extent"
-authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Robert P. Anderson"
+authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Bethany A. Johnson, Robert P. Anderson"
 package: [dismo]
diff --git a/inst/shiny/modules/xfer_time.yml b/inst/shiny/modules/xfer_time.yml
@@ -1,5 +1,5 @@
 component: "xfer"
 short_name: "Transfer to New Time"
 long_name: "Transfer to New Time"
-authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Robert P. Anderson"
+authors: "Jamie M. Kass, Bruno Vilela, Gonzalo E. Pinilla-Buitrago, Bethany A. Johnson, Robert P. Anderson"
 package: [dismo]
diff --git a/inst/shiny/modules/xfer_user.yml b/inst/shiny/modules/xfer_user.yml
@@ -1,5 +1,5 @@
 component: "xfer"
 short_name: "Transfer to User Environments"
 long_name: "Transfer to User Environments"
-authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Robert P. Anderson"
+authors: "Gonzalo E. Pinilla-Buitrago, Jamie M. Kass, Bethany A. Johnson, Robert P. Anderson"
 package: [dismo]
diff --git a/inst/shiny/server.R b/inst/shiny/server.R
@@ -521,8 +521,8 @@ function(input, output, session) {
         mSp <- curSp()
       }
       req(spp[[mSp]]$occDens)
-      ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp1]], title = spName(sp1))
-      ecospat::ecospat.plot.niche(spp[[mSp]]$occDens[[sp2]], title = spName(sp2))
+      ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp1]], title = spName(sp1))
+      ecospat.plot.nicheDEV(spp[[mSp]]$occDens[[sp2]], title = spName(sp2))
       dev.off()
     }
   )

diff --git a/man/ecospat.plot.nicheDEV.Rd b/man/ecospat.plot.nicheDEV.Rd