Merge pull request wallaceEcoMod#405 from bjohnso005/rgeosDEV

[v2.1.0] removed rgeos
bjohnso005 · Sep 25, 2023 · 299ec0a · 299ec0a
2 parents 24e2da2 + 662452f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2.0.6
-Date: 2023-09-05
+Version: 2.1.0
+Date: 2023-09-25
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 
@@ -45,7 +45,6 @@ Imports:
     magrittr,
     methods,
     RColorBrewer,
-    rgeos,
     rJava,
     rlang,
     rmarkdown,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+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)

diff --git a/R/penvs_bgExtent.R b/R/penvs_bgExtent.R
@@ -26,7 +26,7 @@
 #' occs$occID <- 1:nrow(occs)
 #' bgExt <- penvs_bgExtent(occs, bgSel = 'bounding box', bgBuf = 0.5)
 #'
-#' @return A SpatialPolygonsDataFrame object that contains all occurrences from occs
+#' @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>
 # @note
@@ -51,6 +51,10 @@ penvs_bgExtent <- function(occs, bgSel, bgBuf, logger = NULL, spN = NULL) {
   # make spatial pts object of original occs and preserve origID
   occs.sp <- sp::SpatialPointsDataFrame(occs.xy, data = occs['occID'])
 
+  # make an sf obj
+  occs.sf <- sf::st_as_sf(occs.xy, coords = c("longitude", "latitude"))
+  occs.sf <- sf::st_union(occs.sf, by_feature = FALSE)
+
   # generate background extent - one grid cell is added to perimeter of each shape
   # to ensure cells of points on border are included
   if (bgSel == 'bounding box') {
@@ -70,22 +74,29 @@ penvs_bgExtent <- function(occs, bgSel, bgBuf, logger = NULL, spN = NULL) {
     bgExt <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(as.matrix(xy.bord))), 1)))
     msg <- "Study extent: minimum convex polygon."
   } else if (bgSel == 'point buffers') {
-    if (bgBuf == 0) {
+    if (bgBuf <= 0) {
       logger %>%
       writeLog(type = 'error',
-               'Change buffer distance to positive or negative value.')
+               'Change buffer distance to a positive value.')
       return()
     }
-    bgExt <- rgeos::gBuffer(occs.sp, width = bgBuf)
+    bgExt <- sf::st_buffer(occs.sf, dist = bgBuf)
     msg <- paste0("Study extent: buffered points.  Buffered by ", bgBuf, " degrees.")
   }
 
-  if (bgBuf > 0 & bgSel != 'point buffers') {
-    bgExt <- rgeos::gBuffer(bgExt, width = bgBuf)
+  if (bgBuf >= 0 & bgSel != 'point buffers') {
+    bgExt <- sf::st_as_sf(bgExt)
+    bgExt <- sf::st_buffer(bgExt, dist = bgBuf)
     logger %>% writeLog(hlSpp(spN), msg, ' Buffered by ', bgBuf, ' degrees.')
+  } else if (bgBuf < 0 & bgSel != 'point buffers') {
+    logger %>%
+      writeLog(type = 'error',
+               'All localities must be included within extent.
+               Change buffer distance to a positive value.')
+    return()
   } else {
     logger %>% writeLog(hlSpp(spN), msg)
   }
-  bgExt <- methods::as(bgExt, "SpatialPolygonsDataFrame")
+  bgExt <- sf::as_Spatial(bgExt)
   return(bgExt)
 }
diff --git a/R/penvs_drawBgExtent.R b/R/penvs_drawBgExtent.R
@@ -35,9 +35,9 @@
 #'                          ncol = 2)
 #' drawBgBf <- penvs_drawBgExtent(polyExtXY = expertDrawPoly, polyExtID = 1,
 #'                                drawBgBuf = 0.5, occs)
-#' @return This functions returns a SpatialPolygonsDataFrame based on the user
-#' specified coordinates (drawn on map). This SpatialPolygonsDataFrame may be
-#' larger than specified if drawBgBuf > 0. The SpatialPolygonsDataFrame will
+#' @return This functions returns a SpatialPolygons object based on the user
+#' specified coordinates (drawn on map). This SpatialPolygons object may be
+#' larger than specified if drawBgBuf > 0. The SpatialPolygons object will
 #' include all occurrences.
 
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
@@ -56,10 +56,12 @@ penvs_drawBgExtent <- function(polyExtXY, polyExtID, drawBgBuf, occs,
   newPoly <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(polyExtXY)),
                                                    ID = polyExtID)))
   intersect <- sp::over(pts, newPoly)
+  newPoly.sf <- sf::st_as_sf(newPoly)
+
   ptRem <- ifelse(all(!is.na(intersect)), 0, as.numeric(which(is.na(intersect))))
   if (ptRem == 0) {
-    bgExt <- rgeos::gBuffer(newPoly, width = drawBgBuf)
-    bgExt <- methods::as(bgExt, "SpatialPolygonsDataFrame")
+    bgExt <- sf::st_buffer(newPoly.sf, dist = drawBgBuf)
+    bgExt <- sf::as_Spatial(bgExt)
     if (drawBgBuf == 0) {
       logger %>% writeLog(hlSpp(spN), 'Draw polygon without buffer.')
     } else {

diff --git a/R/penvs_userBgExtent.R b/R/penvs_userBgExtent.R
@@ -34,7 +34,7 @@
 #'                                userBgBuf = 0.2, occs = occs)
 #'
 #' @return This function returns a SpatialPolygons object with the user
-#'   provided shape (+ a buffer is userBgBuf >0). The polygon will be at least
+#'   provided shape (+ a buffer if userBgBuf >0). The polygon will be at least
 #'   large enough to contain all occurrences.
 #' @author Jamie Kass <jamie.m.kass@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
@@ -79,8 +79,13 @@ penvs_userBgExtent <- function(bgShp_path, bgShp_name, userBgBuf, occs,
     }
 
     if (userBgBuf >= 0) {
-      bgExt <- rgeos::gBuffer(bgExt, width = userBgBuf)
-      bgExt <- methods::as(bgExt, "SpatialPolygonsDataFrame")
+      bgExt <- sf::st_as_sf(bgExt)
+      bgExt <- sf::st_buffer(bgExt, dist = userBgBuf)
+      bgExt <- sf::as_Spatial(bgExt)
+    } else {
+      bgExt <- sf::st_as_sf(bgExt)
+      bgExt <- sf::st_buffer(bgExt, dist = userBgBuf)
+      bgExt <- sf::as_Spatial(bgExt)
     }
 
     ### Points outside polygon

diff --git a/R/xfer_draw.R b/R/xfer_draw.R
@@ -29,7 +29,7 @@
 #' polygonTest <- xfer_draw(polyXfXY = userDrawPoly, polyXfID,
 #'                          drawXfBuf)
 #'
-#' @return This functions returns a SpatialPolygonsDataFrame based on the user
+#' @return This functions returns a SpatialPolygons object based on the user
 #'   specified coordinates (drawn on map). This SpatialPolygonsDataFrame may be
 #'   larger than specified if drawBgBuf > 0.
 
@@ -41,8 +41,9 @@
 xfer_draw <- function(polyXfXY, polyXfID, drawXfBuf, logger = NULL, spN = NULL) {
   newPoly <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(polyXfXY)),
                                                    ID = polyXfID)))
-  bgExt <- rgeos::gBuffer(newPoly, width = drawXfBuf)
-  bgExt <- methods::as(bgExt, "SpatialPolygonsDataFrame")
+  newPoly.sf <- sf::st_as_sf(newPoly)
+  bgExt <- sf::st_buffer(newPoly.sf, dist = drawXfBuf)
+  bgExt <- sf::as_Spatial(bgExt)
   if (drawXfBuf == 0) {
     logger %>% writeLog(hlSpp(spN), 'Draw polygon without buffer.')
   } else {

diff --git a/R/xfer_userExtent.R b/R/xfer_userExtent.R
@@ -71,15 +71,19 @@ xfer_userExtent <- function(bgShp_path, bgShp_name, userBgBuf,
     return()
   }
 
-  if (userBgBuf >= 0) {
-    bgExt <- rgeos::gBuffer(bgExt, width = userBgBuf)
-    bgExt <- methods::as(bgExt, "SpatialPolygonsDataFrame")
-  }
   if (userBgBuf > 0) {
+    bgExt <- sf::st_as_sf(bgExt)
+    bgExt <- sf::st_buffer(bgExt, dist = userBgBuf)
+    bgExt <- sf::as_Spatial(bgExt)
     logger %>% writeLog(
       hlSpp(spN),
       'Transferring extent user-defined polygon buffered by ',
       userBgBuf, ' degrees.')
+  } else if (userBgBuf < 0) {
+    logger %>%
+      writeLog(type = 'error',
+               'Change buffer distance to a positive value.')
+    return()
   } else {
     logger %>% writeLog(
       hlSpp(spN),

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 (v2.0.6)
+# Wallace (v2.1.0)
 
 *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* v2.0.6 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* v2.1.0 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
 

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* (v2.0.6) 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* (v2.1.0) 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.
 

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* (v2.0.6) 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* (v2.1.0) 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:**  
 

diff --git a/inst/shiny/Rmd/text_team.Rmd b/inst/shiny/Rmd/text_team.Rmd
@@ -15,17 +15,20 @@ output: html_document
 
 <img src="img/gonzalo.png" alt="gonzalo" style="width: 100px;"/>
 
-<a href="https://scholar.google.no/citations?user=xlxAr_EAAAAJ&hl=en" target="_blank">Gonzalo E. Pinilla-Buitrago</a> (co-lead developer) is a PhD candidate at the CUNY Graduate Center and City College of New York.  
+<a href="https://scholar.google.no/citations?user=xlxAr_EAAAAJ&hl=en" target="_blank">Gonzalo E. Pinilla-Buitrago</a> (co-lead developer) received his PhD from the CUNY Graduate Center and City College of New York. He is currently a Postdoctoral Researcher at Yale University.  
 <br>
 
 <img src="img/andrea.png" alt="andrea" style="width: 100px;"/>
 
-<a href="https://andrepazv.github.io" target="_blank">Andrea Paz</a> (developer) received her PhD at CUNY Graduate Center and City College of New York and is now a Postdoctoral Researcher at the Crowther Lab in ETH Zürich.  
+<a href="https://andrepazv.github.io" target="_blank">Andrea Paz</a> (developer) received her PhD at CUNY Graduate Center and City College of New York, after which she was a Postdoctoral Researcher at the Crowther Lab in ETH Zürich. She is now an Assistant Professor at the Biological Sciences Department, University of Montréal.  
 <br>
 
 <img src="img/bethany.jpg" alt="bethany" style="width: 100px;"/>
 
-<a href="https://github.com/bjohnso005" target="_blank">Bethany A. Johnson</a> (developer) is a Master's student at the City College of New York.  
+<a href="https://github.com/bjohnso005" target="_blank">Bethany A. Johnson</a> (developer) received her MS in Biology from the City College of New York and is currently a Visiting Scientist at the Center for Biodiversity & Conservation at the American Museum of Natural History.  
+<br>
+
+<a href="https://www.amnh.org/research/staff-directory/daniel-lopez-lozano" target="_blank">Daniel López Lozano</a> (developer) is a Biodiversity Informatics Specialist at the American Museum of Natural History's Center for Biodiversity & Conservation.   
 <br>
 
 <img src="img/valentina.png" alt="valentina" style="width: 100px;"/>
@@ -57,7 +60,7 @@ output: html_document
 
 <img src="img/mary.png" alt="mary" style="width: 100px;"/>
 
-<a href="https://www.amnh.org/research/staff-directory/mary-e-blair" target="_blank">Mary E. Blair</a> (co-manager) is the Director of Biodiversity Informatics Research at the Center for Biodiversity and Conservation at the American Museum of Natural History.  
+<a href="https://www.amnh.org/research/staff-directory/mary-e-blair" target="_blank">Mary E. Blair</a> (co-manager) is the Director of Biodiversity Informatics Research at the Center for Biodiversity & Conservation at the American Museum of Natural History.  
 <br>
 
 ## Contributors
@@ -74,7 +77,7 @@ Sarah Meenan (contributor) completed her undergraduate degree from the City Coll
 
 <img src="img/peteG.jpg" alt="peteG" style="width: 100px;"/>
 
-<a href="https://www.amnh.org/research/staff-directory/peter-galante" target="_blank">Peter J. Galante</a> (contributor) was a Biodiversity Informatics Scientist at the Center for Biodiversity and Conservation at the American Museum of Natural History and now works as a Project Manager for Storke, LLC, a renewable energy company.
+<a href="https://www.amnh.org/research/staff-directory/peter-galante" target="_blank">Peter J. Galante</a> (contributor) was formerly a Biodiversity Informatics Scientist at the Center for Biodiversity & Conservation at the American Museum of Natural History and now works as a Project Manager for Storke, LLC, a renewable energy company.
 <br>
 
 <img src="img/brianM.jpeg" alt="brianM" style="width: 100px;"/>

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* v2.0.6 session. 
+Please find below the R code history from your *Wallace* v2.1.0 session. 
 
 You can reproduce your session results by running this R Markdown file in RStudio. 
 
@@ -25,7 +25,7 @@ Wallace uses the following R packages that must be installed and loaded before s
 library(spocc)
 library(spThin)
 library(dismo)
-library(rgeos)
+library(sf)
 library(ENMeval)
 library(wallace)
 ```