Merge pull request #9 from danflop/master_fix

Merge and fix conflicts between master and cran_v1 branches

.Rbuildignore

@@ -1,4 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^doc$
+^docs$
 ^Meta$
+^_pkgdown\.yml$
+^CRAN-SUBMISSION$

.gitignore

@@ -8,3 +8,4 @@ DESCRIPTION
 vignettes/fastDiversity_cache/*
 doc
 Meta
+CRAN-SUBMISSION

DESCRIPTION

@@ -2,20 +2,19 @@ Package: changeRangeR
 Type: Package
 Title: Change Metrics for Species Geographic Ranges
 Version: 1.1.0
-Author: c(person('Peter J.', 'Galante',email='pgalante@amnh.org',role=c('aut','cre')),
-    person('Samuel','Chang',email='changalfsam@gmail.com',role=c('aut'))
-    person('Andrea','Paz',email='paz.andreita@gmail.com',role=c('aut'))
-    person('Jamie M.','Kass',email='jamie.kass@oist.jp',role=c('aut'))
-    person('Matthew','Aiello-Lammens',email='maiellolammens@pace.edu',role=c('aut'))
-    person('Beth','Gerstner',email='gerstn11@msu.edu',role=c('aut'))
-    person('Bethany A.','Johnson',email='bjohnso005@citymail.cuny.edu',role=c('aut'))
-    person('Cory','Merow',email='cory.merow@gmail.com',role=c('aut'))
-    person('Elkin','Noguera-Urbano',email='enoguera@humboldt.org.co',role=c('aut'))
-    person('Gonzalo E.','Pinilla-Buitrago',email='gpinillabuitrago@gradcenter.cuny.edu',role=c('aut'))
-    person('Dan','Rosauer',email='dan.rosauer@anu.edu.au',role=c('aut'))
-    person('Mary E.','Blair',email='mblair1@amnh.org',role=c('aut')))
-Maintainer: The package maintainer <mblair1@amnh.org>
-Description: Facilitates workflows to reproducibly transform estimates of species’ distributions into metrics relevant for conservation. For example, combining predictions from species distribution models with other maps of environmental data to characterize the proportion of a species’ range that is under protection, calculating metrics used under the IUCN Criteria A and B guidelines (Area of Occupancy and Extent of Occurrence), and calculating more general metrics such as taxonomic and phylogenetic diversity, as well as endemism. Also facilitates temporal comparisons among biodiversity metrics to inform efforts towards complementarity and consideration of future scenarios in conservation decisions. changeRangeR also provides tools to determine the effects of modeling decisions through sensitivity tests.
+Authors@R: c(person('Peter J.', 'Galante',email='pgalante@amnh.org',role=c('aut')),
+    person('Samuel','Chang',email='changalfsam@gmail.com',role=c('aut')),
+    person('Andrea','Paz',email='paz.andreita@gmail.com',role=c('aut')),
+    person('Jamie M.','Kass',email='jamie.kass@oist.jp',role=c('aut')),
+    person('Matthew','Aiello-Lammens',email='maiellolammens@pace.edu',role=c('aut')),
+    person('Beth','Gerstner',email='gerstn11@msu.edu',role=c('aut')),
+    person('Bethany A.','Johnson',email='bjohnso005@citymail.cuny.edu',role=c('aut')),
+    person('Cory','Merow',email='cory.merow@gmail.com',role=c('aut')),
+    person('Elkin','Noguera-Urbano',email='enoguera@humboldt.org.co',role=c('aut')),
+    person('Gonzalo E.','Pinilla-Buitrago',email='gpinillabuitrago@gradcenter.cuny.edu',role=c('aut')),
+    person('Dan','Rosauer',email='dan.rosauer@anu.edu.au',role=c('aut')),
+    person('Mary E.','Blair',email='mblair1@amnh.org',role=c('aut','cre')))
+Description: Facilitates workflows to reproducibly transform estimates of species’ distributions into metrics relevant for conservation. For example, combining predictions from species distribution models with other maps of environmental data to characterize the proportion of a species’ range that is under protection, calculating metrics used under the IUCN Criteria A and B guidelines (Area of Occupancy and Extent of Occurrence), and calculating more general metrics such as taxonomic and phylogenetic diversity, as well as endemism. Also facilitates temporal comparisons among biodiversity metrics to inform efforts towards complementarity and consideration of future scenarios in conservation decisions. 'changeRangeR' also provides tools to determine the effects of modeling decisions through sensitivity tests.
 License: GPL-3
 VignetteBuilder: knitr
 Encoding: UTF-8
@@ -41,4 +40,4 @@ Suggests:
     R.utils,
     tools,
     dismo
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3

NEWS.md

@@ -1,10 +1,17 @@
 changeRangeR 1.1.0
 =============
-- removed expiring packages (maptools, rgeos, rgdal)
-- updated vignettes, website, & links
-- moved repo to `wallaceEcoMod`
+- Removed expiring packages (maptools, rgeos, rgdal)
+- Updated vignettes, website, & links
+- Moved repo to `wallaceEcoMod`
+
+changeRangeR 1.0.2
+=============
+- Fixed broken links that needed updating in the website and vignette.
+
+changeRangeR 1.0.1
+=============
 
 changeRangeR 1.0.0
 =============
-- on CRAN
+- On CRAN
 - Publication:  https://doi.org/10.1111/csp2.12863

R/SE.R

@@ -2,7 +2,7 @@
 #' @title Calculate species endemism
 #' @description Calculate species endemism as the number of species in a place divided by the total number of places in which those species are found.
 #' @param rStack a rasterStack of binary species presences
-#' @return raster object showing species endemism.
+#' @return Raster object showing species endemism.
 #' @author pgalante@@amnh.org
 #' @examples
 #' # create binary raster

R/aooArea.R

@@ -10,8 +10,8 @@
 #'  (only if locs argument is supplied).
 #' @examples
 #' # create raster
-#' r1 <- raster::raster(nrows=108, ncols=108, xmn=-50, xmx=50)
-#' raster::values(r1)<- runif(n = (108*108))
+#' r1 <- raster::raster(nrows=5, ncols=5, xmn=-5, xmx=5, ymn=-5, ymx=5)
+#' raster::values(r1)<- runif(n = (5*5))
 #' r1[r1 < 0.5] <- NA
 #' r1[!is.na(r1)] <- 1
 #' # calculate aooArea

R/cRRrmm.R

@@ -1,8 +1,8 @@
-#' @title Create metadata objects from changeRangeR
-#' @description Creates and populates a \code{rangeModelMetadata} object from the output of \code{changeRangeR}.
-#' See Merow \emph{et al.} (2019) for more details on the nature of the metadata and the \code{rangeModelMetadata} package.
+#' @title Create metadata objects from 'changeRangeR'
+#' @description Creates and populates a 'rangeModelMetadata' object from the output of 'changeRangeR'.
+#' See Merow et al. (2019) <doi:10.1111/geb.12993> for more details on the nature of the metadata and the 'rangeModelMetadata' package.
 #' To improve reproducibility of the study, this metadata object can be used as supplemental information for a manuscript, shared with collaborators, etc.
-#' @param rmm rangeModelMetadata object: if included, fields are appended to this RMM object as opposed to returning a new RMM object
+#' @param rmm 'rangeModelMetadata' object: if included, fields are appended to this RMM object as opposed to returning a new RMM object
 #' @param binaryRange Raster layer of a binary SDM. Must be either unprojected in the WGS84 datum, or projected in a UTM projection measured in meters.
 #' @param rmm A `rangemodelmetadata` object.
 #' @param locs `data.frame` of occurrence records: Longitude and latitude.

R/envChange.R

@@ -33,16 +33,16 @@
 #' @export
 
 
-#SDM <- raster::raster("inst/extdata/DemoData/SDM/olinguito/olinguitoSDM.tif")
-#binaryRange <- raster::raster("inst/extdata/DemoData/SDM/olinguito/Climatically_suitable_projected1.tif")
+#SDM <- raster::raster("inst/extdata/DemoData/SDM/olinguitoSDM_coarse.tif")
+#binaryRange <- raster::raster("inst/extdata/DemoData/SDM/Climatically_suitable_projected_coarse.tif")
 #binaryRange <- raster::projectRaster(binaryRange, SDM, method = "bilinear")
-#rStack <- raster::stack(list.files(path = "inst/extdata/DemoData/MODIS", pattern = "\\.tif$", full.names = T))
+#rStack <- raster::stack(list.files(path = "inst/extdata/DemoData/MODIS", pattern = "\\.tif$", full.names = TRUE))
 #rStack <- raster::projectRaster(rStack, SDM, method = 'bilinear')
 #threshold <- 50.086735
 #test <- envChange(rStack, binaryRange, threshold, bound = "upper")
 #test2 <- envChange(rStack, binaryRange, threshold, bound = "lower")
 
-envChange <- function(rStack, binaryRange, threshold, bound, correlation = F){
+envChange <- function(rStack, binaryRange, threshold, bound, correlation = FALSE){
   #require(raster)
 
   # if binaryRange is a shapefile, convert to raster then run like normal
@@ -51,7 +51,7 @@ envChange <- function(rStack, binaryRange, threshold, bound, correlation = F){
   }
 
   if(bound == "lower"){
-    #    if(correlation = FALSE){
+    #    if(correlation == FALSE){
     rStack[rStack < threshold] <- NA
     rStack[rStack > threshold] <- 1
     #    } else {
@@ -89,7 +89,7 @@ envChange <- function(rStack, binaryRange, threshold, bound, correlation = F){
   if (!raster::isLonLat(maskStack)){
     areas <- lapply(masks, function(x) raster::res(x)[[1]] * raster::ncell(x[!is.na(x)]))
   } else {
-    area <- lapply(masks, raster::area, na.rm = T)
+    area <- lapply(masks, raster::area, na.rm = TRUE)
     areas.1 <- lapply(area, function(x) x[!is.na(x)])
     areas <- lapply(areas.1, function(x) length(x) * stats::median(x))
     #areas <- lapply(masks, raster::area)

R/mcpSDM.R

@@ -7,7 +7,7 @@
 #' this is then used to delineate the hull
 #' @description Implements the technique to estimate IUCN's extent of occurrence (EOO) geographic range estimate of species
 #' threat level by delineating a minimum convex polygon (i.e., convex hull) around a thresholded SDM prediction, first
-#' described by Syfert et al. (2014). For each increment of 0.01 between a user-specified threshold and the maximum SDM
+#' described by Syfert et al. (2014) <doi:10.1016/j.biocon.2014.06.012>. For each increment of 0.01 between a user-specified threshold and the maximum SDM
 #' prediction value, the prediction is thresholded to this value to make a binary raster. This raster is then converted
 #' to points, which are used to delineate a trial MCP. Each trial MCP is spatially intersected with the original
 #' MCP (based on the occurrence coordinates) and the original occurrence points. The Jaccard similarity index is calculated
@@ -22,10 +22,11 @@
 #' # create continuous raster
 #' p <- raster::raster(nrows=108, ncols=108, xmn=-50, xmx=50)
 #' raster::values(p)<- runif(n = (108*108))
+#' raster::crs(p) <- "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
 #' # create occurrences
 #' xy <- dismo::randomPoints(p, 4)
 #' # create original convex hull
-#' ch.orig <- mcp(xy)
+#' ch.orig <- mcp(xy, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
 #' # set threshold
 #' thr <- 0.5
 #' # mcpSDM
@@ -36,7 +37,6 @@
 mcpSDM <- function(p, xy, ch.orig, thr) {
   #require(raster)
 
-  options(warn=-1)
   vals.p <- raster::getValues(p)
   x <- seq(thr, max(vals.p, na.rm=TRUE), 0.01)
   jsi.vec <- numeric(length(x))
@@ -75,6 +75,5 @@ mcpSDM <- function(p, xy, ch.orig, thr) {
   i.bestfit <- which(jsi.vec.allPts == max(jsi.vec.allPts))
   ch.bestfit <- ch.vec[[i.bestfit]]
 
-  options(warn=0)
   return(list(jsi = jsi.vec, thr = x, ov.pts = ov.pts.vec, best.fit = ch.bestfit, best.fit.ind = i.bestfit))
 }

R/ratioOverlap.R

@@ -28,7 +28,7 @@
 #' @export
 
 # # # # load r
-# r = raster(paste0(system.file(package="changeRangeR"), "/extdata/DemoData/SDM/Forest_suitable_projected1.tif"))
+# r = raster(paste0(system.file(package="changeRangeR"), "/extdata/DemoData/SDM/Forest_suitable_projected_coarse.tif"))
 # # create random polygon based on r
 # mcp <- function (xy) {
 #  xy <- as.data.frame(coordinates(xy))
@@ -37,24 +37,24 @@
 #  xy.bord <- rbind(xy.bord[nrow(xy.bord), ], xy.bord)
 #  return(SpatialPolygons(list(Polygons(list(Polygon(as.matrix(xy.bord))), 1))))
 # }
-# rbuf = gBuffer(mcp(dismo::randomPoints(r, 3)), width = 50000)
+# rbuf <- gBuffer(mcp(dismo::randomPoints(r, 3)), width = 50000)
 # rbuf@proj4string <- crs(r)
-# #r = rbuf
+# #r <- rbuf
 # # load shp and reproject
-# shp = readOGR(paste0(system.file(package="changeRangeR", "/extdata/DemoData/shapefiles")), "WDPA_COL_olinguito")
-# shp = spTransform(shp, CRS("+proj=utm +zone=18 +south +datum=WGS84 +units=m +no_defs"))
+# shp <- readRDS(file.path(system.file(package="changeRangeR", "extdata/DemoData/shapefiles"), "WDPA_COL_olinguito_simp.rds"))
+# shp <- spTransform(shp, CRS("+proj=utm +zone=18 +south +datum=WGS84 +units=m +no_defs"))
 # # convert shp to raster
-# shp = raster::rasterize(shp, r)
+# shp <- raster::rasterize(shp, r)
 # # Define args
-# field = "DESIG_ENG"
-# #category = "All"
-# category = c("National Natural Park", "Regional Natural Parks", "Integrated Management Regional Districts")
-# subfield = TRUE
+# field <- "DESIG_ENG"
+# #category <- "All"
+# category <- c("National Natural Park", "Regional Natural Parks", "Integrated Management Regional Districts")
+# subfield <- TRUE
 # #test
-# t <- ratioOverlap(r, shp, field = field, category = category, subfield= F, quant = c(0.5, 0.75))
+# t <- ratioOverlap(r, shp, field = field, category = category, subfield = FALSE, quant = c(0.5, 0.75))
 # quant = c(0.25, 0.87)
 
-ratioOverlap <- function(r, shp = NULL, rasMask = NULL, field=NULL, category=NULL, subfield = FALSE, quant = "quartile"){
+ratioOverlap <- function(r, shp = NULL, rasMask = NULL, field = NULL, category = NULL, subfield = FALSE, quant = "quartile"){
 
   #setClass("ratioOverlap", slots = list(maskedRange = "RasterLayer", ratio = "character"))
   #require(sf)

tests/testthat/test_mcpSDM.R

@@ -1,13 +1,17 @@
+library(sf)
+
 # create continuous raster
 p <- raster::raster(nrows=108, ncols=108, xmn=-50, xmx=50)
 raster::values(p)<- runif(n = (108*108))
+raster::crs(p) <- "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
 # create occurrences
 xy <- dismo::randomPoints(p, 4)
 # create original convex hull
-ch.orig <- mcp(xy)
+ch.orig <- mcp(xy, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
 # set threshold
 thr <- 0.5
 # mcpSDM
+sf_use_s2(FALSE)
 out <- mcpSDM(p, xy, ch.orig, thr)