Merge pull request #35 from adamlilith/solstice_2022_2023

Solstice 2022 2023
adamlilith · Sep 15, 2023 · b83e17b · b83e17b
2 parents 804c84d + 817bace
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: enmSdmX
 Type: Package
 Title: Species Distribution Modeling and Ecological Niche Modeling
-Version: 1.1.1
-Date: 2023-06-22
+Version: 1.1.3
+Date: 2023-09-15
 Authors@R: 
 	c(
 		person(

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# enmSdmX 1.1.3 2023-09-15
+- Added European Datrim 1950 (ED50) to coordinate reference systems table (mea cupla!)
+
+# enmSdmX 1.1.2 2023-09-07
+- Minor issue fixes with undocumented arguments for non-exported functions
+- Bug fix in `squareCellRast()` that occurred on Linux/Fedora
+
 # enmSdmX 1.1.1 2023-06-11
 - Backwards incompatible: `trainRF()` uses `ranger` package for random forests (changed from `randomForest` package)
 - Backwards incompatible: `geoFold()` uses `complete` clustering method by default (changed from `single`)

diff --git a/R/bioticVelocity.r b/R/bioticVelocity.r
@@ -33,7 +33,7 @@
 #'			\item Root-mean squared difference
 #'			\item Expected Fraction of Shared Presences or ESP (Godsoe, W. 2014. \emph{Ecography} 37:130-136 \doi{10.1111/j.1600-0587.2013.00403.x})
 #'			\item D statistic (Schoener, T.W. 1968. \emph{Ecology} 49:704-726. \doi{10.2307/1935534})
-#'			\item I statistic (Warren, D.L., et al. 2008. \emph{Evolution} 62:2868-2883 \doi{10.111/j.1558-5646.2008.00482.x})
+#'			\item I statistic (Warren, D.L., et al. 2008. \emph{Evolution} 62:2868-2883 \doi{10.1111/j.1558-5646.2008.00482.x})
 #'			\item Pearson correlation
 #'			\item Spearman rank correlation
 #'		}
@@ -933,7 +933,6 @@ bioticVelocity <- function(
 #' @param x1 Matrix of weights in time 1 (i.e., population size).
 #' @param x2 Matrix of weights in time 2 (i.e., population size).
 #' @param refCoord Numeric, latitude or longitude (depending on \code{longOrLat}) of reference point from which to partition the weights into a northern, southern, eastern, or western portion.
-#' @param refLat Numeric, latitude of reference point.
 #' @param x1weightedLongs Matrix of longitudes weighted (i.e., by population size, given by \code{x1}).
 #' @param x1weightedLats Matrix of latitudes weighted (i.e., by population size, given by \code{x1}).
 #' @param x2weightedLongs Matrix of longitudes weighted (i.e., by population size, given by \code{x2}).
@@ -1051,6 +1050,7 @@ bioticVelocity <- function(
 #' @param weightedElev Raster of elevations weighted by x1 or x2 or \code{NULL}.
 #' @param warn Logical. Show warnings.
 #' @keywords internal
+#' @keywords internal
 .interpCoordFromQuantile <- compiler::cmpfun(
 	function(latOrLong, quants, x, coordVect, weightedElev=NULL, warn=TRUE) {
 

diff --git a/R/evalTjursR2.r b/R/evalTjursR2.r
@@ -10,7 +10,7 @@
 #'
 #' @return Numeric value.
 #'
-#' @references Tjur, T. 2009. Coefficients of determination in logistic regression models—A new proposal: The coefficient of discrimination. \emph{The American Statistician} 63:366–372. \doi{10.1198/tast.2009.08210}.
+#' @references Tjur, T. 2009. Coefficients of determination in logistic regression models-A new proposal: The coefficient of discrimination. \emph{The American Statistician} 63:366-372. \doi{10.1198/tast.2009.08210}
 #'
 #' @seealso \code{\link[dismo]{evaluate}}, \code{\link{evalAUC}}, \code{\link{evalMultiAUC}}, \code{\link{evalContBoyce}}, \code{\link{evalThreshold}}, \code{\link{evalThresholdStats}}, \code{\link{evalTSS}}
 #'

diff --git a/R/extentToVect.r b/R/extentToVect.r
@@ -15,7 +15,6 @@
 #' plot(mad0[1], add=TRUE)
 #'
 #' @export
-
 extentToVect <- function(x, ...) {
 
 	if (inherits(x, c('numeric'))) {
@@ -29,7 +28,7 @@ extentToVect <- function(x, ...) {
 
 		proj <- terra::crs(x)
 
-		x <- terra::ext(x)@ptr$vector
+		x <- as.vector(terra::ext(x))
 		xCorners <- c(x[1L], x[2L], x[2L], x[1L])
 		yCorners <- c(x[3L], x[3L], x[4L], x[4L])
 		corners <- cbind(xCorners, yCorners)
@@ -49,7 +48,7 @@ extentToVect <- function(x, ...) {
 		out <- sf::st_as_sf(out, crs=proj)
 
 	} else {
-		stop('Argument "x" must be a vector of 4 numbers, a SpatVector, a SpatRaster, or an sf object.')
+		stop('Argument x must be a vector of 4 numbers, a SpatVector, a SpatRaster, or an sf object.')
 	}
 
 	out

diff --git a/R/geoFoldContrast.r b/R/geoFoldContrast.r
@@ -3,12 +3,10 @@
 #' This function generates geographically-distinct cross-validation folds, or "geo-folds" of background or absence sites (i.e., "contrast" sites). Each contrast site is assigned to a fold based on the fold of the presence site that is closest. Typically, this function is run after \code{\link{geoFold}} is run to assign presences to folds.
 #'
 #' @param contrast	A "spatial points" object representing contrast sites:
-#' \itemize{
 #'	\itemize{
 #'		\item A \code{SpatVector} or \code{sf} vector with points
 #'  	\item A \code{data.frame} or \code{matrix}: Points will be assumed to have the WGS84 coordinate system (i.e., unprojected), and \code{contrastLongLat} should denote the columns with coordinates.
 #' }
-#' }
 #' @param pres 		A "spatial points" object representing presence sites:
 #'	\itemize{
 #'		\item A \code{SpatVector} or \code{sf} vector with points

diff --git a/R/nicheOverlapMetrics.r b/R/nicheOverlapMetrics.r
@@ -22,7 +22,7 @@
 #' @return List object with one element per value specified by the argument in \code{method}.
 #' @references Warren, D.L., Glor, R.E., and Turelli, M.  2008.  Environmental niche equivalency versus conservatism: Quantitative approaches to niche evolution. \emph{Evolution} 62:2868-2883. \doi{10.1111/j.1558-5646.2008.00482.x}
 #' @references Warren, D.L., Glor, R.E., and Turelli, M.  2008.  Erratum.  \emph{Evolution} 62:2868-2883. \doi{10.1111/j.1558-5646.2010.01204.x}
-#' @references Godsoe, W.  2014.  Inferring the similarity of species distributions using Species’ Distribution Models.  \emph{Ecography} 37:130-136. \doi{10.1111/j.1600-0587.2013.00403.x}
+#' @references Godsoe, W. 2014. Inferring the similarity of species distributions using Species' Distribution Models.  \emph{Ecography} 37:130-136. \doi{10.1111/j.1600-0587.2013.00403.x}
 #' 
 #' @seealso \code{\link[enmSdmX]{compareResponse}}
 #' @examples

diff --git a/R/predictEnmSdm.r b/R/predictEnmSdm.r
@@ -235,11 +235,11 @@ predictEnmSdm <- function(
 
 			} else {
 
-				preds <- predictRanger(model, data=nd, predict.all=binary, type='response', ...)
+				out <- predictRanger(model, data=newdata, predict.all=binary, type='response', ...)
 
 				if (binary) {
-					preds <- rowMeans(preds$predictions)
-					preds <- preds - 1
+					out <- rowMeans(out$predictions)
+					out <- out - 1
 				}
 
 			}

diff --git a/R/private_calcWeights.r b/R/private_calcWeights.r
@@ -3,8 +3,9 @@
 #' Calculates weighting for a model. Each record receives a numeric weight.
 #'
 #' @param w Either logical in which case \code{TRUE} (default) causes the total weight of presences to equal the total weight of absences (if \code{family='binomial'}) \emph{or} a numeric list of weights, one per row in \code{data} \emph{or} the name of the column in \code{data} that contains site weights. If \code{FALSE}, then each datum gets a weight of 1.
-#' @param Data frame
+#' @param data Data frame
 #' @param resp Name of response column
+#' @param family Name of family
 #'
 #' @returns A numeric vector.
 #' @keywords internal

diff --git a/R/private_scalePredictors.r b/R/private_scalePredictors.r
@@ -9,7 +9,7 @@
 #' @param data A data frame.
 #'
 #' @import data.table
-#' @noRd
+#' @keywords internal
 .scalePredictors <- function(scale, preds, data) {
 
 	# which predictors are not factors?

diff --git a/R/squareCellRast.r b/R/squareCellRast.r
@@ -53,7 +53,7 @@ squareCellRast <- function(
 	if (inherits(x, 'sf')) x <- terra::vect(x)
 
 	crs <- terra::crs(x)
-	ext <- terra::ext(x)@ptr$vector
+	ext <- as.vector(terra::ext(x))
 	names(ext) <- c('xmin', 'xmax', 'ymin', 'ymax')
 
 	longDist <- ext['xmax'] - ext['xmin']

diff --git a/data/crss.rda b/data/crss.rda
diff --git a/enmSdmX.Rcheck/00_pkg_src/enmSdmX/DESCRIPTION b/enmSdmX.Rcheck/00_pkg_src/enmSdmX/DESCRIPTION
@@ -0,0 +1,45 @@
+Package: enmSdmX
+Type: Package
+Title: Species Distribution Modeling and Ecological Niche Modeling
+Version: 1.1.2
+Date: 2023-09-07
+Authors@R: 
+	c(
+		person(
+			given = 'Adam B.',
+			family = 'Smith',
+			role = c('cre', 'aut'),
+			email = '[email protected]',
+			comment = c(ORCID = '0000-0002-6420-1659')
+		)
+	)
+Maintainer: Adam B. Smith <[email protected]>
+Description: Implements species distribution modeling and ecological niche
+	modeling, including: bias correction, spatial cross-validation, model
+	evaluation, raster interpolation, biotic "velocity" (speed and
+	direction of movement of a "mass" represented by a raster), interpolating
+	across a time series of rasters, and use of spatially imprecise records.
+	The heart of the package is a set of "training" functions which
+	automatically optimize model complexity based number of available
+	occurrences. These algorithms include MaxEnt, MaxNet, boosted regression
+	trees/gradient boosting machines, generalized additive models,
+	generalized linear models, natural splines, and random forests. To enhance
+	interoperability with other modeling packages, no new classes are created.
+	The package works with 'PROJ6' geodetic objects and coordinate reference
+	systems.
+Depends: R (>= 4.0.0)
+Imports: boot, data.table, dismo, doParallel, DT, foreach, gbm,
+        graphics, ks, maxnet, methods, mgcv, MuMIn, omnibus, parallel,
+        ranger, rJava, scales, sf, shiny, statisfactory, stats, terra,
+        utils
+Suggests: geodata
+LazyData: true
+LazyLoad: yes
+URL: https://github.com/adamlilith/enmSdmX
+BugReports: https://github.com/adamlilith/enmSdmX
+Encoding: UTF-8
+License: MIT + file LICENSE
+RoxygenNote: 7.2.3
+NeedsCompilation: no
+Packaged: 2023-09-08 17:12:43 UTC; adam
+Author: Adam B. Smith [cre, aut] (<https://orcid.org/0000-0002-6420-1659>)
diff --git a/enmSdmX.Rcheck/00_pkg_src/enmSdmX/LICENSE b/enmSdmX.Rcheck/00_pkg_src/enmSdmX/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2022
+COPYRIGHT HOLDER: Adam B. Smith
diff --git a/enmSdmX.Rcheck/00_pkg_src/enmSdmX/NAMESPACE b/enmSdmX.Rcheck/00_pkg_src/enmSdmX/NAMESPACE
@@ -0,0 +1,51 @@
+# Generated by roxygen2: do not edit by hand
+
+export(bioticVelocity)
+export(compareResponse)
+export(coordImprecision)
+export(countPoints)
+export(customAlbers)
+export(customLambert)
+export(customVNS)
+export(decimalToDms)
+export(dmsToDecimal)
+export(elimCellDuplicates)
+export(evalAUC)
+export(evalContBoyce)
+export(evalMultiAUC)
+export(evalTSS)
+export(evalThreshold)
+export(evalThresholdStats)
+export(evalTjursR2)
+export(extentToVect)
+export(geoFold)
+export(geoFoldContrast)
+export(geoThin)
+export(getCRS)
+export(getValueByCell)
+export(globalx)
+export(interpolateRasts)
+export(longLatRasts)
+export(modelSize)
+export(nearestEnvPoints)
+export(nearestGeogPoints)
+export(nicheOverlapMetrics)
+export(plotExtent)
+export(predictEnmSdm)
+export(predictMaxEnt)
+export(predictMaxNet)
+export(sampleRast)
+export(setValueByCell)
+export(spatVectorToSpatial)
+export(squareCellRast)
+export(summaryByCrossValid)
+export(trainBRT)
+export(trainByCrossValid)
+export(trainGAM)
+export(trainGLM)
+export(trainMaxEnt)
+export(trainMaxNet)
+export(trainNS)
+export(trainRF)
+export(weightByDist)
+import(data.table)
diff --git a/enmSdmX.Rcheck/00_pkg_src/enmSdmX/NEWS.md b/enmSdmX.Rcheck/00_pkg_src/enmSdmX/NEWS.md
@@ -0,0 +1,42 @@
+# enmSdmX 1.1.2 2023-09-07
+- Minor issue fixes with undocumented arguments for non-exported functions
+- Bug fix in `squareCellRast()` that occurred on Linux/Fedora
+
+# enmSdmX 1.1.1 2023-06-11
+- Backwards incompatible: `trainRF()` uses `ranger` package for random forests (changed from `randomForest` package)
+- Backwards incompatible: `geoFold()` uses `complete` clustering method by default (changed from `single`)
+- New feature: `trainGLM()` and `trainNS()` can automatically scale predictors
+- New feature: Reworked `trainGLM()` to handle cases with large numbers of predictors
+- New feature: Added `geoFoldContrast()` for assigning geo-folds to background or absence sites
+- Better functionality: `trainRF()` now indicates if the response is binary using a `binary` argument (vs. `family`, which falsely implied more functionality than RFs have)
+
+# enmSdmX 1.0.6 2023-05-22
+- Better functionality: Expanded capacity of .calcWeights() (a hidden function) to handle different values for `family`
+
+# enmSdmX 1.0.5 2023-05-12
+- new feature: Added help page for troubleshooting running functions that support parallel operation
+- Bug fix: `predictEnmSdm()` when using a BRT model and predicting to a `SpatRaster` (thank you, Nikki C!)
+
+# enmSdmX 1.0.4 2023-04-10
+- New feature: Users can select clustering method in `geoThin()` and `geoFold()` (thank you, Pascal T!)
+- Bug fix: Example in `customCRS()` when GADM server is down
+- Bug fix:`geoThin()` which returned input if it was a `data.frame`*
+- Bug fix:`geoThin()` which returned a `data.frame` lacking coordinates if input was a `data.frame` (thank you, Pascal T!)
+
+# enmSdmX 1.0.3 2023-03-07
+- Bug fix: Removed Fedora issue with external link to `raster` package
+- Bug fix: Added `rJava` dependency
+
+# enmSdmX 1.0.2 2023-03-04
+- New feature: `getCRS()` (no arguments) now displays `shiny` table of all available CRSs
+- Bug fix: Fixed issue in `nearestGeogPoints()` when polygon lay under centroid
+- Bug fix: Fixed bug with "table" call of `getCRS()`
+
+# enmSdmX 1.0.1
+- New feature: `summarizeByCrossValid()` now summarizes natural spline (NS) models
+- Bug fix: Bug experienced by some users using `predictEnmSdm()` and `predictMaxNet()` (Thank you, Nikki!)
+- Bug fix: `trainByCrossValid()` using improper call to `evalContBoyce()`
+- Bug fix: `extract()` bug in some examples
+
+# enmSdmX 1.0.0
+- First release on CRAN
diff --git a/enmSdmX.Rcheck/00_pkg_src/enmSdmX/R/00_datatable_aware.r b/enmSdmX.Rcheck/00_pkg_src/enmSdmX/R/00_datatable_aware.r
@@ -0,0 +1,3 @@
+# needed to use data.table in functions
+# https://cran.r-project.org/web/packages/data.table/vignettes/datatable-importing.html
+.datatable.aware <- TRUE
diff --git a/enmSdmX.Rcheck/00_pkg_src/enmSdmX/R/aaa.r b/enmSdmX.Rcheck/00_pkg_src/enmSdmX/R/aaa.r
@@ -0,0 +1,13 @@
+# .onLoad <- function(lib, pkg) {
+
+# }
+
+.onAttach <- function(lib, pkg) {
+
+	ver <- read.dcf(file=system.file('DESCRIPTION', package=pkg), fields='Version')
+	packageStartupMessage(paste0('This is ', pkg, ' ', ver, '.'))
+	packageStartupMessage(paste0('* Back-incompatible changes starting starting with enmSdmX version 1.1.1:'))
+	packageStartupMessage(paste0('* trainRF() replaces use of the randomForest package with the faster ranger package, which produces random forests that are statistically equivalent.'))
+	packageStartupMessage(paste0('geoFold() uses ', dQuote('complete'), ' clustering by default (was ', dQuote('single'), ').'))
+
+}