minor changes to description and examples

Author: flaviomoc

DESCRIPTION

@@ -10,7 +10,7 @@ Authors@R: c(
            comment = c(ORCID = "0000-0001-5661-3381"))
   )
 Maintainer: Flávio M. M. Mota <flaviomoc@gmail.com>
-Description: The divraster package calculates diversity patterns (alpha and beta) from raster data for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions. Spatial and temporal beta diversity can be partitioned into replacement and richness difference components. It also calculates standardized effect size for FD and PD alpha diversity and the average individual traits across multilayer rasters. The raster's layers represent species, while the cells represent communities.
+Description: Alpha and beta diversity for taxonomic (TD), functional (FD), and phylogenetic (PD) dimensions based on rasters. Spatial and temporal beta diversity can be partitioned into replacement and richness difference components. It also calculates standardized effect size for FD and PD alpha diversity and the average individual traits across multilayer rasters. The layers of the raster represent species, while the cells represent communities. Methods details can be found at Cardoso et al. 2022 <https://CRAN.R-project.org/package=BAT> and Heming et al. 2023 <https://CRAN.R-project.org/package=SESraster>.
 License: GPL (>= 3)
 URL: https://github.com/flaviomoc/divraster
 BugReports: https://github.com/flaviomoc/divraster/issues

R/alpha.R

@@ -39,7 +39,7 @@ spat.alpha.vec <- function(x, tree, resu, ...) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' library(terra)
 #' bin1 <- terra::rast(system.file("extdata", "ref.tif",
 #' package = "divraster"))

R/beta_spatial.R

@@ -1,10 +1,5 @@
 #' Spatial beta diversity for vector
 #'
-#' This function will compute beta diversity on vectors containing
-#' multiple species at multiple sites. Species at sites should be
-#' placed sequentially, so that the vector can be transformed in a
-#' matrix with species at columns and sites at rows.
-#'
 #' @param x A numeric vector with presence-absence data (0 or 1)
 #' for a set of species.
 #' @param tree It can be a data frame with species traits or a
@@ -17,7 +12,8 @@
 #' @param ... Additional arguments to be passed passed down from a
 #' calling function.
 #'
-#' @return A SpatRaster with beta results.
+#' @return A SpatRaster with beta results (total, replacement,
+#' and richness differences).
 spat.beta.vec <- function(x, tree, global = FALSE, spp, nspp, ...) {
   x <- matrix(x, ncol = nspp, byrow = FALSE,
               dimnames = list(NULL, spp))
@@ -47,10 +43,6 @@ spat.beta.vec <- function(x, tree, global = FALSE, spp, nspp, ...) {
 
 #' Spatial beta diversity for raster
 #'
-#' This function will compute beta diversity on spatRast objects
-#' that contain binary (presence/absence) species distribution data.
-#' @description Compute alpha diversity for taxonomic, functional,
-#' and phylogenetic diversity.
 #' @param x A SpatRaster with presence-absence data (0 or 1) for a
 #' set of species.
 #' @param tree A data.frame with species traits or a phylogenetic
@@ -67,11 +59,12 @@ spat.beta.vec <- function(x, tree, global = FALSE, spp, nspp, ...) {
 #' @param ... Additional arguments to be passed passed down from
 #' a calling function.
 #'
-#' @return A SpatRaster with beta results.
+#' @return A SpatRaster with beta results (total, replacement,
+#' and richness differences).
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' library(terra)
 #' bin1 <- terra::rast(system.file("extdata", "ref.tif",
 #' package = "divraster"))

R/beta_temporal.R

@@ -10,7 +10,8 @@
 #' @param ... Additional arguments to be passed passed down from
 #' a calling function.
 #'
-#' @return A SpatRaster with beta results.
+#' @return A SpatRaster with beta results (total, replacement,
+#' and richness differences).
 temp.beta.vec <- function(x, nspp, spp, tree, resu, ...) {
   if (all(is.na(x))) {
     resu[] <- NA
@@ -39,11 +40,11 @@ temp.beta.vec <- function(x, nspp, spp, tree, resu, ...) {
 #' @param ... Additional arguments to be passed passed down from
 #' a calling function.
 #'
-#' @return A SpatRaster with beta results.
+#' @return A SpatRaster with beta results (total, replacement,
+#' and richness differences).
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' library(terra)
 #' bin1 <- terra::rast(system.file("extdata", "ref.tif",
 #' package = "divraster"))
@@ -56,7 +57,6 @@ temp.beta.vec <- function(x, nspp, spp, tree, resu, ...) {
 #' temp.beta(bin1, bin2)
 #' temp.beta(bin1, bin2, traits)
 #' temp.beta(bin1, bin2, tree)
-#' }
 temp.beta <- function(bin1, bin2, tree, filename = NULL,
                       cores = 1, ...) {
   # Check if rasters are NULL or invalid

R/data.R

@@ -17,10 +17,8 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' data <- load.data()
 #' data
-#' }
 load.data <- function() {
   ref <- terra::rast(system.file("extdata",
                                  "ref_frugivor.tif",

R/rand.R

@@ -2,37 +2,38 @@
 #' diversity
 #'
 #' @description Calculates the standardized effect size for
-#' functional and phylogenetic diversity. See SESraster package for details.
-#'
+#' functional and phylogenetic diversity.
+#' See \code{\link[SESraster]{bootspat_str}} and
+#' \code{\link[SESraster]{bootspat_naive}}
+
+
 #' @param x SpatRaster. A SpatRaster containing presence-absence
 #' data (0 or 1) for a set of species.
 #' @param tree a data.frame with species traits or a phylogenetic
 #' tree.
 #' @param aleats positive integer. A positive integer indicating
 #' how many times the calculation should be repeated.
 #' @param random character. A character indicating the type of
-#' randomization. The currently available randomization methods are "spat",
-#'  "site", "species" or "both" (site and species).
+#' randomization. The currently available randomization methods
+#' are "spat", "site", "species" or "both" (site and species).
 #' @param cores positive integer. If cores > 1, a 'parallel'
 #' package cluster with that many cores is created and used.
 #' @param filename character. Output filename.
-#' @param ... additional arguments to be passed passed down from a
-#'  calling function.
+#' @param ... additional arguments to be passed passed down from
+#' a calling function.
 #'
 #' @return SpatRaster with Mean, SD, Observed, and SES.
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' x <- terra::rast(system.file("extdata", "ref.tif",
 #' package = "divraster"))
 #' traits <- read.csv(system.file("extdata", "traits.csv",
 #' package = "divraster"), row.names = 1)
 #' tree <- ape::read.tree(system.file("extdata", "tree.tre",
 #' package = "divraster"))
-#' spat.rand(x, traits, 10, "spat")
-#' spat.rand(x, tree, 10, "spat")
-#' }
+#' spat.rand(x, tree, 3, "site")
+#' spat.rand(x, traits, 3, "site")
 spat.rand <- function(x,
                       tree,
                       aleats,

R/traits.R

@@ -28,14 +28,12 @@ spat.trait.vec <- function(x, col_trait, ...) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' library(terra)
 #' bin1 <- terra::rast(system.file("extdata", "ref.tif",
 #' package = "divraster"))
 #' traits <- read.csv(system.file("extdata", "traits.csv",
 #' package = "divraster"), row.names = 1)
 #' spat.trait(bin1, traits)
-#' }
 spat.trait <- function(x,
                        trait,
                        cores = 1,

cran-comments.md

@@ -3,3 +3,13 @@
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
+
+## Maintainer comments
+
+* The description was updated, and now it no longer starts with "This package", the package name, title, or anything similar.
+
+* Package names, software names, and API without single quotes in titles and descriptions were checked.
+
+* References describing the methods have been added to the description file: Cardoso et al. 2022 <https://CRAN.R-project.org/package=BAT> and Heming et al. 2023 <https://CRAN.R-project.org/package=SESraster>
+
+* \dontrun{} was either removed or replaced with \donttest{}