minor changes to function documentation and citation

Author: flaviomoc

NEWS.md

@@ -1,7 +1,8 @@
 # divraster 1.0.4
 
 * New function added for initial testing [#3](https://github.com/flaviomoc/divraster/issues/3).
-* Minor corrections in function tests to align with BAT update.
+* Minor changes in function documentation.
+* Minor changes in function tests.
 * Citation updated.
 
 # divraster 1.0.3

R/alpha.R

@@ -30,8 +30,9 @@ spat.alpha.vec <- function(x, tree, resu, ...) {
 #'
 #' @param bin A SpatRaster 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
-#' phylogenetic tree.
+#' @param tree It can be a 'data.frame' with species traits or a
+#' 'phylo' with a rooted phylogenetic tree. Species names in 'tree'
+#' and 'bin' must match!
 #' @param cores A positive integer. If cores > 1, a 'parallel'
 #' package cluster with that many cores is created and used.
 #' @param filename Character. Save results if a name is provided.

R/beta_spatial.R

@@ -75,13 +75,13 @@ spat.beta.vec <- function(x,
 #'
 #' @description Calculates spatial beta diversity for
 #' taxonomic (TD), functional (FD), and phylogenetic (PD)
-#' dimensions. Adapted from \code{\link[BAT]{beta}}. Species
-#' names in 'x' and 'tree' objects must match!
+#' dimensions. Adapted from \code{\link[BAT]{beta}}.
 #'
 #' @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
-#' tree.
+#' @param tree It can be a 'data.frame' with species traits or a
+#' 'phylo' with a rooted phylogenetic tree. Species names in 'tree'
+#' and 'x' must match!
 #' @param filename Character. Save results if a name is provided.
 #' @param global Logical. Mean of pairwise comparisons between
 #' focal cell and its neighbors (default) or mean of all pairwise
@@ -97,7 +97,6 @@ spat.beta.vec <- function(x,
 #' @details The TD beta diversity partitioning framework we used
 #' was developed by Podani and Schmera (2011) and Carvalho et al.
 #' (2012) and expanded to PD and FD by Cardoso et al. (2014).
-#' Species names in 'x' and 'tree' objects must match!.
 #'
 #' @references Cardoso, P. et al. 2014. Partitioning taxon,
 #' phylogenetic and functional beta diversity into replacement

R/beta_temporal.R

@@ -47,9 +47,11 @@ temp.beta.vec <- function(x, nspp, spp, tree, resu, ...) {
 #' @param bin1 A SpatRaster with presence-absence data (0 or 1)
 #' for a set of species.
 #' @param bin2 A SpatRaster 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
-#' phylogenetic tree.
+#' for a set of species. Species names in 'bin2' and 'bin1' must
+#' match!
+#' @param tree It can be a 'data.frame' with species traits or a
+#' 'phylo' with a rooted phylogenetic tree. Species names in 'tree',
+#' 'bin1', and 'bin2' must match!
 #' @param filename Character. Save results if a name is provided.
 #' @param cores A positive integer. If cores > 1, a 'parallel'
 #' package cluster with that many cores is created and used.

R/data.R

@@ -1,7 +1,6 @@
 .onAttach <- function(libname, pkgname) {
-packageStartupMessage("Thank you for using divraster!")
-packageStartupMessage("To acknowledge our work, please cite the package:")
-packageStartupMessage(paste0("Mota, F. M. M., Alves-Ferreira, G., Talora, D. C., and Heming, N. M. (2023). divraster: an R package to calculate taxonomic, functional and phylogenetic diversity from rasters. - Ecography, e06905."))
+packageStartupMessage("Welcome to divraster!")
+packageStartupMessage("To acknowledge our work use: citation('divraster')")
 }
 #' Load data adapted from Mota et al. (2022), Tobias et al. (2022),
 #'  and Jetz et al. (2014)
@@ -17,8 +16,10 @@ packageStartupMessage(paste0("Mota, F. M. M., Alves-Ferreira, G., Talora, D. C.,
 #' Conservation of Evolutionary Distinctness in Birds. -
 #' Current Biology 24: 919–930.
 #'
-#' @return List with climate scenarios, traits, and phylogenetic
-#' tree
+#' @return A list with binary maps of species for the reference
+#' and future climate scenarios, species traits, and a rooted
+#' phylogenetic tree for the species. The species names across
+#' these objects must match!
 #' @export
 #'
 #' @examples

R/inputs_chk.R

@@ -3,11 +3,13 @@
 #' @param bin1 A SpatRaster with presence-absence data (0 or 1)
 #' for a set of species.
 #' @param bin2 A SpatRaster 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
-#' phylogenetic tree.
+#' for a set of species. Species names in 'bin2' and 'bin1' must
+#' match!
+#' @param tree It can be a 'data.frame' with species traits or a
+#' 'phylo' with a rooted phylogenetic tree. Species names in 'tree',
+#' 'bin1', and 'bin2' must match!
 #'
-#' @return A message.
+#' @return Either a success message or an error.
 #' @export
 #'
 #' @examples

R/rand.R

@@ -7,8 +7,9 @@
 #'
 #' @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 tree It can be a 'data.frame' with species traits or a
+#' 'phylo' with a rooted phylogenetic tree. Species names in 'tree'
+#' and 'x' must match!
 #' @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

R/traits.R

@@ -17,7 +17,8 @@ spat.trait.vec <- function(x, col_trait, ...) {
 #' @description Compute average for each trait.
 #' @param x A SpatRaster with presence-absence data (0 or 1) for a
 #'  set of species.
-#' @param trait A data.frame with species traits.
+#' @param trait A 'data.frame' with species traits. Rownames must
+#' have species names that match with 'x'!
 #' @param cores A positive integer. If cores > 1, a 'parallel'
 #' package cluster with that many cores is created and used.
 #' @param filename Character. Save results if a name is provided.

inst/CITATION

@@ -1,13 +1,4 @@
-citHeader("Thank you for using divraster! Please cite also BAT package and the related articles in your publications:")
-
-bibentry(
-  bibtype  = "Misc",
-  title    = "{divraster}: an R package to calculate taxonomic, functional and phylogenetic diversity from rasters",
-  author   = c("F. M. M. Mota", "N. M. Heming", "G. Alves-Ferreira"),
-  year     = "2023",
-  note     = "R package version 1.0.3",
-  url      = "https://CRAN.R-project.org/package=divraster"
-)
+citHeader("Thank you for using divraster! Please remember to cite BAT as well.")
 
 bibentry(
   bibtype  = "Article",
@@ -19,15 +10,6 @@ bibentry(
   doi      = "10.1111/ecog.06905"
 )
 
-bibentry(
-  bibtype  = "Misc",
-  title    = "{BAT}: Biodiversity Assessment Tools",
-  author   = c("P. Cardoso", "S. Mammola", "F. Rigal", "J. Carvalho"),
-  year     = "2022",
-  note     = "R package version 2.9.2",
-  url      = "https://CRAN.R-project.org/package=BAT"
-)
-
 bibentry(
   bibtype  = "Article",
   title    = "BAT -- Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity",