change in the description of functions

correction of spelling errors

NEWS.md

@@ -2,9 +2,10 @@
 
 # phyloraster 2.1.0
 
--  added functions to compute full and tip branch lengths: 'species.tip.length()' and 'species.branch.length()'
-- added new function to compute ED for each species
+- added functions to compute full and tip branch lengths: 'species.tip.length()' and 'species.branch.length()'
+- added new function to compute ED for each species: 'species.ed()'
 - fixed ED calculation for raster data
+- added new tests for the new functions
 
 # phyloraster 2.0.1
 

R/delta.grid.R

@@ -1,18 +1,16 @@
 .delta.vec <- function(x) {
-  diff <- x[2] - x[1] # diference between metric in time 2 and 1
+  diff <- x[2] - x[1] # difference between metric in time 2 and 1
 }
 
-#' Calculates the delta of spatialized diversity metrics (richness,
-#' phylogenetic endemism, phylogenetic diversity, weighted endemism,
-#' evolutionary distinctiveness) between different time periods
+#' Delta of Diversity Metrics
 #'
-#' @description Calculates the delta of spatialized diversity metrics
+#' @description Calculates the difference of rasterized diversity metrics
 #' (richness, phylogenetic endemism, phylogenetic diversity, weighted endemism,
-#' evolutionary distinctiveness) between different time periods.
-#' @param r1 SpatRaster Spatialized diversity metrics for time 1 (e.g
+#' evolutionary distinctiveness) between time periods.
+#' @param r1 SpatRaster Rasterized diversity metrics for time 1 (e.g
 #' phylogenetic diversity in present). To calculate some diversity metrics for
 #' rasters see phyloraster::geo.phylo function.
-#' @param r2 SpatRaster Spatialized diversity metrics for time 2 (e.g
+#' @param r2 SpatRaster Rasterized diversity metrics for time 2 (e.g
 #' phylogenetic diversity in future).
 #' @param filename character. Output filename.
 #' @param ... additional arguments to be passed passed down from a calling

R/df2rast.R

@@ -8,9 +8,7 @@
 #' @param ... additional arguments to be passed passed down from a calling
 #' function.
 #' @param CRS character. Description of the Coordinate Reference System
-#' (map projection) in PROJ.4, WKT or authority:code notation. See crs. If
-#' this argument is missing, and the x coordinates are within -360 .. 360 and
-#' the y coordinates are within -90 .. 90, longitude/latitude is assigned
+#' (map projection) in PROJ.4.
 #' @return SpatRaster
 #' @export
 #' @examples

R/geo.phylo.R

@@ -95,9 +95,9 @@ rast.sr <- function(x, filename = "", ...){
 #' @references Williams, P.H., Humphries, C.J., Forey, P.L., Humphries, C.J. and
 #' VaneWright, R.I. (1994). Biodiversity, taxonomic relatedness, and endemism in
 #' conservation. In: Systematics and Conservation Evaluation (eds Forey PL,
-#' Humphries CJ, Vane-Wright RI), p. 438. Oxford University Press, Oxford.
+#' Humphries C.J., Vane-Wright RI), p. 438. Oxford University Press, Oxford.
 #' @references Crisp, M., Laffan, S., Linder, H. and Monro, A. (2001). Endemism
-#' in theAustralian flora. Journal of Biogeography, 28, 183–198.
+#' in the Australian flora. Journal of Biogeography, 28, 183–198.
 #' @references Isaac, N. J., Turvey, S. T., Collen, B., Waterman, C. and
 #' Baillie, J. E. (2007). Mammals on the EDGE: conservation priorities based on
 #' threat and phylogeny. PLoS ONE 2, e296.
@@ -196,10 +196,10 @@ rast.sr <- function(x, filename = "", ...){
 #' @references Williams, P.H., Humphries, C.J., Forey, P.L., Humphries, C.J.
 #' and VaneWright, R.I. (1994). Biodiversity, taxonomic relatedness, and
 #' endemism in conservation. In: Systematics and Conservation Evaluation
-#' (eds Forey PL, Humphries CJ, Vane-Wright RI), p. 438. Oxford University
+#' (eds Forey PL, Humphries C.J., Vane-Wright RI), p. 438. Oxford University
 #' Press, Oxford.
 #' @references Crisp, M., Laffan, S., Linder, H. and Monro, A. (2001).
-#' Endemism in theAustralian flora. Journal of Biogeography, 28, 183–198.
+#' Endemism in the Australian flora. Journal of Biogeography, 28, 183–198.
 #' @references Isaac, N. J., Turvey, S. T., Collen, B., Waterman, C. and
 #' Baillie, J. E. (2007). Mammals on the EDGE: conservation priorities based on
 #' threat and phylogeny. PLoS ONE 2, e296.
@@ -323,7 +323,7 @@ geo.phylo <- function(x, tree,
 #' @references Williams, P.H., Humphries, C.J., Forey, P.L., Humphries, C.J.,
 #' VaneWright, R.I. (1994). Biodiversity, taxonomic relatedness, and endemism
 #' in conservation. In: Systematics and Conservation Evaluation (eds Forey PL,
-#' Humphries CJ, Vane-Wright RI), p. 438. Oxford University Press, Oxford.
+#' Humphries C.J., Vane-Wright RI), p. 438. Oxford University Press, Oxford.
 #' @references Crisp, M., Laffan, S., Linder, H., Monro, A. (2001). Endemism
 #' in the Australian flora. Journal of Biogeography, 28, 183–198.
 #'

cran-comments.md

@@ -4,7 +4,11 @@
 
 * This is a new release.
 
-* \dontrun{} has been replaced with \donttest{}.
+* added functions to compute full and tip branch lengths: 'species.tip.length()' and 'species.branch.length()'
 
-* Comments in the example code lines have been removed.
+* added new function to compute ED for each species: 'species.ed()'
+
+* fixed ED calculation for raster data
+
+* added new tests for the new functions
 

tests/testthat/test-geo.phylo.R

@@ -162,8 +162,8 @@ test_that("names are reordened in the function geo.phylo", {
 
   # tests
   expect(geo.phylo(data$x, tree, #range.BL = area.branch$range.BL,
-                   inv.R = inv.R,
-                   edge.path = data$edge.path[sample(1:nrow(data$edge.path)),],
+                inv.R = inv.R,
+                edge.path = data$edge.path[sample(1:nrow(data$edge.path)),],
                    branch.length = data$branch.length,
                    n.descen = data$n.descendants), ok = T)
 

vignettes/phyloraster-vignette.Rmd

@@ -95,7 +95,7 @@ library(phylobase)
 
 ## Data processing {#data}
 
-In the step of pre processing, we offer support to manipulate matrices, 
+In the step of pre-processing, we offer support to manipulate matrices, 
 shapefiles, rasters, and phylogenetic trees.
 In the processing step, we provide functions to calculate Faith's phylogenetic 
 diversity (Faith, 1992), phylogenetic endemism (Rosauer et al., 2009), 
@@ -410,7 +410,7 @@ plot(t)
 -   **Function** `delta.grid`
 
 The package also brings the function `delta.grid` that allows you to calculate 
-the difference between spatialized diversity metrics between two different times.
+the difference between rasterized diversity metrics between two different times.
 This function would allow assessing how species richness varies between 
 different times, which could be useful in a climate change scenario.
 For example, imagine that we currently have 33 tree frog species of the 
@@ -474,7 +474,7 @@ Gotelli, N. J., and McCabe, D. J.
 Species co-occurrence: A meta-analysis of J.
 M. Diamond's assembly rules model.
 Ecology, 83(8), 2091--2096.
-[https://doi.org/10.1890/0012-9658(2002)083[2091:SCOAMA]2.0.CO;2](https://doi.org/10.1890/0012-9658(2002)083%5B2091:SCOAMA%5D2.0.CO;2){.uri}
+<https://doi.org/10.1890/0012-9658(2002)083%5B2091:SCOAMA%5D2.0.CO;2>
 
 Gotelli, N. J., and Ulrich, W.
 (2012).