caught up master branch

Merge branch 'master' into version_0.5

# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/plot.phylo_divent.R
#	R/plot.species_distribution.R

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: divent
 Type: Package
 Title: Entropy Partitioning to Measure Diversity
-Version: 0.4-99.9002
+Version: 0.4-99.9003
 Authors@R: c(
     person("Eric", "Marcon", email="eric.marcon@agroparistech.fr", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5249-321X"))
     )

NEWS.md

@@ -1,8 +1,9 @@
-# divent 0.4-99.9002
+# divent 0.4-99.9003
 
 ## Features
 
 - Hurlbert's diversity: `ent_hurlbert()` and `div_hurlbert()`.
+- Methods for 
 
 
 # divent 0.3-16

R/abd_species.R

@@ -2,12 +2,12 @@
 #' 
 #' Utilities for community abundances (objects of class "abundances").
 #' 
-#' `abd_species()` returns a tibble containing the species abundance columns only,
+#' @returns `abd_species()` returns a tibble containing the species abundance columns only,
 #' to simplify numeric operations.
+#' 
 #' `prob_species()` returns the same tibble but values are probabilities.
 #' 
-#' `abd_sum()` returns the sample sizes of the communities.
-#'
+#' `abd_sum()` returns the sample sizes of the communities in a numeric vector.
 #' @inheritParams check_divent_args
 #'
 #' @examples

R/package.R

@@ -1058,9 +1058,9 @@ ent_gamma_similarity <- function(
 #' @noRd
 #' 
 error_message <- function(message, argument, parent_function) {
-  cat(deparse(substitute(argument)), "cannot be:\n")
-  print(utils::head(argument))
-  cat(paste(paste("Error in ", parent_function, ":"), message, "\n"))
+  message(deparse(substitute(argument)), " cannot be:", appendLF = TRUE)
+  message(utils::head(argument))
+  message("In function ", parent_function, ": ", message)
   stop("Check the function arguments.", call. = FALSE)
 }
 

R/plot.phylo_divent.R

@@ -6,6 +6,8 @@
 #' @param x An object of class "phylo_divent".
 #' @param ... Arguments passed to [stats::plot.dendrogram].
 #'
+#' @returns `NULL`. Called for side effects.
+#' 
 #' @export
 #'
 #' @examples

R/plot.species_distribution.R

@@ -29,6 +29,8 @@ NULL
 #' @param palette The name of a color palette, recognized by [RColorBrewer::brewer.pal].
 #' RAC plot only.
 #'
+#' @returns `NULL`. Called for side effects.
+#' 
 #' @export
 plot.species_distribution <- function(
     x, 

R/probabilities.R

@@ -28,6 +28,9 @@
 #' 
 #' @param ... Unused.
 #' 
+#' @returns An object of class "probabilities", which is a [species_distribution] 
+#' or a numeric vector with argument `as_numeric = TRUE`.
+#' 
 #' @references
 #' \insertAllCited{}
 #' 

R/species_distribution.R

@@ -2,6 +2,13 @@
 #' 
 #' A Species Distribution is a [tibble::tibble] containing species abundances 
 #' or probabilities.
+
+#' Rows of the tibble are communities and column are species. 
+#' Values are either abundances or probabilities. 
+#' Special columns contain the site names, and their weights 
+#' (e.g. their area or number of individuals):
+#' their names must be "site" and "weight". 
+#' All other column names are considered as species names.
 #' 
 #' `species_distribution` objects include `abundances` and `probabilities` 
 #' objects.
@@ -22,17 +29,19 @@
 #' the same output as `probabilities()` with `estimator = "naive"`.
 #' 
 #' `species_distribution` objects objects can be plotted by [plot] and [autoplot].
+#'
+#' @inheritParams check_divent_args
+#' @param x an object.
+#' @param ... Unused.
+
+#' @returns An object of classes "species_distribution" and "abundances" or "probabilities".
 #' 
 #' `as.double()` and its synonymous `as.numeric()` return a numeric vector 
 #' that contains species abundances or probabilities of a single-row 
 #' `species_distribution`. 
 #' `as.matrix()` returns a numeric matrix if the `species_distribution` contains 
 #' several rows.
 #' These are methods of the generic functions for class `species_distribution`.
-#'
-#' @inheritParams check_divent_args
-#' @param x an object.
-#' @param ... Unused.
 #' 
 #' @references
 #' \insertAllCited{}