Merge pull request #258 from grunwaldlab/release-2.9.5

release 2.9.5 (CRAN chore)

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.9.4
-Date: 2023-03-23 00:53:20 UTC
-SHA: b43ac8e7096d534fab19e3a7834a42215b6e9081
+Version: 2.9.5
+Date: 2024-01-15 13:20:49 UTC
+SHA: 963d5f60cda1447ce150d78c12c2cd2d38f58d80

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.9.4
+Version: 2.9.5
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "zkamvar@gmail.com", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",

NEWS.md

@@ -1,3 +1,13 @@
+poppr 2.9.5
+===========
+
+CRAN MAINTENANCE
+----------------
+
+* The `usenames` option from xcolor has been removed from the algorithms and
+  equations vignette.
+* Old documentation has been fixed to conform with CRAN standards.
+
 poppr 2.9.4
 ===========
 

R/filter_stats.R

@@ -75,7 +75,7 @@
 #' @seealso \code{\link{mlg.filter}} \code{\link{cutoff_predictor}} 
 #'   \code{\link{bitwise.dist}} \code{\link{diss.dist}}
 #' @note This function originally appeared in 
-#'   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
+#'   \doi{10.5281/zenodo.17424}
 #' @references ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary 
 #'   Material for Frontiers Plant Genetics and Genomics 'Novel R tools for 
 #'   analysis of genome-wide population genetic data with emphasis on
@@ -137,7 +137,7 @@ filter_stats <- function(x, distance = bitwise.dist,
   }
   return(fanlist)
 }
-#==============================================================================#
+
 #' Predict cutoff thresholds for use with mlg.filter
 #' 
 #' Given a series of thresholds for a data set that collapse it into one giant 
@@ -153,7 +153,7 @@ filter_stats <- function(x, distance = bitwise.dist,
 #'   lineages should be defined.
 #' @seealso \code{\link{filter_stats}} \code{\link{mlg.filter}}
 #' @note This function originally appeared in 
-#'   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}. 
+#'   \doi{10.5281/zenodo.17424}. 
 #'   This is a bit of a blunt instrument.
 #' @export
 #' @references ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary
@@ -188,7 +188,6 @@ cutoff_predictor <- function(thresholds, fraction = 0.5){
   mean(thresholds[diffmax:(diffmax + 1)])
 }
 
-#==============================================================================#
 #' Plot the results of filter_stats
 #' 
 #' @param x a genlight of genind object
@@ -203,7 +202,7 @@ cutoff_predictor <- function(thresholds, fraction = 0.5){
 #' @export
 #' @seealso \code{\link{filter_stats}}
 #' @note This function originally appeared in 
-#'   \doi{10.5281/zenodo.17424}{DOI: 10.5281/zenodo.17424}
+#'   \doi{10.5281/zenodo.17424}
 #' @author Zhian N. Kamvar
 #' @references ZN Kamvar, JC Brooks, and NJ Grünwald. 2015. Supplementary
 #' Material for Frontiers Plant Genetics and Genomics 'Novel R tools for

R/methods.r

@@ -515,7 +515,6 @@ is.genclone <- function(x){
 #==============================================================================#
 #' @rdname genclone-method
 #' @param .Object a character, "genclone"
-#' @param gen \code{"\linkS4class{genind}"} object
 #' @param mlg a vector where each element assigns the multilocus genotype of 
 #'   that individual in the data set.
 #' @param mlgclass a logical value specifying whether or not to translate the 
@@ -552,9 +551,6 @@ setMethod(
 #' @param drop set to \code{FALSE}
 #' @param mlg.reset logical. Defaults to \code{FALSE}. If \code{TRUE}, the mlg
 #'   vector will be reset
-#' @param loc passed on to \code{\linkS4class{genind}} object.
-#' @param treatOther passed on to \code{\linkS4class{genind}} object.
-#' @param quiet passed on to \code{\linkS4class{genind}} object.
 #' @author Zhian N. Kamvar
 #==============================================================================#
 setMethod(

R/mlg.r

@@ -41,88 +41,95 @@
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
+
 #' Create counts, vectors, and matrices of multilocus genotypes.
 #' 
 #' @name mlg
+#' @md
 #'   
-#' @param gid a \code{\linkS4class{genind}}, \code{\linkS4class{genclone}},
-#'   \code{\linkS4class{genlight}}, or \code{\linkS4class{snpclone}} object.
-#'  
+#' @param gid a [adegenet::genind], [genclone][genclone-class], [adegenet::genlight], or [snpclone][snpclone-class] object.
 #' @param strata a formula specifying the strata at which computation is to be
 #'   performed.
-#' 
-#' @param sublist a \code{vector} of population names or indices that the user 
+#' @param sublist a `vector` of population names or indices that the user 
 #'   wishes to keep. Default to "ALL".
-#'   
-#' @param exclude a \code{vector} of population names or indexes that the user
-#' wishes to discard. Default to \code{NULL}.
-#'
+#' @param exclude a `vector` of population names or indexes that the user
+#' wishes to discard. Default to `NULL`.
 #' @param blacklist DEPRECATED, use exclude.
-#'
-#' @param mlgsub a \code{vector} of multilocus genotype indices with which to 
-#'   subset \code{mlg.table} and \code{mlg.crosspop}. NOTE: The resulting table 
-#'   from \code{mlg.table} will only contain countries with those MLGs
-#'   
-#' @param quiet \code{Logical}. If FALSE, progress of functions will be printed 
+#' @param mlgsub a `vector` of multilocus genotype indices with which to 
+#'   subset `mlg.table` and `mlg.crosspop`. NOTE: The resulting table 
+#'   from `mlg.table` will only contain countries with those MLGs
+#' @param quiet `Logical`. If FALSE, progress of functions will be printed 
 #'   to the screen.
-#'   
-#' @param bar deprecated. Same as \code{plot}. Retained for compatibility.
-#'   
-#' @param plot \code{logical} If \code{TRUE}, a bar graph for each population 
+#' @param bar deprecated. Same as `plot`. Retained for compatibility.
+#' @param plot `logical` If `TRUE`, a bar graph for each population 
 #'   will be displayed showing the relative abundance of each MLG within the 
 #'   population.
-#'   
-#' @param indexreturn \code{logical} If \code{TRUE}, a vector will be returned 
-#'   to index the columns of \code{mlg.table}.
-#'   
-#' @param df \code{logical} If \code{TRUE}, return a data frame containing the 
+#' @param indexreturn `logical` If `TRUE`, a vector will be returned 
+#'   to index the columns of `mlg.table`.
+#' @param df `logical` If `TRUE`, return a data frame containing the 
 #'   counts of the MLGs and what countries they are in. Useful for making graphs
-#'   with \code{\link{ggplot}}.
-#'   
-#' @param total \code{logical} If \code{TRUE}, a row containing the sum of all 
+#'   with [ggplot].
+#' @param total `logical` If `TRUE`, a row containing the sum of all 
 #'   represented MLGs is appended to the matrix produced by mlg.table.
 #'   
-#' @return \subsection{mlg}{ an integer describing the number of multilocus
-#' genotypes observed. } \subsection{mlg.table}{ a matrix with columns
-#' indicating unique multilocus genotypes and rows indicating populations. 
-#' This table can be used with the funciton \code{\link{diversity_stats}} to calculate
-#' the Shannon-Weaver index (H), Stoddart and Taylor's 
-#' index (aka inverse Simpson's index; G), Simpson's index (lambda), and evenness (E5).} 
-#' \subsection{mlg.vector}{ a numeric vector naming the multilocus genotype of
-#' each individual in the dataset. } \subsection{mlg.crosspop}{ \itemize{ 
-#' \item{default}{ a \code{list} where each element contains a named integer
-#' vector representing the number of individuals represented from each
-#' population in that MLG} \item{\code{indexreturn = TRUE}}{ a \code{vector} of
-#' integers defining the multilocus genotypes that have individuals crossing
-#' populations} \item{\code{df = TRUE}}{ A long form data frame with the
-#' columns: MLG, Population, Count. Useful for graphing with ggplot2} } } 
-#' \subsection{mlg.id}{ a list of multilocus genotypes with the associated
-#' individual names per MLG. }
+#' @return 
+#' 
+#' ## mlg
+#'
+#' an integer describing the number of multilocus genotypes observed. 
+#'
+#' ## mlg.table
+#'
+#' a matrix with columns indicating unique multilocus genotypes and rows
+#' indicating populations. This table can be used with the funciton
+#' [diversity_stats] to calculate the Shannon-Weaver index (H), Stoddart and
+#' Taylor's index (aka inverse Simpson's index; G), Simpson's index (lambda),
+#' and evenness (E5).
+#' 
+#' ## mlg.vector
+#'
+#' a numeric vector naming the multilocus genotype of each individual in the
+#' dataset. 
+#'
+#' ## mlg.crosspop
+#'
+#' - **default** a `list` where each element contains a named integer
+#'   vector representing the number of individuals represented from each
+#'   population in that MLG 
+#' - `indexreturn = TRUE` a `vector` of integers defining the multilocus
+#'   genotypes that have individuals crossing populations 
+#' - `df = TRUE` A long form data frame with the columns: MLG, Population,
+#'   Count. Useful for graphing with ggplot2   
+#'
+#' ## mlg.id
+#'
+#' a list of multilocus genotypes with the associated individual names per MLG. 
 #' 
 #' @details Multilocus genotypes are the unique combination of alleles across
-#'   all loci. For details of how these are calculated see \code{vignette("mlg",
-#'   package = "poppr")}. In short, for genind and genclone objects, they are
+#'   all loci. For details of how these are calculated see `vignette("mlg",
+#'   package = "poppr")`. In short, for genind and genclone objects, they are
 #'   calculated by using a rank function on strings of alleles, which is
 #'   sensitive to missing data. For genlight and snpclone objects, they are
-#'   calculated with distance methods via \code{\link{bitwise.dist}} and
-#'   \code{\link{mlg.filter}}, which means that these are insensitive to missing
-#'   data. Three different types of MLGs can be defined in \pkg{poppr}: \itemize{ 
-#'   \item{original - }{the default definition of multilocus genotypes as
-#'   detailed above} \item{contracted - }{these are multilocus genotypes
-#'   collapsed into multilocus lineages (\code{\link{mll}}) with genetic
-#'   distance via \code{\link{mlg.filter}}} \item{custom - }{user-defined
-#'   multilocus genotypes. These are useful for information such as mycelial
-#'   compatibility groups}}
-#'   \strong{All of the functions documented here will work on any of the MLG
-#'   types defined in \pkg{poppr}}
-#'   
+#'   calculated with distance methods via [bitwise.dist] and
+#'   [mlg.filter], which means that these are insensitive to missing
+#'   data. Three different types of MLGs can be defined in \pkg{poppr}: 
+#'
+#' - **original** the default definition of multilocus genotypes as
+#'   detailed above 
+#' - **contracted** these are multilocus genotypes collapsed into multilocus
+#'   lineages ([mll]) with genetic distance via [mlg.filter] 
+#' - **custom** user-defined multilocus genotypes. These are useful for
+#'   information such as mycelial compatibility groups
+#'
+#' **All of the functions documented here will work on any of the MLG types
+#' defined in \pkg{poppr}**
 #' 
-#' @seealso \code{\link[vegan]{diversity}} 
-#'  \code{\link{diversity_stats}}
-#'  \code{\link{popsub}}
-#'  \code{\link{mll}}
-#'  \code{\link{mlg.filter}}
-#'  \code{\link{mll.custom}}
+#' @seealso [vegan::diversity()]
+#'  [diversity_stats]
+#'  [popsub]
+#'  [mll]
+#'  [mlg.filter]
+#'  [mll.custom]
 #'  
 #' @author Zhian N. Kamvar
 #' @examples
@@ -235,13 +242,13 @@ mlg <- function(gid, quiet=FALSE){
 #' @rdname mlg 
 #' 
 #' @param color an option to display a single barchart for mlg.table, colored by
-#'   population (note, this becomes facetted if \code{background = TRUE}).
+#'   population (note, this becomes facetted if `background = TRUE`).
 #'   
 #' @param background an option to display the the total number of MLGs across
 #'   populations per facet in the background of the plot.
 #'
-#' @note The resulting matrix of \code{mlg.table} can be used for analysis with 
-#' the \code{\link{vegan}} package.
+#' @note The resulting matrix of `mlg.table` can be used for analysis with 
+#' the \pkg{vegan} package.
 #' 
 #' @export
 #==============================================================================#
@@ -316,21 +323,19 @@ mlg.table <- function(gid, strata = NULL, sublist = "ALL", exclude = NULL, black
   return(mlgtab)
 }
 
-#==============================================================================#
 #' @rdname mlg
 #' 
 #' @param reset logical. For genclone objects, the MLGs are defined by the input
 #'   data, but they do not change if more or less information is added (i.e.
-#'   loci are dropped). Setting \code{reset = TRUE} will recalculate MLGs.
-#'   Default is \code{FALSE}, returning the MLGs defined in the @@mlg slot.
+#'   loci are dropped). Setting `reset = TRUE` will recalculate MLGs.
+#'   Default is `FALSE`, returning the MLGs defined in the @@mlg slot.
 #'   
 #' @note mlg.vector will recalculate the mlg vector for
-#'   \code{\linkS4class{genind}} objects and will return the contents of the mlg
-#'   slot in \code{\linkS4class{genclone}} objects. This means that MLGs will be
-#'   different for subsetted \code{\linkS4class{genind}} objects.
+#'   [adegenet::genind] objects and will return the contents of the mlg
+#'   slot in [genclone][genclone-class] objects. This means that MLGs will be
+#'   different for subsetted [adegenet::genind] objects.
 #'   
 #' @export
-#==============================================================================#
 mlg.vector <- function(gid, reset = FALSE){
 
   # This will return a vector indicating the multilocus genotypes.
@@ -401,19 +406,8 @@ mlg.vector <- function(gid, reset = FALSE){
 
 
 
-#==============================================================================#
 #' @rdname mlg
-# Multilocus Genotypes Across Populations
-#
-# Show which multilocus genotypes exist accross populations. 
-#
-# @param gid a \code{\link{genind}} object.
-# 
-#' @return a \code{list} containing vectors of population names for each MLG. 
-#' 
 #' @export
-#==============================================================================#
-
 mlg.crosspop <- function(gid, strata = NULL, sublist = "ALL", exclude = NULL, blacklist = NULL, 
                          mlgsub = NULL,
                          indexreturn = FALSE, df = FALSE, quiet = FALSE){
@@ -516,12 +510,8 @@ mlg.crosspop <- function(gid, strata = NULL, sublist = "ALL", exclude = NULL, bl
 
 
 
-#==============================================================================#
 #' @rdname mlg
 #' @export
-#==============================================================================#
-
-
 mlg.id <- function (gid){
   if (!is.genind(gid) & !is(gid, "snpclone")){
     stop(paste(substitute(gid), "is not a genind or genclone object"))

cran-comments.md

@@ -1,5 +1,3 @@
-# Poppr version 2.9.4
-
-This fixes broken tests, provides a declaration for an exported C function, and fixes object class comparison to use identical()
-This also removes RClone from Suggests. There is no user-facing code that contains RClone and it is an archived package on CRAN.
+# Poppr version 2.9.5
 
+This removes the xcolor.sty option usenames