Merge pull request #264 from grunwaldlab/znk/ggplot2-maintenance/263

use modern ggplot2 labs idiom

Author: zkamvar

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.9.6
-Date: 2024-03-15 16:50:51 UTC
-SHA: ef69ace403850e8149c4c1728de6190d36195bd3
+Version: 2.9.7
+Date: 2025-06-18 23:41:37 UTC
+SHA: 43eb0047542d0bc739f6ea19bc95e008431f2119

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.9.6
+Version: 2.9.7
 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",
@@ -67,4 +67,4 @@ Suggests:
 Config/Needs/check: dbailleul/RClone
 License: GPL-2 | GPL-3
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2.9000

NEWS.md

@@ -1,3 +1,13 @@
+poppr 2.9.7
+===========
+
+MISC
+----
+
+* compatibility fix for ggplot2 4.0.0 (reported: @teunbrand, #263, 
+  fixed: @zkamvar, #264)
+* CRAN maintenance: documentaiton fixes
+
 poppr 2.9.6
 ===========
 

R/Index_calculations.r

@@ -161,7 +161,7 @@
 #'
 #' This function outputs a \pkg{ggplot2} graphic of histograms. These can be
 #' manipulated to be visualized in another manner by retrieving the plot with
-#' the [last_plot()] command from \pkg{ggplot2}. A useful manipulation would
+#' the last plot command from \pkg{ggplot2}. A useful manipulation would
 #' be to arrange the graphs into a single column so that the values of the
 #' statistic line up: `p <- last_plot(); p + facet_wrap(~population,
 #' ncol = 1, scales = "free_y")` The name for the groupings is

R/aaaMLGmethods.R

@@ -353,7 +353,7 @@ setMethod(
 #' @export
 #' @keywords internal
 #' @seealso \code{\link{MLG}} \code{\linkS4class{genclone}} 
-#'   \code{\linkS4class{genlight}} \code{\link{initialize,MLG-method}}
+#'   \code{\link[adegenet:genlight-class]{genlight}} \code{\link{initialize,MLG-method}}
 #'   \code{\link{levels,MLG-method}} \code{\link{unique,MLG-method}}
 #'   
 #' @examples

R/bruvo.r

@@ -54,7 +54,7 @@
 #' 
 #' Calculate the average Bruvo's distance over all loci in a population.
 #' 
-#' @param pop a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param pop a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #'   
 #' @param replen a \code{vector} of \code{integers} indicating the length of the
 #'   nucleotide repeats for each microsatellite locus. E.g. a locus with a (CAT) 
@@ -243,9 +243,9 @@ bruvo.dist <- function(pop, replen = 1, add = TRUE, loss = TRUE, by_locus = FALS
 #' Only diferences between query individuals and reference individuals will be reported
 #' All other values are NaN
 #' 
-#' @param query a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param query a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #' 
-#' @param ref a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param ref a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #' 
 #' @export
 #' @author David Folarin
@@ -282,7 +282,7 @@ bruvo.between <- function(query, ref, replen = 1, add = TRUE, loss = TRUE, by_lo
 #
 #' Create a tree using Bruvo's Distance with non-parametric bootstrapping.
 #' 
-#' @param pop a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param pop a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #'   
 #' @param replen a \code{vector} of \code{integers} indicating the length of the
 #'   nucleotide repeats for each microsatellite locus.
@@ -315,15 +315,15 @@ bruvo.between <- function(query, ref, replen = 1, add = TRUE, loss = TRUE, by_lo
 #'   \code{FALSE}. By default, it is set to \code{NULL}, which will assume an
 #'   unrooted phylogeny unless the function name contains "upgma".
 #' 
-#' @param ... any argument to be passed on to \code{\link{boot.phylo}}. eg. 
+#' @param ... any argument to be passed on to \code{\link[ape]{boot.phylo}}. eg. 
 #'   \code{quiet = TRUE}.
 #'   
 #'   
 #' @return a tree of class phylo with nodelables
 #'   
-#' @seealso \code{\link{bruvo.dist}}, \code{\link{nancycats}}, 
-#'   \code{\link{upgma}}, \code{\link{nj}}, \code{\link{boot.phylo}}, 
-#'   \code{\link{nodelabels}}, \code{\link{tab}}, 
+#' @seealso \code{\link{bruvo.dist}}, \code{\link[adegenet]{nancycats}}, 
+#'   \code{\link{upgma}}, \code{\link[ape]{nj}}, \code{\link[ape]{boot.phylo}}, 
+#'   \code{\link[ape]{nodelabels}}, \code{\link[adegenet]{tab}}, 
 #'   \code{\link{missingno}}.
 #'   
 #' @details This function will calculate a tree based off of Bruvo's distance
@@ -455,7 +455,7 @@ bruvo.boot <- function(pop, replen = 1, add = TRUE, loss = TRUE, sample = 100,
 #' Create minimum spanning network of selected populations using Bruvo's 
 #' distance.
 #' 
-#' @param gid a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param gid a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #'   
 #' @param replen a \code{vector} of \code{integers} indicating the length of the
 #'   nucleotide repeats for each microsatellite locus.
@@ -516,7 +516,7 @@ bruvo.boot <- function(pop, replen = 1, add = TRUE, loss = TRUE, sample = 100,
 #'   used to filter un-contracted data sets.
 #'   }
 #'   
-#' @seealso \code{\link{bruvo.dist}}, \code{\link{nancycats}}, 
+#' @seealso \code{\link{bruvo.dist}}, \code{\link[adegenet]{nancycats}}, 
 #'   \code{\link{plot_poppr_msn}}, \code{\link[igraph]{mst}} 
 #'   \code{\link{bruvo.boot}}, \code{\link{greycurve}} \code{\link{poppr.msn}}
 #'   
@@ -663,7 +663,7 @@ bruvo.msn <- function (gid, replen = 1, add = TRUE, loss = TRUE,
 #' 
 #' This function will test for consistency in the sense that all alleles are 
 #' able to be represented as discrete units after division and rounding.
-#' @param gid a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param gid a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #' @param replen a numeric vector of repeat motif lengths.
 #' @return a logical vector indicating whether or not the repeat motif length is
 #'   consistent.
@@ -711,7 +711,7 @@ consistent_replen <- function(index, alleles, replen){
 #' 
 #' Attempts to fix inconsistent repeat lengths found by \code{test_replen}
 #' 
-#' @param gid a \code{\link{genind}} or \code{\link{genclone}} object
+#' @param gid a \code{\link[adegenet]{genind}} or \code{\link{genclone}} object
 #' @param replen a numeric vector of repeat motif lengths.
 #' @param e a number to be subtracted or added to inconsistent repeat lengths to
 #'   allow for proper rounding.

R/classes.r

@@ -50,19 +50,19 @@ setClassUnion("mlgORnumeric", c("MLG", "numeric"))
 #' GENclone and SNPclone classes
 #' 
 #' @description \strong{GENclone} is an S4 class that extends the 
-#'   \code{\linkS4class{genind}} object.\cr \strong{SNPclone} is an S4 class
-#'   that extends the \code{\linkS4class{genlight}} object.\cr\cr They will have
+#'   \code{\link[adegenet:genind-class]{genind}} object.\cr \strong{SNPclone} is an S4 class
+#'   that extends the \code{\link[adegenet:genlight-class]{genlight}} object.\cr\cr They will have
 #'   all of the same attributes as their parent classes, but they will contain
 #'   one extra slot to store extra information about multilocus genotypes.
 #'   
 #' @section Extends: The \code{genclone} class extends class 
-#'   \code{"\linkS4class{genind}"}, directly. \cr The \code{snpclone} class 
-#'   extends class \code{"\linkS4class{genlight}"}, directly.
+#'   \code{"\link[adegenet:genind-class]{genind}"}, directly. \cr The \code{snpclone} class 
+#'   extends class \code{"\link[adegenet:genlight-class]{genlight}"}, directly.
 #'   
 #' @details The genclone and snpclone classes will allow for more optimized 
 #'   methods of clone correction.
 #'   
-#'   Previously for \linkS4class{genind} and \linkS4class{genlight} objects, 
+#'   Previously for \link[adegenet:genind-class]{genind} and \link[adegenet:genlight-class]{genlight} objects, 
 #'   multilocus genotypes were not retained after a data set was subset by 
 #'   population. The new \strong{\code{mlg}} slot allows us to assign the 
 #'   multilocus genotypes and retain that information no matter how we subset 
@@ -85,7 +85,7 @@ setClassUnion("mlgORnumeric", c("MLG", "numeric"))
 #'   object of class \code{\linkS4class{MLG}}.
 #' @author Zhian N. Kamvar
 #' @seealso \code{\link{as.genclone}} \code{\link{as.snpclone}} 
-#'   \code{\linkS4class{genind}} \code{\linkS4class{genlight}} 
+#'   \code{\link[adegenet:genind-class]{genind}} \code{\link[adegenet:genlight-class]{genlight}} 
 #'   \code{\link[adegenet:accessors]{strata}} \code{\link[adegenet:accessors]{setPop}} 
 #'   \code{\link{MLG}} \code{\link{mll}} \code{\link{mlg.filter}}
 #' @import methods
@@ -186,7 +186,7 @@ setClass(
 #' An internal object used for bootstrapping. Not intended for user interaction.
 #' 
 #' @section Extends: 
-#' Virtual Class \code{"\linkS4class{gen}"}.
+#' Virtual Class \code{"\link[adegenet:gen-class]{gen}"}.
 #' 
 #' @name bootgen-class
 #' @rdname bootgen-class

R/data_subset.r

@@ -48,7 +48,7 @@
 #' This function removes any duplicated multilocus genotypes from any specified 
 #' population strata.
 #' 
-#' @param pop a \code{\linkS4class{genind}}, \code{\linkS4class{genclone}}, or
+#' @param pop a \code{\link[adegenet:genind-class]{genind}}, \code{\linkS4class{genclone}}, or
 #'   \code{\linkS4class{snpclone}} object
 #'   
 #' @param strata a hierarchical formula or numeric vector. This will define the
@@ -65,7 +65,7 @@
 #'   can set \code{keep = c(1,3)}.
 #'   
 #' @return a clone corrected \code{\linkS4class{genclone}}, 
-#'   \code{\linkS4class{snpclone}}, or \code{\linkS4class{genind}} object.
+#'   \code{\linkS4class{snpclone}}, or \code{\link[adegenet:genind-class]{genind}} object.
 #'   
 #' @details This function will clone correct based on the stratification 
 #'   provided. To clone correct indiscriminately of population structure, set 
@@ -205,8 +205,8 @@ clonecorrect <- function(pop, strata = 1, combine = FALSE, keep = 1){
 #' Create a new dataset with specified populations or exclude specified
 #' populations from the dataset.
 #' 
-#' @param gid a \code{\linkS4class{genind}}, \code{\linkS4class{genclone}},
-#'   \code{\linkS4class{genlight}}, or \code{\linkS4class{snpclone}} object.
+#' @param gid a \code{\link[adegenet:genind-class]{genind}}, \code{\linkS4class{genclone}},
+#'   \code{\link[adegenet:genlight-class]{genlight}}, or \code{\linkS4class{snpclone}} object.
 #' 
 #' @param sublist a \code{vector} of population names or indexes that the user
 #' wishes to keep. Default to \code{"ALL"}.
@@ -351,7 +351,7 @@ popsub <- function(gid, sublist="ALL", exclude=NULL, blacklist=NULL, mat=NULL, d
 #' missingno gives the user four options to deal with missing data: remove loci,
 #' remove samples, replace with zeroes, or replace with average allele counts.
 #'
-#'@param pop a \code{\linkS4class{genclone}} or \code{\linkS4class{genind}} 
+#'@param pop a \code{\linkS4class{genclone}} or \code{\link[adegenet:genind-class]{genind}} 
 #'  object.
 #'  
 #'@param type a \code{character} string: can be "ignore", "zero", "mean", 
@@ -370,7 +370,7 @@ popsub <- function(gid, sublist="ALL", exclude=NULL, blacklist=NULL, mat=NULL, d
 #'  instead.
 #'  
 #'@details These methods provide a way to deal with systematic missing data and 
-#'  to give a wrapper for \code{adegenet}'s \code{ \link{tab}} function. 
+#'  to give a wrapper for \code{adegenet}'s \code{ \link[adegenet]{tab}} function. 
 #'  ALL OF THESE ARE TO BE USED WITH CAUTION. 
 #'  
 #'  Using this function with polyploid data (where missing data is coded as "0")
@@ -389,7 +389,7 @@ popsub <- function(gid, sublist="ALL", exclude=NULL, blacklist=NULL, mat=NULL, d
 #'  more diversity.}
 #'  }
 #'  }
-#'@return a \code{\linkS4class{genclone}} or \code{\linkS4class{genind}} object.
+#'@return a \code{\linkS4class{genclone}} or \code{\link[adegenet:genind-class]{genind}} object.
 #'  
 #'@note \emph{"wild missingno appeared!"}
 #'  
@@ -513,12 +513,12 @@ missingno <- function(pop, type = "loci", cutoff = 0.05, quiet=FALSE, freq = FAL
 #' Remove all non-phylogentically informative loci
 #' 
 #' This function will facilitate in removing phylogenetically uninformative loci
-#' from a \code{\linkS4class{genclone}} or \code{\linkS4class{genind}} object. 
+#' from a \code{\linkS4class{genclone}} or \code{\link[adegenet:genind-class]{genind}} object. 
 #' The user has the ability to define what uninformative means by setting a 
 #' cutoff value for either percentage of differentiating genotypes or minor 
 #' allele frequency.
 #' 
-#' @param pop a \code{\linkS4class{genclone}} or \code{\linkS4class{genind}} 
+#' @param pop a \code{\linkS4class{genclone}} or \code{\link[adegenet:genind-class]{genind}} 
 #'   object.
 #'   
 #' @param cutoff \code{numeric}. A number from 0 to 1 defining the minimum 
@@ -658,12 +658,12 @@ informloci <- function(pop, cutoff = 2/nInd(pop), MAF = 0.01, quiet = FALSE){
 #' diversity statistics. The tradeoff was the fact that this broke all other 
 #' analyses as they relied on allele frequencies and the missing alleles are 
 #' treated as extra alleles. This function removes those alleles and returns a 
-#' \code{\linkS4class{genclone}} or \code{\linkS4class{genind}} object where 
+#' \code{\linkS4class{genclone}} or \code{\link[adegenet:genind-class]{genind}} object where 
 #' allele frequencies are coded based on the number of alleles observed at a 
 #' single locus per individual. See the examples for more details.
 #' 
-#' @param poly a \code{\linkS4class{genclone}}, \code{\linkS4class{genind}}, or 
-#'   \code{\linkS4class{genpop}} object that has a ploidy of > 2
+#' @param poly a \code{\linkS4class{genclone}}, \code{\link[adegenet:genind-class]{genind}}, or 
+#'   \code{\link[adegenet:genpop-class]{genpop}} object that has a ploidy of > 2
 #' @param newploidy for genind or genclone objects: if \code{FALSE} (default),
 #'   the user-defined ploidy will stay constant. if \code{TRUE}, the ploidy for
 #'   each sample will be determined by the maximum ploidy observed for each
@@ -673,8 +673,8 @@ informloci <- function(pop, cutoff = 2/nInd(pop), MAF = 0.01, quiet = FALSE){
 #' if \code{TRUE}, objects with uneven ploidies will have zeroes appended to all
 #' loci to allow conversion to genpop objects. Defaults to \code{FALSE}.
 #'   
-#' @return a \code{\linkS4class{genclone}}, \code{\linkS4class{genind}}, or
-#'   \code{\linkS4class{genpop}} object.
+#' @return a \code{\linkS4class{genclone}}, \code{\link[adegenet:genind-class]{genind}}, or
+#'   \code{\link[adegenet:genpop-class]{genpop}} object.
 #'   
 #' @details The genind object has two caveats that make it difficult to work 
 #'   with polyploid data sets: 

R/distances.r

@@ -52,7 +52,7 @@
 #' individuals who share half of the same alleles will have a distance of 0.5.
 #' This function can analyze distances for any marker system.
 #' 
-#' @param x a \code{\link{genind}} object.
+#' @param x a \code{\link[adegenet]{genind}} object.
 #'   
 #' @param percent \code{logical}. Should the distance be represented as a 
 #'   percent? If set to \code{FALSE} (default), the distance will be reflected 
@@ -139,7 +139,7 @@ diss.dist <- function(x, percent=FALSE, mat=FALSE){
 #' These functions are modified from the function \link[adegenet]{dist.genpop} to
 #' be applicable for distances between individuals.
 #' 
-#' @param x a \linkS4class{genind}, \linkS4class{genclone}, or matrix object.
+#' @param x a \link[adegenet:genind-class]{genind}, \linkS4class{genclone}, or matrix object.
 #'   
 #' @param warning If \code{TRUE}, a warning will be printed if any infinite 
 #'   values are detected and replaced. If \code{FALSE}, these values will be 
@@ -163,7 +163,7 @@ diss.dist <- function(x, percent=FALSE, mat=FALSE){
 #'   compatibility.
 #'   
 #'   These distances were adapted from the \pkg{adegenet} function
-#'   \code{\link{dist.genpop}} to work with \code{\linkS4class{genind}} objects.
+#'   \code{\link[adegenet]{dist.genpop}} to work with \code{\link[adegenet:genind-class]{genind}} objects.
 #' 
 #' @seealso \code{\link{aboot}} \code{\link{diss.dist}} \code{\link{poppr.amova}}
 #' @rdname genetic_distance

R/filter_stats.R

@@ -47,8 +47,8 @@
 #' This function is a wrapper to mlg.filter. It will calculate all of the stats 
 #' for mlg.filter utilizing all of the algorithms.
 #' 
-#' @param x a \code{\link{genind}}, \code{\link{genclone}},
-#'   \code{\link{genlight}}, or \code{\link{snpclone}} object
+#' @param x a \code{\link[adegenet]{genind}}, \code{\link{genclone}},
+#'   \code{\link[adegenet]{genlight}}, or \code{\link{snpclone}} object
 #' @param distance a distance function or matrix
 #' @param threshold a threshold to be passed to \code{\link{mlg.filter}} 
 #'   (Default: 1e6)