Changing the the verb of the function's title to third person.

Add check for duplicated names.

R/gl.amova.r

@@ -1,4 +1,4 @@
-#' Performs AMOVA using genlight data.
+#' Performs AMOVA using genlight data
 #'
 #' This script performs an AMOVA based on the genetic distance matrix from
 #' stamppNeisD() [package StAMPP] using the amova() function from the package

R/gl.assign.pa.r

@@ -1,5 +1,5 @@
 #' @name gl.assign.pa
-#' @title Eliminate populations as possible source populations for an individual
+#' @title Eliminates populations as possible source populations for an individual
 #'  of unknown provenance, using private alleles
 #' @description
 #' This script eliminates from consideration as putative source populations,

R/gl.check.verbosity.r

@@ -1,4 +1,4 @@
-#' A function to check the current global verbosity
+#' Checks the current global verbosity
 #'
 #' The verbosity can be set in one of two ways -- (a) explicitly by the user by
 #' passing a value using the parameter verbose= in a function, or (b) by setting

R/gl.collapse.r

@@ -1,15 +1,15 @@
 #' @name gl.collapse
-#' @title Collapse a distance matrix by amalgamating populations with pairwise
+#' @title Collapses a distance matrix by amalgamating populations with pairwise
 #' fixed difference count less that a threshold
 #' @description
-#' This script takes a the file generated by gl.fixed.diff and amalgamates
+#' This script takes a file generated by gl.fixed.diff and amalgamates
 #' populations with distance less than or equal to a specified threshold. The
 #' distance matrix is generated by gl.fixed.diff().
 #'
 #' The script then applies the new population assignments to the genlight object
 #'  and recalculates the distance and associated matrices.
 #'
-#' @param fd Name of the list of matricies produced by gl.fixed.diff() [required].
+#' @param fd Name of the list of matrices produced by gl.fixed.diff() [required].
 #' @param tloc Threshold defining a fixed difference (e.g. 0.05 implies 95:5 vs
 #'  5:95 is fixed) [default 0].
 #' @param tpop Threshold number of fixed differences above which populations

R/gl.compliance.check.r

@@ -69,7 +69,8 @@ gl.compliance.check <- function(x,
         locNames(x) <- paste0("Loc", 1:nLoc(x))
     }
 
-    # Check that the data exist, and that they are restricted to the appropriate values
+    # Check that the data exist, and that they are restricted to the
+    # appropriate values
 
     if (datatype == "SNP") {
         mat <- as.matrix(x)
@@ -115,7 +116,8 @@ gl.compliance.check <- function(x,
         }
     }
 
-    # Check for the locus metrics, and create if they do not exist.  Check for the locus metrics flags, and create if they do not exist.
+    # Check for the locus metrics, and create if they do not exist.
+    # Check for the locus metrics flags, and create if they do not exist.
     # Check for the verbosity flag, and create if it does not exist.
 
     if (verbose >= 2) {
@@ -146,7 +148,8 @@ gl.compliance.check <- function(x,
         x@other$loc.metrics.flags$monomorphs <- FALSE
     }
 
-    # Check that the number of values in the loc.metrics dataframe is the same as the number of loci
+    # Check that the number of values in the loc.metrics dataframe is the same
+    # as the number of loci
     if (nLoc(x) != nrow(x@other$loc.metrics)) {
         cat(
             warn(
@@ -155,6 +158,23 @@ gl.compliance.check <- function(x,
         )
     }
 
+    # check that individual names are unique, and if not, add underscore and
+    # letters
+    if (verbose >= 2) {
+        cat(report("  Checking whether individual names are unique.\n"))
+    }
+
+    if (any(duplicated(indNames(x)))) {
+        if (verbose >= 2) {
+            cat(
+                warn(
+                    "  Individual names are not unique. Appending an extra number to make them unique.\n"
+                )
+            )
+        }
+        indNames(x) <- make.unique(indNames(x), sep = '_')
+    }
+
     # Check that the individual metrics exist, and if not, create the df
 
     if (verbose >= 2) {
@@ -171,7 +191,8 @@ gl.compliance.check <- function(x,
         }
     }
 
-    # Check that the population variable exists, and if it does not, create it with a single population 'pop1'
+    # Check that the population variable exists, and if it does not, create it
+    # with a single population 'pop1'
 
     if (verbose >= 2) {
         cat(report("  Checking for population assignments\n"))

R/gl.define.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.define.pop
-#' @title Define a new population in a genlight object for specified individuals
+#' @title Defines a new population in a genlight object for specified individuals
 #' @description
 #' The script reassigns existing individuals to a new population and removes
 #' their existing population assignment.

R/gl.dist.ind.r

@@ -1,5 +1,5 @@
 #' @name gl.dist.ind
-#' @title Calculate a distance matrix for individuals defined in an \{adegenet\}
+#' @title Calculates a distance matrix for individuals defined in an \{adegenet\}
 #'  genlight object
 #' @description
 #' This script calculates various distances between individuals based on allele

R/gl.dist.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.dist.pop
-#' @title Calculate a distance matrix for populations with SNP genotypes in a
+#' @title Calculates a distance matrix for populations with SNP genotypes in a
 #' genlight object
 #' @description
 #' This script calculates various distances between populations based on allele

R/gl.drop.ind.r

@@ -1,5 +1,5 @@
 #' @name gl.drop.ind
-#' @title Remove specified individuals from a genlight \{adegenet\} object
+#' @title Removes specified individuals from a genlight \{adegenet\} object
 #' @description
 #' The script, having deleted individuals, optionally identifies resultant
 #' monomorphic loci or loci with all values missing and deletes them

R/gl.drop.loc.r

@@ -1,5 +1,5 @@
 #' @name gl.drop.loc
-#' @title Remove specified loci from a genlight \{adegenet\} object
+#' @title Removes specified loci from a genlight \{adegenet\} object
 #' @description
 #' The script returns a genlight object with specified loci deleted.
 #'

R/gl.drop.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.drop.pop
-#' @title Remove specified populations from a genlight object
+#' @title Removes specified populations from a genlight object
 #' @description
 #' Individuals are assigned to populations based on the specimen metadata data
 #' file (csv) used with \code{\link{gl.read.dart}}.

R/gl.edit.recode.ind.r

@@ -1,6 +1,6 @@
 #' @name gl.edit.recode.ind
-#' @title Create or edit a individual (=specimen) names, create an recode_ind
-#'  file amd apply the changes to a genlight object.
+#' @title Creates or edits an individual (=specimen) names, creates an recode_ind
+#'  file and applies the changes to a genlight object.
 #' @description
 #' A script to edit individual names in a genlight object, or to create a
 #' reassignment table taking the individual labels from a genlight object, or to

R/gl.edit.recode.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.edit.recode.pop
-#' @title Create or edit a population re-assignment table
+#' @title Creates or edits a population re-assignment table
 #' @description
 #' A script to edit population assignments in a genlight object, or to
 #' create a reassignment table taking the population assignments

R/gl.evanno.r

@@ -1,5 +1,5 @@
 #' @name gl.evanno
-#' @title Create an Evanno plot from an sr structure run object
+#' @title Creates an Evanno plot from an sr structure run object
 #' @description
 #' This function takes a genlight object and runs a STRUCTURE analysis based on
 #' functions from \code{strataG}

R/gl.fdsim.r

@@ -1,5 +1,5 @@
 #' @name gl.fdsim
-#' @title Estimate the rate of false positives in a fixed difference analysis
+#' @title Estimates the rate of false positives in a fixed difference analysis
 #' @description
 #' This function takes two populations and generates allele frequency profiles
 #' for them. It then samples an allele frequency for each, at random, and

R/gl.filter.allna.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.allna
-#' @title Remove loci that are all NA across individuals and/or individuals with
+#' @title Removes loci that are all NA across individuals and/or individuals with
 #'  all NA across loci
 #'
 #' @description

R/gl.filter.callrate.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.callrate
-#' @title Filter loci or specimens in a genlight \{adegenet\} object based on
+#' @title Filters loci or specimens in a genlight \{adegenet\} object based on
 #' call rate
 #' @description
 #' SNP datasets generated by DArT have missing values primarily arising from

R/gl.filter.locmetric.r

@@ -1,5 +1,5 @@
-#' @title gl.filter.locmetrics
-#' @title Filter loci on the basis of numeric information stored in
+#' @name gl.filter.locmetrics
+#' @title Filters loci on the basis of numeric information stored in
 #' other$loc.metrics in a genlight \{adegenet\} object
 #' @description
 #' This script uses any field with numeric values stored in $other$loc.metrics

R/gl.filter.maf.r

@@ -1,5 +1,5 @@
-#' @title gl.filter.maf
-#' @title Filter loci on the basis of minor allele frequency (MAF) in a genlight
+#' @name gl.filter.maf
+#' @title Filters loci on the basis of minor allele frequency (MAF) in a genlight
 #'  {adegenet} object
 #' @description
 #' This script calculates the minor allele frequency for each locus and updates

R/gl.filter.monomorphs.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.monomorphs
-#' @title Remove monomorphic loci, including those with all NAs
+#' @title Removes monomorphic loci, including those with all NAs
 #' @description
 #' This script deletes monomorphic loci from a genlight \{adegenet\} object
 #'

R/gl.filter.pa.r

@@ -1,7 +1,7 @@
-#' Filter loci that contain private (and fixed alleles) between two populations.
+#' Filters loci that contain private (and fixed alleles) between two populations
 #'
 #' This script is meant to be used prior to \code{gl.nhybrids} to maximise the
-#' information content of the snps used to identify hybrids (currently
+#' information content of the SNPs used to identify hybrids (currently
 #'  newhybrids does allow only 200 SNPs). The idea is to use first all loci that
 #'   have fixed alleles between the potential source populations and then 'fill
 #'    up' to 200 loci using loci that have private alleles between those. The

R/gl.filter.parent.offspring.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.parent.offspring
-#' @title Filter putative parent offspring within a population
+#' @title Filters putative parent offspring within a population
 #' @description
 #' This script removes individuals suspected of being related as
 #' parent-offspring,using the output of the function

R/gl.filter.rdepth.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.rdepth
-#' @title Filter loci based on counts of sequence tags scored at a locus (read
+#' @title Filters loci based on counts of sequence tags scored at a locus (read
 #' depth)
 #'
 #' @description

R/gl.filter.reproducibility.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.reproducibility
-#' @title Filter loci in a genlight \{adegenet\} object based on average
+#' @title Filters loci in a genlight \{adegenet\} object based on average
 #' repeatability of alleles at a locus
 #' @description
 #' SNP datasets generated by DArT have an index, RepAvg, generated by

R/gl.filter.secondaries.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.secondaries
-#' @title Filter loci that represent secondary SNPs in a genlight object
+#' @title Filters loci that represent secondary SNPs in a genlight object
 #' @description
 #' SNP datasets generated by DArT include fragments with more than one SNP and
 #' record them separately with the same CloneID (=AlleleID). These multiple SNP

R/gl.filter.sexlinked.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.sexlinked
-#' @title Filter loci that are sex linked
+#' @title Filters loci that are sex linked
 #' @description
 #' Alleles unique to the Y or W chromosome and monomorphic on the X chromosomes
 #' will appear in the SNP dataset as genotypes that are heterozygotic in all

R/gl.filter.taglength.r

@@ -1,5 +1,5 @@
 #' @name gl.filter.taglength
-#' @title Filter loci in a genlight \{adegenet\} object based on sequence tag
+#' @title Filters loci in a genlight \{adegenet\} object based on sequence tag
 #' length
 #' @description
 #' SNP datasets generated by DArT typically have sequence tag lengths ranging

R/gl.fixed.diff.r

@@ -1,5 +1,5 @@
 #' @name gl.fixed.diff
-#' @title Generate a matrix of fixed differences and associated statistics for
+#' @title Generates a matrix of fixed differences and associated statistics for
 #' populations taken pairwise
 #' @description
 #' This script takes SNP data or sequence tag P/A data grouped into populations

R/gl.fst.pop.r

@@ -1,4 +1,4 @@
-#' Calculate a pairwise Fst values for populations in a genlight object
+#' Calculates a pairwise Fst values for populations in a genlight object
 #'
 #' This script calculates pairwise Fst values based on the implementation in the
 #' StAMPP package (?stamppFst). It allows to run bootstrap to estimate

R/gl.install.vanilla.dartR.r

@@ -1,4 +1,4 @@
-#' This functions installs all required packages for using all functions
+#' Installs all required packages for using all functions
 #' available in dartR
 #'
 #' The function compares the installed packages with the the currently available

R/gl.keep.ind.r

@@ -1,5 +1,5 @@
 #' @name gl.keep.ind
-#' @title Remove all but the specified individuals from a genlight \{adegenet\}
+#' @title Removes all but the specified individuals from a genlight \{adegenet\}
 #' object
 #' @description
 #' The script, having deleted individuals, optionally identifies resultant

R/gl.keep.loc.r

@@ -1,5 +1,5 @@
 #' @name gl.keep.loc
-#' @title Remove all but the specified loci from a genlight \{adegenet\} object
+#' @title Removes all but the specified loci from a genlight \{adegenet\} object
 #' @description
 #' The script returns a genlight object with the all but the specified loci
 #' deleted.

R/gl.keep.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.keep.pop
-#' @title Remove all but specified populations from a genlight \{adegenet\}
+#' @title Removes all but specified populations from a genlight \{adegenet\}
 #' object
 #' @description
 #' Individuals are assigned to populations based on the specimen metadata data

R/gl.list.reports.r

@@ -1,4 +1,5 @@
-#' Prints dartR reports saved in tempdir
+#' @name gl.list.reports
+#' @title Prints dartR reports saved in tempdir
 #'
 #' @return Prints a table with all reports saved in tempdir. Currently the style
 #' cannot be changed.

R/gl.load.r

@@ -1,4 +1,4 @@
-#' Load an object from compressed binary format produced by gl.save()
+#' Loads an object from compressed binary format produced by gl.save()
 #'
 #' This is a wrapper for readRDS()
 #'

R/gl.make.recode.ind.r

@@ -1,5 +1,5 @@
 #' @name gl.make.recode.ind
-#' @title Create a proforma recode_ind file for reassigning individual
+#' @title Creates a proforma recode_ind file for reassigning individual
 #'  (=specimen) names
 #' @description
 #' Renaming individuals may be required when there have been errors in

R/gl.make.recode.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.make.recode.pop
-#' @title Create a proforma recode_pop_table file for reassigning population
+#' @title Creates a proforma recode_pop_table file for reassigning population
 #' names
 #' @description
 #' Renaming populations may be required when there have been errors in

R/gl.map.structure.r

@@ -1,5 +1,5 @@
 #' @name gl.map.structure
-#' @title Map a STRUCTURE plot using a genlight object
+#' @title Maps a STRUCTURE plot using a genlight object
 #' @description
 #' This function takes the output of plotstructure (the q matrix) and maps the
 #' q-matrix across using the population centers from the genlight object that

R/gl.merge.pop.r

@@ -1,5 +1,5 @@
 #' @name gl.merge.pop
-#' @title Merge two or more populations in a genlight object into one population
+#' @title Merges two or more populations in a genlight object into one population
 #' @description
 #' Individuals are assigned to populations based on the specimen metadata data
 #' file (csv) used with gl.read.dart().

R/gl.nhybrids.r

@@ -1,5 +1,5 @@
 #' @name gl.nhybrids
-#' @title Create an input file for the program NewHybrids and run it if
+#' @title Creates an input file for the program NewHybrids and runs it if
 #'  NewHybrids is installed
 #' @description
 #' This function compares two sets of parental populations to identify loci that

R/gl.outflank.r

@@ -1,7 +1,7 @@
-#' Function to identify loci under selection per population using the outflank
+#' Identifies loci under selection per population using the outflank
 #' method of Whitlock and Lotterhos (2015)
 #'
-#' @param gi a genlight or genind object, with a defined population structure
+#' @param gi A genlight or genind object, with a defined population structure
 #' [required].
 #' @param plot A switch if a barplot is wanted [default TRUE].
 #' @param LeftTrimFraction The proportion of loci that are trimmed from the
@@ -14,8 +14,8 @@
 #' from a locus [default 0.1].
 #' @param qthreshold The desired false discovery rate threshold for calculating
 #' q-values [default 0.05].
-#' @param ... additional parameters (see documentation of outflank on github)
-#' @return returns an index of outliers and the full outflank list
+#' @param ... additional parameters (see documentation of outflank on github). 
+#' @return Returns an index of outliers and the full outflank list
 #' @details
 #' This function is a wrapper around the outflank function provided by
 #' Whitlock and Lotterhos. To be able to run this function the packages qvalue

R/gl.percent.freq.r

@@ -1,4 +1,4 @@
-#' Generate percentage allele frequencies by locus and population
+#' Generates percentage allele frequencies by locus and population
 #'
 #' This is a support script, to take SNP data or SilicoDArT presence/absence
 #' data grouped into populations in a genlight object \{adegenet\} and generate

R/gl.plot.heatmap.r

@@ -1,5 +1,5 @@
-#' @title gl.plot.heatmap
-#' @title Represent a distance matrix as a heatmap
+#' @name gl.plot.heatmap
+#' @title Represents a distance matrix as a heatmap
 #' @description
 #' The script plots a heat map to represent the distances in the distance or
 #' dissimilarity matrix. This function is a wrapper for

R/gl.plot.structure.r

@@ -1,6 +1,6 @@
 #' @name gl.plot.structure
 #'
-#' @title Plot a STRUCTURE analysis using a genlight object
+#' @title Plots a STRUCTURE analysis using a genlight object
 #'
 #' @description
 #' This function takes a structure run object (output from