Added needed tests for MSNs and misc tests

Also, the case change is back, so of course all of the man pages are changed again.
grunwaldlab · Jul 8, 2015 · e850924 · e850924
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 1.1.5.99-686
+Version: 1.1.5.99-690
 Date: 2015-07-07
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "[email protected]"),

diff --git a/man/Aeut.Rd b/man/Aeut.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/internal.R
+% Please edit documentation in R/internal.r
 \docType{data}
 \name{Aeut}
 \alias{Aeut}

diff --git a/man/Pinf.Rd b/man/Pinf.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/internal.R
+% Please edit documentation in R/internal.r
 \docType{data}
 \name{Pinf}
 \alias{Pinf}

diff --git a/man/Pram.Rd b/man/Pram.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/internal.R
+% Please edit documentation in R/internal.r
 \docType{data}
 \name{Pram}
 \alias{Pram}

diff --git a/man/bitwise.IA.Rd b/man/bitwise.IA.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bitwise.R
+% Please edit documentation in R/bitwise.r
 \name{bitwise.IA}
 \alias{bitwise.IA}
 \title{Calculate the index of association between samples in a genlight object.}

diff --git a/man/bitwise.dist.Rd b/man/bitwise.dist.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bitwise.R
+% Please edit documentation in R/bitwise.r
 \name{bitwise.dist}
 \alias{bitwise.dist}
 \title{Calculate a distance matrix comparing samples based on the number of alleles

diff --git a/man/bootgen-class.Rd b/man/bootgen-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/classes.R
+% Please edit documentation in R/classes.r
 \docType{class}
 \name{bootgen-class}
 \alias{bootgen-class}

diff --git a/man/bootgen-methods.Rd b/man/bootgen-methods.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{[,bootgen,ANY,ANY,ANY-method}
 \alias{$,bootgen-method}

diff --git a/man/bruvo.boot.Rd b/man/bruvo.boot.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bruvo.R
+% Please edit documentation in R/bruvo.r
 \name{bruvo.boot}
 \alias{bruvo.boot}
 \title{Create a tree using Bruvo's Distance with non-parametric bootstrapping.}

diff --git a/man/bruvo.dist.Rd b/man/bruvo.dist.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bruvo.R
+% Please edit documentation in R/bruvo.r
 \name{bruvo.dist}
 \alias{bruvo.dist}
 \title{Bruvo's distance for microsatellites}

diff --git a/man/bruvo.msn.Rd b/man/bruvo.msn.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bruvo.R
+% Please edit documentation in R/bruvo.r
 \name{bruvo.msn}
 \alias{bruvo.msn}
 \alias{msn.bruvo}

diff --git a/man/bruvomat-class.Rd b/man/bruvomat-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/classes.R
+% Please edit documentation in R/classes.r
 \docType{class}
 \name{bruvomat-class}
 \alias{bruvomat-class}

diff --git a/man/bruvomat-methods.Rd b/man/bruvomat-methods.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{initialize,bruvomat-method}
 \alias{[,bruvomat,ANY,ANY,ANY-method}

diff --git a/man/clonecorrect.Rd b/man/clonecorrect.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/data_subset.R
+% Please edit documentation in R/data_subset.r
 \name{clonecorrect}
 \alias{clonecorrect}
 \title{Remove potential bias caused by cloned genotypes in genind or genclone

diff --git a/man/coercion-methods.Rd b/man/coercion-methods.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{as.genclone}
 \alias{as.genclone}

diff --git a/man/diss.dist.Rd b/man/diss.dist.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/distances.R
+% Please edit documentation in R/distances.r
 \name{diss.dist}
 \alias{diss.dist}
 \title{Calculate a distance matrix based on relative dissimilarity}

diff --git a/man/fix_replen.Rd b/man/fix_replen.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bruvo.R
+% Please edit documentation in R/bruvo.r
 \name{fix_replen}
 \alias{fix_replen}
 \title{Find and fix inconsistent repeat lengths}

diff --git a/man/genclone-class.Rd b/man/genclone-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/classes.R
+% Please edit documentation in R/classes.r
 \docType{class}
 \name{genclone-class}
 \alias{genclone}

diff --git a/man/genclone-method.Rd b/man/genclone-method.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{initialize,genclone-method}
 \alias{[,genclone,ANY,ANY,ANY-method}

diff --git a/man/genetic_distance.Rd b/man/genetic_distance.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/distances.R
+% Please edit documentation in R/distances.r
 \name{nei.dist}
 \alias{edwards.dist}
 \alias{nei.dist}

diff --git a/man/genind2genalex.Rd b/man/genind2genalex.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/file_handling.R
+% Please edit documentation in R/file_handling.r
 \name{genind2genalex}
 \alias{genind2genalex}
 \title{Exporting data from genind objects to genalex formatted *.csv files.}

diff --git a/man/genotype_curve.Rd b/man/genotype_curve.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/visualizations.R
+% Please edit documentation in R/visualizations.r
 \name{genotype_curve}
 \alias{genotype_curve}
 \title{Produce a genotype accumulation curve}

diff --git a/man/getfile.Rd b/man/getfile.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/file_handling.R
+% Please edit documentation in R/file_handling.r
 \name{getfile}
 \alias{getfile}
 \title{Get a file name and path and store them in a list.}

diff --git a/man/greycurve.Rd b/man/greycurve.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/visualizations.R
+% Please edit documentation in R/visualizations.r
 \name{greycurve}
 \alias{greycurve}
 \title{Display a greyscale gradient adjusted to specific parameters}

diff --git a/man/ia.Rd b/man/ia.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/Index_calculations.R
+% Please edit documentation in R/Index_calculations.r
 \name{ia}
 \alias{ia}
 \alias{pair.ia}

diff --git a/man/info_table.Rd b/man/info_table.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/visualizations.R
+% Please edit documentation in R/visualizations.r
 \name{info_table}
 \alias{info_table}
 \title{Create a table summarizing missing data or ploidy information of a genind or

diff --git a/man/informloci.Rd b/man/informloci.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/data_subset.R
+% Please edit documentation in R/data_subset.r
 \name{informloci}
 \alias{informloci}
 \title{Remove all non-phylogentically informative loci}

diff --git a/man/is.clone.Rd b/man/is.clone.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \name{is.snpclone}
 \alias{is.clone}
 \alias{is.genclone}

diff --git a/man/locus_table.Rd b/man/locus_table.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/Index_calculations.R
+% Please edit documentation in R/Index_calculations.r
 \name{locus_table}
 \alias{locus_table}
 \title{Create a table of summary statistics per locus.}

diff --git a/man/missingno.Rd b/man/missingno.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/data_subset.R
+% Please edit documentation in R/data_subset.r
 \name{missingno}
 \alias{missingno}
 \title{How to deal with missing data in a genind object.}

diff --git a/man/mlg.Rd b/man/mlg.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/mlg.R
+% Please edit documentation in R/mlg.r
 \name{mlg}
 \alias{mlg}
 \alias{mlg.crosspop}

diff --git a/man/mlg.filter.Rd b/man/mlg.filter.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{mlg.filter}
 \alias{mlg.filter}

diff --git a/man/mll-method.Rd b/man/mll-method.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{mll}
 \alias{mll}

diff --git a/man/mll.custom.Rd b/man/mll.custom.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{mll.custom}
 \alias{mll.custom}

diff --git a/man/mll.reset-method.Rd b/man/mll.reset-method.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{mll.reset}
 \alias{mll.reset}

diff --git a/man/monpop.Rd b/man/monpop.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/internal.R
+% Please edit documentation in R/internal.r
 \docType{data}
 \name{monpop}
 \alias{monpop}

diff --git a/man/old2new_genclone.Rd b/man/old2new_genclone.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \name{old2new_genclone}
 \alias{old2new_genclone}
 \title{Convert an old genclone object to a new genclone object}

diff --git a/man/partial_clone.Rd b/man/partial_clone.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/internal.R
+% Please edit documentation in R/internal.r
 \docType{data}
 \name{partial_clone}
 \alias{old_partial_clone}

diff --git a/man/plot_poppr_msn.Rd b/man/plot_poppr_msn.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/visualizations.R
+% Please edit documentation in R/visualizations.r
 \name{plot_poppr_msn}
 \alias{plot_poppr_msn}
 \title{Plot minimum spanning networks produced in poppr.}

diff --git a/man/poppr.Rd b/man/poppr.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/Index_calculations.R
+% Please edit documentation in R/Index_calculations.r
 \name{poppr}
 \alias{poppr}
 \title{Produce a basic summary table for population genetic analyses.}

diff --git a/man/poppr.all.Rd b/man/poppr.all.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/Index_calculations.R
+% Please edit documentation in R/Index_calculations.r
 \name{poppr.all}
 \alias{poppr.all}
 \title{Process a list of files with poppr}

diff --git a/man/poppr.amova.Rd b/man/poppr.amova.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/amova.R
+% Please edit documentation in R/amova.r
 \name{poppr.amova}
 \alias{amova}
 \alias{poppr.amova}

diff --git a/man/poppr.msn.Rd b/man/poppr.msn.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/visualizations.R
+% Please edit documentation in R/visualizations.r
 \name{poppr.msn}
 \alias{msn.poppr}
 \alias{poppr.msn}

diff --git a/man/poppr_has_parallel.Rd b/man/poppr_has_parallel.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bitwise.R
+% Please edit documentation in R/bitwise.r
 \name{poppr_has_parallel}
 \alias{poppr_has_parallel}
 \title{Determines whether openMP is support on this system.}

diff --git a/man/popsub.Rd b/man/popsub.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/data_subset.R
+% Please edit documentation in R/data_subset.r
 \name{popsub}
 \alias{popsub}
 \title{Subset a \code{\linkS4class{genclone}} or \code{\linkS4class{genind}} object by population}

diff --git a/man/private_alleles.Rd b/man/private_alleles.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/Index_calculations.R
+% Please edit documentation in R/Index_calculations.r
 \name{private_alleles}
 \alias{private_alleles}
 \title{Tabulate alleles the occur in only one population.}

diff --git a/man/read.genalex.Rd b/man/read.genalex.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/file_handling.R
+% Please edit documentation in R/file_handling.r
 \name{read.genalex}
 \alias{read.genalex}
 \title{Importing data from genalex formatted *.csv files.}

diff --git a/man/recode_polyploids.Rd b/man/recode_polyploids.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/data_subset.R
+% Please edit documentation in R/data_subset.r
 \name{recode_polyploids}
 \alias{recode_polyploids}
 \title{Recode polyploid microsatellite data for use in frequency based statistics.}

diff --git a/man/samp.ia.Rd b/man/samp.ia.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bitwise.R
+% Please edit documentation in R/bitwise.r
 \name{samp.ia}
 \alias{samp.ia}
 \title{Calculate random samples of the index of association for genlight objects.}

diff --git a/man/shufflepop.Rd b/man/shufflepop.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/sample_schemes.R
+% Please edit documentation in R/sample_schemes.r
 \name{shufflepop}
 \alias{shufflepop}
 \title{Shuffle individuals in a \code{\linkS4class{genclone}} or

diff --git a/man/snpclone-class.Rd b/man/snpclone-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/classes.R
+% Please edit documentation in R/classes.r
 \docType{class}
 \name{snpclone-class}
 \alias{snpclone}

diff --git a/man/snpclone-coercion-methods.Rd b/man/snpclone-coercion-methods.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{as.snpclone}
 \alias{as.snpclone}

diff --git a/man/snpclone-method.Rd b/man/snpclone-method.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/methods.R
+% Please edit documentation in R/methods.r
 \docType{methods}
 \name{[,snpclone,ANY,ANY,ANY-method}
 \alias{[,snpclone,ANY,ANY,ANY-method}

diff --git a/man/test_replen.Rd b/man/test_replen.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bruvo.R
+% Please edit documentation in R/bruvo.r
 \name{test_replen}
 \alias{test_replen}
 \title{Test repeat length consistency.}

diff --git a/man/win.ia.Rd b/man/win.ia.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/bitwise.R
+% Please edit documentation in R/bitwise.r
 \name{win.ia}
 \alias{win.ia}
 \title{Calculate windows of the index of association for genlight objects.}