A toolkit for analyzing stratified population genetic data.
Functions are provided for summarizing and checking loci
(haploid, diploid, and polyploid), single stranded DNA sequences,
calculating most population subdivision metrics, and running external programs
such as structure and fastsimcoal. The package is further described in
Archer et al (2016)
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
To install the stable version from CRAN:
install.packages('strataG')
To install the latest version from GitHub:
# make sure you have Rtools installedif (!require('devtools')) install.packages('devtools')# install from GitHubdevtools::install_github('ericarcher/strataG', build_vignettes = TRUE)
# To see the list of available vignettesbrowseVignettes("strataG") # To open a specific vignettevignette("gtypes")
The paper can be obtained here, and is cited as (preferred):
Archer, F. I., Adams, P. E. and Schneiders, B. B. (2016), strataG: An R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour. doi:10.1111/1755-0998.12559
If desired, the current release version of the package can be cited as:
Archer, F. 2016. strataG: An R package for manipulating, summarizing and analysing population genetic data. R package version 1.0.6. Zenodo. http://doi.org/10.5281/zenodo.60416
gtypes
object by replacing the @loci
data.frame slot with a @data
data.table slot. The data.table has a id
character column, a strata
character column, and every column afterwards represents one locus. The @strata
slot has been removed.loci
accessor has been removed.as.array
which returns a 3-dimensional array with dimensions of [id, locus, allele].gtypes
objects no longer shows a by-locus summary. The display was getting too slow for data sets with a large number of loci.summary
function now includes by-sample results.maf
to return minimum allele frequency for each locus.ldNe
to calculate Ne.read.arlequin
back. Fixed missing function error with write.arlequin
.summarizeSamples
evanno
from base graphics to ggplot2labelHaplotypes
to assign haplotypes if possible alternative site combinations match a present haplotypestrataGUI
) for creating gtypes objects, QA/QC, and population structure analysestype
argument to structurePlot
to select between area and bar chartshaplotypeLikelihoods
to sequenceLikelihoods
neiDa
now creates haplotypes before calculating metricwritePhase
that was creating improper input files for PHASE