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:
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
gtypesobject by replacing the
@locidata.frame slot with a
@datadata.table slot. The data.table has a
idcharacter column, a
stratacharacter column, and every column afterwards represents one locus. The
@strataslot has been removed.
lociaccessor has been removed.
as.arraywhich returns a 3-dimensional array with dimensions of [id, locus, allele].
gtypesobjects no longer shows a by-locus summary. The display was getting too slow for data sets with a large number of loci.
summaryfunction now includes by-sample results.
mafto return minimum allele frequency for each locus.
ldNeto calculate Ne.
read.arlequinback. Fixed missing function error with
evannofrom base graphics to ggplot2
labelHaplotypesto assign haplotypes if possible alternative site combinations match a present haplotype
strataGUI) for creating gtypes objects, QA/QC, and population structure analyses
structurePlotto select between area and bar charts
neiDanow creates haplotypes before calculating metric
writePhasethat was creating improper input files for PHASE