strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure. One can select select specific individuals, loci, or strata using standard R '[' indexing methods. . The package contains functions for summarizing haploid and diploid loci (e.g., allelic richness, heterozygosity, haplotypic diversity, etc.), and haploid sequences by locus and by strata as well as functions for computing by-site base frequencies and identifying variable and fixed sites among strata. There are both overall and pairwise standard tests of population structure like PHIst, Fst, Gst, and Jost's D. If individuals are stratified according to multiple schemes, these stratifications can be changed with the
stratify() function and summaries or tests can be re-run on the new object. The package also includes wrappers for several external programs like fastsimcoal2, STRUCTURE, and mafft. There are also multiple conversion functions for data objects for other population packages such as adegenet, pegas, and phangorn.
To install the stable version from CRAN:
To install the latest version from GitHub:
# make sure you have Rtools installed if (!require('devtools')) install.packages('devtools') # install from GitHub devtools::install_github('ericarcher/strataG', build_vignettes = TRUE)
Vignettes are available on several topics:
- Creating and manipulating gtypes ("gtypes")
- Genotype and sequence summaries ("summaries")
- Working with sequences ("sequences")
- Tests of population structure ("population.structure")
- Installing external programs ("external.programs")
To see the list of all available vignettes:
To open a specific vignette:
There is also a tutorial detailing running fastsimcoal2 through strataG available through the function
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
- submit suggestions and bug-reports: https://github.com/ericarcher/strataG/issues
- send a pull request: https://github.com/ericarcher/strataG/
- e-mail: email@example.com
version 2.4.910 (devel)
- removed melt from structurePlot
- fixed ldNe error when one individual is present
- fixed mafft error and now have mafft .fasta files written to temporary file rather than working directory
- fixed error with
version 2.4.905 (on CRAN)
- Deleted functions:
- Changed structure of
gtypesobject, making it no longer compatible with previous versions
- Fixed and enhanced
arlequinRead()so that it will read and parse all .arp files. Added
gtypesobject from parsed .arp files.
- Improved performance of several standard summary functions, most notably
- Full rework of fastsimcoal2 wrapper.
- fixed error in ldNe when missing data are present
- added STANDARD marker type to fastsimcoal
na.rm = TRUEto calculation of mean locus summaries by strata in
summary.gtypes. This avoids
NaNs when there is a locus with genotypes missing for all samples.
- explicitly convert
df2gtypesin case it is a
- NOTE: In order to speed up indexing the data in large data sets, this version changes the underlying structure of the
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].
- The print (show) function for
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.
- Fixed computational errors in population structure metrics due to incorrect sorting of stratification.
mafto return minimum allele frequency for each locus.
ldNeto calculate Ne.
expandHaplotypesto expand the haplotypes in a
gtypesobject to one sequence per individual.
read.arlequinback. Fixed missing function error with
evannofrom base graphics to ggplot2
- Updated logic in
labelHaplotypesto assign haplotypes if possible alternative site combinations match a present haplotype
- Added Zenodo DOI
- Added shiny app (
strataGUI) for creating gtypes objects, QA/QC, and population structure analyses
structurePlotto select between area and bar charts
neiDanow creates haplotypes before calculating metric
- Fixed error in
writePhasethat was creating improper input files for PHASE
- Fixed error in dupGenotypes, propSharedLoci, and propSharedIDs where missing genotypes were not being properly counted.
- Added as.data.frame.gtypes.
- Removed gtypes2df.
- Added arguments to as.matrix.gtypes to include id and strata columns in output.
- Removed the jmodeltest function as this functionality is available in the modeltest function in the phangorn package.
- Added conversion functions gtypes2phyDat and phyDat2gtypes to facilitate interoperability with the phangorn package.
- Removed read.arlequin.
- Added alleleNames accessor for gtypes object, which returns list of allele names for each locus.
- New version with different gtypes format from previous versions. See vignettes for instructions and examples.