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 installed if (!require('devtools')) install.packages('devtools') # install from GitHub devtools::install_github('ericarcher/strataG', build_vignettes = TRUE)
# To see the list of available vignettes browseVignettes("strataG") # To open a specific vignette vignette("gtypes")
- Creating and Manipulating gtypes Objects ( gtypes)
- By-Locus Summaries ( summaries)
- Working with sequences ( sequences)
- Tests of Population Structure (population.structure)
- Quality Assurance / Quality Control (qaqc)
- Installing External Programs (external.programs)
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: firstname.lastname@example.org
- 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
version 2.0.2 (current on GitHub)
- 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.