strataG

Description

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

Installation

To install the stable version from CRAN:

install.packages('strataG')

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

# 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)

Citation

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

Contact

• submit suggestions and bug-reports: https://github.com/ericarcher/strataG/issues
• send a pull request: https://github.com/ericarcher/strataG/
• e-mail: eric.archer@noaa.gov

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 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.
• The loci accessor has been removed.
• Added as.array which returns a 3-dimensional array with dimensions of [id, locus, allele].
• The print (show) function for gtypes objects no longer shows a by-locus summary. The display was getting too slow for data sets with a large number of loci.
• The summary function now includes by-sample results.
• Fixed computational errors in population structure metrics due to incorrect sorting of stratification.
• Added maf to return minimum allele frequency for each locus.
• Added ldNe to calculate Ne.

version 1.0.6

• Added read.arlequin back. Fixed missing function error with write.arlequin.
• Added summarizeSamples
• Changed evanno from base graphics to ggplot2
• Updated logic in labelHaplotypes to 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
• Added type argument to structurePlot to select between area and bar charts
• Changed haplotypeLikelihoods to sequenceLikelihoods
• neiDa now creates haplotypes before calculating metric
• Fixed error in writePhase that was creating improper input files for PHASE

version 1.0.5

• 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.

version 1.0

• New version with different gtypes format from previous versions. See vignettes for instructions and examples.