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

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

version 2.1

  • fixed error in ldNe when missing data are present
  • added STANDARD marker type to fastsimcoal
  • added na.rm = TRUE to 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 x to a data.frame in df2gtypes in case it is a data.table or tibble.

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.
  • Added expandHaplotypes to expand the haplotypes in a gtypes object to one sequence per individual.

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.