convertHapSNPsToArlequin() is an R function to convert a file containing population-specific haplotype SNPs in a simple format to an Arlequin project file. A number of options are provided for controlling the output.
plotGFF() is an R function to produce a simple graphical plot of the annotatation contained within a GFF file. See plotGFF-example.png below for an example.
plotSpatialPies() is an R function to plot pie charts representing fractions of a code at particular lat/long locations. Useful for examining e.g., genotype proportions in space. Requires the R package "plotrix", for its very useful floating.pie() function.
pmi() is an R function to calculate PMI (Probability of Maternal Identity) statistics, as described in Grivet et al. (2005) and Scofield et al. (2010).
An R source file that provides a function to read GenAlEx-format genotype files into an annotated data.frame, and several functions for accessing and printing this data. GenAlEx and its documentation are available from http://www.anu.edu.au/BoZo/GenAlEx/.
Relative frequencies of seed sources within Acorn Woodpecker granaries in the Figueroa valley of Sedgwick Reserve, Santa Barbara County, California, among acorns sampled in 2006. For more information, see Scofield, Smouse and Sork, J. Ecol. 2010.
Read GenAlEx-format genotype files into an annotated data.frame, and provides several functions for accessing and printing this data. GenAlEx and its documentation are available from http://www.anu.edu.au/BoZo/GenAlEx/.
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