Whyp provides R functions for maximum-likelihood assignment of parentage of progeny based on genotypes from progeny and/or progeny-associated maternal tissue (e.g. pericarps), and genotypes of potential parents. Whyp handles two kinds of genotyping error: null alleles (common in maternal tissue), and mistyping (completely wrong genotype).
Development of whyp to date has focused on identifying the maternal parent when potentially error-containing pericarp genotypes are available.
The whyp API is very rough at this stage. Genotype input for parents,
pericarps and progeny is each in the form of an annotated data.frame produced by
readGenalex() (available at https://github.com/douglasgscofield/popgen).
assemble.whyp.data() : load data for a whyp run into a large list
whyp() : calculate parental assignments
The file example.R contains some example code which uses these functions. The data files themselves are not included. assemble.v1() and assemble.v2() load data for a whyp run. whyp.analysis() runs a whyp analysis on a loaded dataset, and includes alternatives for specifying an analysis and returning results.
The file whyp.R and the entire folder whyp_functions/ are required. See what I mean about a rough API? :-)
These statistical tools were developed in collaboration with Peter Smouse (Rutgers University) and Victoria Sork (UCLA) and were funded by U.S. National Science Foundation awards NSF-DEB-0514956 and NSF-DEB-0516529.
Whyp (including earlier versions) has been used the following publications:
Smouse, P. E., V. L. Sork, D. G. Scofield, and D. Grivet. 2012. Using Seedling and Pericarp Tissues to Determine Maternal Parentage of Dispersed Valley Oak Recruits. Journal of Heredity 103:250-259.
Scofield, D. G., V. L. Sork, and P. E. Smouse. 2010. Influence of acorn woodpecker social behaviour on transport of coast live oak (Quercus agrifolia) acorns in a southern California oak savanna. Journal of Ecology 98:561-572.
Scofield, D. G., V. R. Alfaro, V. L. Sork, D. Grivet, E. Martinez, J. Papp, A. R. Pluess et al. 2011. Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata Née) in two California oak savanna-woodlands. Oecologia 166:187-196.