Package: pgacmdr 0.1.0

pgacmdr: Interactive Shiny Application for Population Genetics

PGA-cmdr is an interactive 'shiny' application for population genetics analyses of multilocus individual genotype data from codominant markers (microsatellites, allozymes, SNPs). It covers data import and formatting, allele frequencies and missing data, observed and expected heterozygosity, F-statistics (FIS, FST, FIT) following Weir and Cockerham (1984) <doi:10.1111/j.1558-5646.1984.tb05657.x>, and gene diversities (HS, HT) following Nei and Chesser (1983) <doi:10.1111/j.1469-1809.1983.tb00993.x>. Analyses include local and global panmixia tests, population subdivision with a G-based test of genotypic differentiation, pairwise linkage disequilibrium tests, null allele frequency estimation with the ENA correction of Chapuis and Estoup (2007) <doi:10.1093/molbev/msl191>, and isolation by distance using the regression of Rousset (1997) <doi:10.1093/genetics/145.4.1219> and a Mantel test. Confidence intervals are obtained by bootstrap over individuals, sub-samples or loci, and p-values by Monte Carlo permutation, computed in parallel in C++ via 'Rcpp' and 'OpenMP'. All computations run locally and no data leave the user's computer.

Authors:Naffiou Kadiri [aut, cre], Vincent Manzanilla [aut], Thierry de Meeûs [aut], INTERTRYP, IRD, CIRAD [cph]