R Population Genetic Functions

Functions for fast forward population genetic analyses in R. Most functions are based on genind-objects, which is the adegenet formal class (S4) for individual genotypes.

Among others, it includes functions for:

• calculating summaries, e.g. number of alleles, allele distribution of single loci
• estimating linkage disequilibrium
• reformatting genind-objects to formats required by other programs, e.g. BOTTLENECK, GENEPOP, FreeNA, ARLEQUIN, STRUCTURE, EEMS, SPAGEDI, TESS, CERVUS

These functions were compiled/developed during the analyses of microsatellite data for the manuscript: "High gene flow and complex treeline dynamics of Larix Mill. stands on the Taymyr Peninsula (north-central Siberia) revealed by nuclear microsatellites" by Kruse, S., Epp, L. S., Wieczorek, M., Pestryakova, L. A., Stoof-Leichsenring, K. R., Herzschuh, U., accepted for publication in Tree Genetics & Genomes, doi:10.1007/s11295-018-1235-3