assignment_genodive: Prepare and summarise the assignment results from GENODIVE

In eriqande/assigner: Assignment Analysis with GBS/RADseq Data using R

Description

Import assignment results from GENODIVE. Current version needs results from both statistics, the home likelihood and likelihood ratio.

Usage

assignment_genodive(assignment.lmax, assignment.lhome, lmax.migrant.skip,
  lmax.number.migrant, lmax.skip, lhome.migrant.skip, lhome.number.migrant,
  lhome.skip, sites.levels, pop.labels, pop.levels, pop.id.start, pop.id.end,
  number.individuals, number.pop)

Arguments

assignment.lmax	The file with likelihood ratio assignment results from GENODIVE.
assignment.lhome	The file with home likelihood assignment results from GENODIVE.
lmax.migrant.skip	The number of lines to skip before the migrant info in the likelihood ratio assignment results. Usually = 11.
lmax.number.migrant	The number of migrant detected in the likelihood ratio assignment results.
lmax.skip	The number of lines to skip before the individuals info in the likelihood ratio assignment results.
lhome.migrant.skip	The number of lines to skip before the migrant info in the home likelihood assignment results. Usually = 11.
lhome.number.migrant	The number of migrant detected in the home likelihood assignment results.
lhome.skip	The number of lines to skip before the individuals info in the home likelihood assignment results.
sites.levels	An optional character string with your sites names in the same order as the pop levels.
pop.labels	The pop label to identify your sampling sites.
pop.levels	An optional character string with your populations ordered.
pop.id.start	The start of your population id in the name of your individual sample.
pop.id.end	The end of your population id in the name of your individual sample.
number.individuals	The number of individuals analysed.
number.pop	The number of populations analysed.

Author(s)

Thierry Gosselin [e-mail]

References

Meirmans PG, Van Tienderen PH (2004) genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794.

eriqande/assigner documentation built on May 16, 2019, 8:45 a.m.