dlr: Genotype likelihood ratio distance (Dlr)

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

Description

The function computes Paetkau's et al. (1997) genotype likelihood ratio distance (Dlr).

Arguments

data	The output assignment file (home likelihood or likelihood ratio statistics) from GENODIVE.
l.skip	(integer) The number of lines to skip before the individuals info in GenoDive assignment results (see Vignette).
number.individuals	(integer) The number of individuals analysed.
number.pop	(integer) The number of populations analysed.
pop.id.start	(Optional) The start of your population id in the name of your individual sample. Your individuals are identified in this form : SPECIES-POPULATION-MATURITY-YEAR-ID = CHI-QUE-ADU-2014-020, then, pop.id.start = 5. If you didn't name your individuals with the pop id in it, use the strata argument.
pop.id.end	(Optional) The end of your population id in the name of your individual sample. Your individuals are identified in this form : SPECIES-POPULATION-MATURITY-YEAR-ID = CHI-QUE-ADU-2014-020, then, pop.id.end = 7. If you didn't name your individuals with the pop id in it, use the strata argument.
strata	(optional) A tab delimited file with 2 columns with header: INDIVIDUALS and STRATA. Default: strata = NULL. The STRATA column is used here as the populations id of your sample.
pop.levels	A character string with your sampling sites or populations in the order you prefer (for tables and figure).
pop.labels	(optional) A character string for your populations labels. If you need to rename sampling sites in pop.levels or combined sites/pop into a different names, here is the place.
filename	(optional) Name of the file prefix for the matrix and the table written in the working directory.

Value

A list with 3 objects of class: table ($dlr.table), dist (a lower diagonal matrix, $dlr.dist), data.frame (a mirrored matrix, $dlr.matrix).

Author(s)

Thierry Gosselin [e-mail]

References

Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13, 55-65.

Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobeck C (1997) An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics, 147, 1943-1957.

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.