The function computes Paetkau's et al. (1997) genotype likelihood ratio distance (Dlr).
dlr( data, strata, plots = FALSE, filename = NULL, parallel.core = parallel::detectCores() - 1 )
data | The output assignment file (home likelihood or likelihood ratio statistics) from GENODIVE. |
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strata | A tab delimited file with 2 columns with header:
|
plots | (optional) Generate Dlr plots for all the pairwise populations
in the dataset. The plots are |
filename | (optional) Name of the file prefix for the matrix and the table written in the working directory. |
parallel.core | (optional) The number of core for parallel computation.
Default: |
A list with 5 objects:
the assignment results ($assignment),
the dlr pairwise table ($dlr.table),
the lower diagonal dlr distance matrix ($dlr.dist),
a data.frame with the dlr distance mirrored ($dlr.matrix),
the list of dlr plots ($dlr.plots)
Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13, 55-65.
Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobeck C (1997) An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics, 147, 1943-1957.
Meirmans PG, Van Tienderen PH (2004) genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794.
Thierry Gosselin thierrygosselin@icloud.com
if (FALSE) { dlr <- assigner::dlr( data = "assignment.gdv", strata = "my.strata.tsv", plots = TRUE) # to get the plots list: plot.list <- dlr$dlr.plots # access and isolate in different object a plot with $ }