Genotype likelihood ratio distance (Dlr)

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

Usage

dlr(
  data,
  strata,
  plots = FALSE,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1
)

Arguments

data: The output assignment file (home likelihood or likelihood ratio statistics) from GENODIVE.
strata: A tab delimited file with 2 columns with header: INDIVIDUALS and STRATA. The STRATA column is used here as the populations id of your sample.
plots: (optional) Generate Dlr plots for all the pairwise populations in the dataset. The plots are ggplot2 objects that can be modified with the proper ggplot2 syntax. Default: plots = FALSE.
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: parallel.core = parallel::detectCores() - 1.

Value

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)

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.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
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 $
} # }