R: Assigns individuals to populations with an associated...

gl.mahal.assign {dartR.base}

R Documentation

Assigns individuals to populations with an associated probability

Description

Uses Mahalanobis Distances between individuals and group centroids to calculate probability of group membership

Usage

gl.mahal.assign(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

Arguments

`x`	Name of the genlight object [required].
`plot.display`	If TRUE, resultant plots are displayed in the plot window [default TRUE].
`plot.theme`	Theme for the plot. See Details for options [default theme_dartR()].
`plot.colors`	List of two color names for the borders and fill of the plots [default c("#2171B5","#6BAED6")].
`plot.file`	Name for the RDS binary file to save (base name only, exclude extension) [default NULL]
`plot.dir`	Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]
`verbose`	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity]

Details

The function generates 200 simulated individuals for each group (=population in the genlight object) drawing from the observed allele frequencies for each group. The group centroids and covariance matricies are calculated for these simulated groups. The covariance matrix is inverted using package MASS::ginv to overcome the singularities that would otherwise arise with typical SNP data. Mahanobilis Distances are calculated using stats::mahanalobis for each individual in the dataset and associated Chi Square probabilities of group membership are calculated for each individual in the original genlight object. The resultant table can be used for decisions on group membership. A special group (=population in the genlight object) called 'unknowns' can be used to specifically identify individuals with unknown group membership.

A color vector can be obtained with gl.select.colors() and then passed to the function with the plot.colors parameter. Themes can be obtained from in

If a plot.file is given, the ggplot arising from this function is saved as an "RDS" binary file using saveRDS(); can be reloaded with readRDS(). A file name must be specified for the plot to be saved. If a plot directory (plot.dir) is specified, the ggplot binary is saved to that directory; otherwise to the tempdir().

Value

The unchanged genlight object

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr