Utility function to run Structure — utils.structure.run • dartR

These functions were copied from package strataG, which is no longer on CRAN (maintained by Eric Archer)

Usage

utils.structure.run(
  g,
  k.range = NULL,
  num.k.rep = 1,
  label = NULL,
  delete.files = TRUE,
  exec = "structure",
  ...
)

g: a gtypes object [see strataG].
k.range: vector of values to for maxpop in multiple runs. If set to NULL, a single STRUCTURE run is conducted with maxpops groups. If specified, do not also specify maxpops.
num.k.rep: number of replicates for each value in k.range.
label: label to use for input and output files
delete.files: logical. Delete all files when STRUCTURE is finished?
exec: name of executable for STRUCTURE. Defaults to "structure".
...: arguments to be passed to structureWrite.

structureRun

a list where each element is a list with results from structureRead and a vector of the filenames used

structureWrite

a vector of the filenames used by STRUCTURE

structureRead

a list containing:

summary: new locus name, which is a combination of loci in group
q.mat: data.frame of assignment probabilities for each id
prior.anc: list of prior ancestry estimates for each individual where population priors were used
files: vector of input and output files used by STRUCTURE
label: label for the run