utils.structure.run {dartR}

Utility function to run Structure

Description

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",
  ...
)

Arguments

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.

Value

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

Author(s)

Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr); original implementation of Eric Archer https://github.com/EricArcher/strataG