utils.structure.run: Utility function to run Structure

In dartR.popgen: Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

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,
  num.k.rep,
  label,
  delete.files = TRUE,
  exec,
  burnin,
  numreps,
  noadmix,
  freqscorr,
  randomize,
  seed,
  pop.prior,
  locpriorinit,
  maxlocprior,
  gensback,
  migrprior,
  pfrompopflagonly,
  popflag,
  inferalpha,
  alpha,
  unifprioralpha,
  alphamax,
  alphapriora,
  alphapriorb
)

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".
burnin	Number of burnin reps [default 10000].
numreps	Number of MCMC replicates [default 1000].
noadmix	Logical. No admixture? [default TRUE].
freqscorr	Logical. Correlated frequencies? [default FALSE].
randomize	Randomize [default TRUE].
seed	Set random seed [default 0].
pop.prior	A character specifying which population prior model to use: "locprior" or "usepopinfo" [default NULL].
locpriorinit	Parameterizes locprior parameter r - how informative the populations are. Only used when pop.prior = "locprior" [default 1].
maxlocprior	Specifies range of locprior parameter r. Only used when pop.prior = "locprior" [default 20].
gensback	Integer defining the number of generations back to test for immigrant ancestry. Only used when pop.prior = "usepopinfo" [default 2].
migrprior	Numeric between 0 and 1 listing migration prior. Only used when pop.prior = "usepopinfo" [default 0.05].
pfrompopflagonly	Logical. update allele frequencies from individuals specified by popflag. Only used when pop.prior = "usepopinfo" [default TRUE].
popflag	A vector of integers (0, 1) or logicals identifiying whether or not to use strata information. Only used when pop.prior = "usepopinfo" [default NULL].
inferalpha	Logical. Infer the value of the model parameter # from the data; otherwise is fixed at the value alpha which is chosen by the user. This option is ignored under the NOADMIX model. Small alpha implies that most individuals are essentially from one population or another, while alpha > 1 implies that most individuals are admixed [default FALSE].
alpha	Dirichlet parameter for degree of admixture. This is the initial value if inferalpha = TRUE [default 1].
unifprioralpha	Logical. Assume a uniform prior for alpha which runs between 0 and alphamax. This model seems to work fine; the alternative model (when unfprioralpha = 0) is to take alpha as having a Gamma prior, with mean alphapriora × alphapriorb, and variance alphapriora × alphapriorb^2 [default TRUE].
alphamax	Maximum for uniform prior on alpha when unifprioralpha = TRUE [default 20].
alphapriora	Parameters of Gamma prior on alpha when unifprioralpha = FALSE [default 0.05].
alphapriorb	Parameters of Gamma prior on alpha when unifprioralpha = FALSE [default 0.001].

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

dartR.popgen documentation built on June 28, 2024, 1:06 a.m.