utils.structure.run {dartR.popgen}

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