run.single.Structure: Run Structure anaylsis for a single MAXPOPS parameter.
In jeffreyhanson/structurer: Structure Analysis in R

Description Usage Arguments See Also Examples

This function analyses data using Structure. It generates replicate runs for a single MAXPOPS parameter.

run.single.Structure(x, NUMRUNS = 2, MAXPOPS = 2, BURNIN = 10000,
  NUMREPS = 20000, NOADMIX = FALSE, ADMBURNIN = 500, FREQSCORR = TRUE,
  UPDATEFREQ = max(floor(BURNIN + NUMREPS)/1000, 1), M = "Greedy",
  W = TRUE, S = FALSE, REPEATS = 1000, dir = tempdir(), clean = TRUE,
  verbose = FALSE, threads = 1, SEED = sample.int(1e+05, NUMRUNS))

`x`	`StructureData` object.
`NUMRUNS`	`numeric` Number of replicate Structure runs. Defaults to 2.
`MAXPOPS`	`numeric` Number of populations assumed. Defaults to 2.
`BURNIN`	`numeric` Length of burnin period. Defaults to 10000.
`NUMREPS`	`numeric` Number of MCMC iterations for inference. Defaults to 20000.
`NOADMIX`	`logical` Do not use admixture model. Defaults to `FALSE`.
`ADMBURNIN`	`numeric` Initial period of burnin with admixture model. Defaults to 500.
`FREQSCORR`	`logical` Allele frequencies are correlated among populations? Defaults to `TRUE`.
`UPDATEFREQ`	`numeric` Frequency to store updates to loglikelihood for traceplots. Defaults to yield 1000 frequencies.
`M`	`character` name of search method. Valid arguments are 'FullSearch', 'Greedy', or 'LargeKGreedy'. Defaults to 'Greedy'.
`W`	`logical` weight populations by number of individuals? Defaults to `TRUE`.
`S`	`logical` if `TRUE` the G matrix similarity statistic used used. Else the G \prime statistic is used. Defaults to codeFALSE.
`REPEATS`	`numeric` Number of random input orders tested. Defaults to 1000.
`dir`	`character` with directory to use for analysis.
`clean`	`logical` should input and output files be deleted after analysis is finished?
`verbose`	`logical` should messages be printed during processing?
`threads`	`numeric` number of threads to use for processing. Defaults to 1.
`SEED`	`numeric` Seed for random number generator. Defaults to NA so a random seed is used.

StructureData, StructureOpts.

# run Structure using low number of iterations
dat <- read.StructureData(system.file('extdata', 'example_fstat_aflp.dat', package='structurer'))
x <- run.single.Structure(dat, NUMRUNS=1, MAXPOPS=2, BURNIN=10,
NUMREPS=10, NOADMIX=FALSE, ADMBURNIN=10)