maverickRun: Run MavericK
In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

maverickRun

R Documentation

Run MavericK

Description

Run MavericK clustering algorithm

Usage

maverickRun(
  g,
  params = NULL,
  label = "MavericK_files",
  data_fname = "data.txt",
  param_fname = "parameters.txt",
  exec = "Maverick1.0.5"
)

Arguments

`g`	a gtypes object.
`params`	a list specifying parameters for MavericK. All parameters are available and can be specified by partial matching. The function will automatically specify parameters related to data formatting (data, headerRow_on, missingData, ploidy, ploidyCol_on, popCol_on), so those will be ignored. For a full list of available parameters and their definitions, see the MavericK documentation distributed with the program.
`label`	folder where input and output files will be written to.
`data_fname`	file name of data input file.
`param_fname`	file name of parameters file.
`exec`	name of executable for MavericK.

Note

MavericK is not included with strataG and must be downloaded separately. It can be obtained from http://www.bobverity.com/. Additionally, it must be installed such that it can be run from the command line in the current working directory. See the vignette for external.programs for OS-specific installation instructions.

Author(s)

Eric Archer eric.archer@noaa.gov

References

Robert Verity and Richard Nichols. (2016) Estimating the number of subpopulations (K) in structured populations. Genetics
Robert Verity and Richard Nichols. (2016) Documentation for MavericK software: Version 1.0

EricArcher/strataG documentation built on May 17, 2024, 12:41 p.m.