gl.run.EMIBD9 {dartR.captive}

Run program EMIBD9

Description

Run program EMIBD9

Usage

gl.run.EMIBD9(
  x,
  outfile = "EMIBD9_Res.ibd9",
  outpath = tempdir(),
  emibd9.path = getwd(),
  Inbreed = TRUE,
  ISeed = 42,
  plot.out = TRUE,
  plot.dir = NULL,
  plot.file = NULL,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data [required].

outfile

A string, giving the path and name of the output file [default "EMIBD9_Res.ibd9"].

outpath

Path where to save the output file. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working or current directory [default tempdir(), mandated by CRAN].

emibd9.path

Path to the folder emidb files. Please note there are 2 different executables depending on your OS: EM_IBD_P.exe (=Windows) EM_IBD_P (=Mac, Linux). You only need to pointto the folder (the function will recognise which OS you are running) [default getwd()].

Inbreed

A Boolean, taking values 0 or 1 to indicate inbreeding is not and is allowed in estimating IBD coefficients [default 1].

ISeed

An integer used to seed the random number generator [default 42].

plot.out

A boolean that indicates whether to plot the results [default TRUE].

plot.dir

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]

plot.file

Name for the RDS binary file to save (base name only, exclude extension) [default NULL]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity]

Details

Download the program from here:

https://www.zsl.org/about-zsl/resources/software/emibd9

For Windows, Mac and Linux install the program then point to the folder where you find: EM_IBD_P.exe (=Windows) and EM_IBD_P (=Mac, Linux). If running really slow you may want to create the files using the function and then run in parallel using the documentation provided by the authors [you need to have mpiexec installed].

Value

A matrix with pairwise relatedness

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

References

• Wang, J. (2022). A joint likelihood estimator of relatedness and allele frequencies from a small sample of individuals. Methods in Ecology and Evolution, 13(11), 2443-2462.

Examples

## Not run: 
#To run this function needs EMIBD9 installed in your computer
t1 <- gl.filter.allna(platypus.gl)
res_rel <- gl.run.EMIBD9(t1)

## End(Not run)