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Creates a proforma recode_ind file for reassigning individual (=specimen) names

gl.make.recode.ind.Rd

Renaming individuals may be required when there have been errors in labelling arising in the process from sample to DArT files. There may be occasions where renaming individuals is required for preparation of figures. Caution needs to be exercised because of the potential for breaking the 'chain of evidence' between the samples themselves and the analyses. Recoding individuals can be done with a recode table (csv).

Usage

gl.make.recode.ind(
  x,
  out.recode.file = "default_recode_ind.csv",
  outpath = tempdir(),
  verbose = NULL
)

Arguments

x

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

out.recode.file

File name of the output file (including extension) [default default_recode_ind.csv].

outpath

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

verbose

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

Value

A vector containing the new individual names.

Details

This script facilitates the construction of a recode table by producing a proforma file with current individual (=specimen) names in two identical columns. Edit the second column to reassign individual names. Use keyword Delete to delete an individual.

Apply the recoding using gl.recode.ind(). Deleting individuals can potentially generate monomorphic loci or loci with all values missing. Clean this up with gl.filter.monomorphic().

Author

Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr

Examples

result <- gl.make.recode.ind(testset.gl, out.recode.file ='Emmac_recode_ind.csv',outpath=tempdir())
#> Starting gl.make.recode.ind 
#>   Processing genlight object with SNP data
#>   Writing draft lookup table to /tmp/RtmpMqupE6/Emmac_recode_ind.csv . Edit before use
#> Completed: gl.make.recode.ind 
#>