dartR (version 1.1.11)

gl.make.recode.ind: Create a proforma recode_ind file for reassigning individual (=specimen) names

Description

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, outfile = "default_recode_ind.csv",
  outpath = tempdir())

Arguments

x

-- name of the genlight object containing the SNP data, or the genind object containing the SilocoDArT data [required]

outfile

-- name of the new proforma file [default default_recode_ind.csv]

outpath

-- path where to save the output file (set to tempdir by default)

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().

Examples

# NOT RUN {
result <- gl.make.recode.ind(testset.gl, outfile="Emmac_recode_ind.csv")
# }