Converts DarT to genlight — utils.dart2genlight • dartR

Converts a DArT file (read via read.dart) into an genlight object adegenet. Internal function called by gl.read.dart

Usage

utils.dart2genlight(
  dart,
  ind.metafile = NULL,
  covfilename = NULL,
  probar = TRUE,
  verbose = NULL
)

Arguments

dart: A dart object created via read.dart [required].
ind.metafile: Optional file in csv format with metadata for each individual (see details for explanation) [default NULL].
covfilename: Depreciated, use parameter ind.metafile.
probar: Show progress bar [default TRUE].
verbose: Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL].

Value

A genlight object. Including all available slots are filled. loc.names, ind.names, pop, lat, lon (if provided via the ind.metadata file)

Details

The ind.metadata file needs to have very specific headings. First a heading called id. Here the ids have to match the ids in the dart object colnames(dart[[4]]). The following column headings are optional. pop: specifies the population membership of each individual. lat and lon specify spatial coordinates (in decimal degrees WGS1984 format). Additional columns with individual metadata can be imported (e.g. age, gender).