Checks a genlight object to see if it complies with dartR expectations and amends it to comply if necessary

Source: R/gl.compliance.check.r

This function will check to see that the genlight object conforms to expectation in regard to dartR requirements (see details), and if it does not, will rectify it.

gl.compliance.check(x, verbose = NULL)

Arguments

x

Name of the input genlight object [required].

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 genlight object that conforms to the expectations of dartR

Details

A genlight object used by dartR has a number of requirements that allow functions within the package to operate correctly. The genlight object comprises:

  1. The SNP genotypes or Tag Presence/Absence data (SilicoDArT);

  2. An associated dataframe (gl@other$loc.metrics) containing the locus metrics (e.g. Call Rate, Repeatability, etc);

  3. An associated dataframe (gl@other$ind.metrics) containing the individual/sample metrics (e.g. sex, latitude (=lat), longitude(=lon), etc);

  4. A specimen identity field (indNames(gl)) with the unique labels applied to each individual/sample;

  5. A population assignment (popNames) for each individual/specimen;

  6. Flags that indicate whether or not calculable locus metrics have been updated.

Author

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

Examples

x <- gl.compliance.check(testset.gl)
#> Starting gl.compliance.check 
#>   Processing genlight object with SNP data
#>   Checking coding of SNPs
#>     SNP data scored NA, 0, 1 or 2 confirmed
#>   Checking locus metrics and flags
#>   Recalculating locus metrics
#>   Checking for monomorphic loci
#>     Dataset contains monomorphic loci
#>   Checking for loci with all missing data
#>     No loci with all missing data detected
#>   Checking whether individual names are unique.
#>   Checking for individual metrics
#>     Individual metrics confirmed
#>   Checking for population assignments
#>     Population assignments confirmed
#>   Spelling of coordinates checked and changed if necessary to 
#>             lat/lon
#> Completed: gl.compliance.check 
#> 
x <- gl.compliance.check(testset.gs)
#> Starting gl.compliance.check 
#>   Processing genlight object with Presence/Absence (SilicoDArT) data
#>   Checking coding of Tag P/A data
#>     Tag P/A data (SilicoDArT) scored 1, 0 (present or 
#>                         absent) confirmed
#>   Checking locus metrics and flags
#>   Recalculating locus metrics
#>   Checking for monomorphic loci
#>     Dataset contains monomorphic loci
#>   Checking for loci with all missing data
#>     No loci with all missing data detected
#>   Checking whether individual names are unique.
#>   Checking for individual metrics
#>     Individual metrics confirmed
#>   Checking for population assignments
#>     Population assignments confirmed
#>   Spelling of coordinates checked and changed if necessary to 
#>             lat/lon
#> Completed: gl.compliance.check 
#>