ConGenR now supports matching of multilocus genotypes
Following the determination of consensus genotypes, it is often desirable to identify samples with identical (full match) or similar (partial match) multilocus genotypes. The congen.matching() function can be used to identify samples with fully or partially matching multilocus genotypes. Users can define the number of matching loci required to report two samples as being a match; in practice, the number of matches required will often be set to the number of loci required to meet desired levels of probability of identity (Waits et al. 2001). An option to consider or ignore loci with uncertainty (coded as an allele size = 0) provides a flexible framework for identifying matches even when uncertainty exists. When uncertainty is ignored, two samples are considered a match if the number of loci that are full matches and the number of loci with uncertainty sum to a value greater than the number of matches required. Matching methods employed by ConGenR allow the user to provide sample location data, which can be numeric (i.e., XY data, such as UTMs) or categorical (e.g., region, county, study area). Sample locations are provided in a separate file or data frame. When numeric locations are provided, the results will include a distance between each focal sample (the sample to which other samples are being compared) and each sample determined to be a match. Alternatively, if locations are categorical, the location of each sample will be added to the result file, facilitating comparisons between the focal sample and matching samples.