Produce a dissimilarity matrix for pairs of multilocus genotypes
Given an amDataset object find the dissimilarities between pairs of multilocus genotypes, taking missing data into account.
amMatrix(amDatasetFocal, missingMethod = 2)
An amDataset object. See
The method used to determine the similarity of multilocus genotypes when data is missing. The default (=2) is preferable in all cases. Please see details.
This function is the behind-the-scenes workhorse of AlleleMatch, and typically
will not be called by the user.
missingMethod=2 is the recommended value, and the default, as it has performed
better in simulations. In this method, missing data matches perfectly with missing data,
while missing data matches partially with non-missing data.
missingMethod=1 is retained for experimental purposes. Here, missing data
matches partially with missing and non-missing data.
A distance/dissimilarity matrix of S3 class "amMatrix".
Paul Galpern (email@example.com)
Please see the supplementary documentation for more information. This is available as a vignette. Click on the index link at the bottom of this page to find it.
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