Produce a dissimilarity matrix for pairs of multilocus genotypes

Description

Given an amDataset object find the dissimilarities between pairs of multilocus genotypes, taking missing data into account.

Usage

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amMatrix(amDatasetFocal, missingMethod = 2)

Arguments

amDatasetFocal

An amDataset object. See amDataset.

missingMethod

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.

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.

Value

A distance/dissimilarity matrix of S3 class "amMatrix".

Author(s)

Paul Galpern (pgalpern@gmail.com)

References

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.

See Also

amPairwise, amUnique

Examples

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## Not run: 

data("amExample1")

## Produce amDataset object
myDataset <- amDataset(amExample1, missingCode="-99", indexColumn=1,
    metaDataColumn=2)

## Produce dissimilarity matrix
dissimMatrix <- amMatrix(myDataset)

## End(Not run)