amMatrix: Produce a dissimilarity matrix for pairs of multilocus...

Description Usage Arguments Details Value Author(s) References See Also Examples

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)


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