amMatrix {allelematch}

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

	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, (missingMethod = 2), is preferable in all cases.
See amMatrix.

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 ([e-mail])

References

For a complete vignette, please access via the Data S1 Supplementary documentation and tutorials (PDF) located at <doi:10.1111/j.1755-0998.2012.03137.x>.

See Also

amPairwise, amUnique

Examples

	## 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)