allelematch (version 2.5.5)

amMatrix: 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
		)

Value

A distance/dissimilarity matrix of S3 class amMatrix.

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.

Author

Paul Galpern ()

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.

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

	if (FALSE) {
	data("amExample1")
	
	## Produce amDataset object
	myDataset <- 
		amDataset(
			amExample1, 
			missingCode = "-99", 
			indexColumn = 1, 
			metaDataColumn = 2
			)
	
	## Produce dissimilarity matrix
	dissimMatrix <- amMatrix(myDataset)
	}