allelematch v2.5.1

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Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present

Tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present. The package is targeted at those working with large datasets and databases containing multiple samples of each individual, a situation that is common in conservation genetics, and particularly in non-invasive wildlife sampling applications. Functions explicitly incorporate missing data, and can tolerate allele mismatches created by genotyping error. If you use this tool, please cite the package using the journal article in Molecular Ecology Resources (Galpern et al., 2012). Please use citation('allelematch') to call the full citation. For users with access to the associated journal article, tutorial material is also available as supplementary material to the article describing this software, the citation for which can be called using citation('allelematch').

Functions in allelematch

Name Description
amDataset Prepare a dataset for use with allelematch
allelematch-package Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present
amAlleleFreq Determine allele frequencies
amUniqueProfile Determine optimal parameter values for the identification of unique genotypes
amUnique Identification of unique genotypes
amMatrix Produce a dissimilarity matrix for pairs of multilocus genotypes
amPairwise Pairwise matching of multilocus genotypes
amCSSForHTML Produce cascading style sheet (CSS) for HTML
amCluster Clustering of multilocus genotypes
amExampleData Data sets to support the tutorials in the supplementary documentation and examples in the manual.
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Vignettes of allelematch

Name
allelematchSuppDoc.pdf.asis
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Details

VignetteBuilder R.rsp
License GPL-3
LazyLoad yes
Packaged 2019-04-15 16:01:22 UTC; tbcross
NeedsCompilation no
Repository CRAN
Date/Publication 2019-04-15 21:22:47 UTC

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