allelematch: Identifying unique multilocus genotypes where genotyping error and missing data may be present

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This package provides 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 find this. Due to changing CRAN policy, and the size and compile time of the vignettes, they can no longer be distributed with this package. Please contact the package primary author, or visit the allelematch site for a complete vignette (http://nricaribou.cc.umanitoba.ca/allelematch/). For users with access to academic literature, tutorial material is also available as supplementary material to the article describing this software.

Author
Paul Galpern <pgalpern@gmail.com>
Date of publication
2014-09-19 00:14:49
Maintainer
Paul Galpern <pgalpern@gmail.com>
License
GPL (>= 2)
Version
2.5
URLs

View on CRAN

Man pages

allelematch-package
Identification of unique multilocus genotypes
amAlleleFreq
Determine allele frequencies
amCluster
Clustering of multilocus genotypes
amCSSForHTML
Produce cascading style sheet (CSS) for HTML
amDataset
Prepare a dataset for use with allelematch
amExampleData
Data sets to support the tutorials in the supplementary...
amMatrix
Produce a dissimilarity matrix for pairs of multilocus...
amPairwise
Pairwise matching of multilocus genotypes
amUnique
Identification of unique genotypes
amUniqueProfile
Determine optimal parameter values for the identification of...

Files in this package

allelematch
allelematch/inst
allelematch/inst/CITATION
allelematch/NAMESPACE
allelematch/data
allelematch/data/amExample4.RData
allelematch/data/amExample1.RData
allelematch/data/amExample5.RData
allelematch/data/amExample3.RData
allelematch/data/amExample2.RData
allelematch/R
allelematch/R/allelematch.r
allelematch/MD5
allelematch/DESCRIPTION
allelematch/man
allelematch/man/amExampleData.Rd
allelematch/man/amCluster.Rd
allelematch/man/amUniqueProfile.Rd
allelematch/man/amPairwise.Rd
allelematch/man/amMatrix.Rd
allelematch/man/amAlleleFreq.Rd
allelematch/man/amDataset.Rd
allelematch/man/allelematch-package.Rd
allelematch/man/amUnique.Rd
allelematch/man/amCSSForHTML.Rd