Package: allelematch 2.5.4

allelematch: 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; targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, 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 package, please cite the original publication in Molecular Ecology Resources (Galpern et al., 2012), the details for which can be generated using citation('allelematch'). 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>.

Authors:Paul Galpern <[email protected]>

allelematch_2.5.4.tar.gz
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allelematch.pdf |allelematch.html
allelematch/json (API)

# Install 'allelematch' in R:
install.packages('allelematch', repos = c('https://noreastermt.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • amExample1 - Data sets to support the tutorials in the supplementary documentation and examples in the manual
  • amExample2 - Data sets to support the tutorials in the supplementary documentation and examples in the manual
  • amExample3 - Data sets to support the tutorials in the supplementary documentation and examples in the manual
  • amExample4 - Data sets to support the tutorials in the supplementary documentation and examples in the manual
  • amExample5 - Data sets to support the tutorials in the supplementary documentation and examples in the manual

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.26 score 1 packages 8 scripts 427 downloads 6 mentions 19 exports 1 dependencies

Last updated 8 months agofrom:1695b8e07a. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winNOTEOct 25 2024
R-4.5-linuxNOTEOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:amAlleleFreqamClusteramCSSForHTMLamCSV.amClusteramCSV.amPairwiseamCSV.amUniqueamDatasetamHTML.amClusteramHTML.amPairwiseamHTML.amUniqueamMatrixamPairwiseamUniqueamUniqueProfileprint.amAlleleFreqprint.amDatasetsummary.amClustersummary.amPairwisesummary.amUnique

Dependencies:dynamicTreeCut

Readme and manuals

Help Manual

Help pageTopics
Identification of unique multilocus genotypesallelematch-package allelematch allelematch-tutorial
Determine allele frequenciesamAlleleFreq print.amAlleleFreq
Clustering of multilocus genotypesamCluster amCSV.amCluster amHTML.amCluster summary.amCluster
Produce cascading style sheet (CSS) for HTMLamCSSForHTML
Prepare a dataset for use with allelematchamDataset print.amDataset
Data sets to support the tutorials in the supplementary documentation and examples in the manualamExample1 amExample2 amExample3 amExample4 amExample5 amExampleData
Produce a dissimilarity matrix for pairs of multilocus genotypesamMatrix
Pairwise matching of multilocus genotypesamCSV.amPairwise amHTML.amPairwise amPairwise summary.amPairwise
Identification of unique genotypesamCSV.amUnique amHTML.amUnique amUnique summary.amUnique
Determine optimal parameter values for the identification of unique genotypesamUniqueProfile