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:
allelematch_2.5.4.tar.gz
allelematch_2.5.4.zip(r-4.5)allelematch_2.5.4.zip(r-4.4)allelematch_2.5.4.zip(r-4.3)
allelematch_2.5.4.tgz(r-4.4-any)allelematch_2.5.4.tgz(r-4.3-any)
allelematch_2.5.4.tar.gz(r-4.5-noble)allelematch_2.5.4.tar.gz(r-4.4-noble)
allelematch_2.5.4.tgz(r-4.4-emscripten)allelematch_2.5.4.tgz(r-4.3-emscripten)
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')) |
- 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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 months agofrom:1695b8e07a. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 26 2024 |
| R-4.5-win | NOTE | Aug 26 2024 |
| R-4.5-linux | NOTE | Aug 26 2024 |
| R-4.4-win | OK | Aug 26 2024 |
| R-4.4-mac | OK | Aug 26 2024 |
| R-4.3-win | OK | Aug 26 2024 |
| R-4.3-mac | OK | Aug 26 2024 |
Exports:amAlleleFreqamClusteramCSSForHTMLamCSV.amClusteramCSV.amPairwiseamCSV.amUniqueamDatasetamHTML.amClusteramHTML.amPairwiseamHTML.amUniqueamMatrixamPairwiseamUniqueamUniqueProfileprint.amAlleleFreqprint.amDatasetsummary.amClustersummary.amPairwisesummary.amUnique
Dependencies:dynamicTreeCut
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identification of unique multilocus genotypes | allelematch-package allelematch allelematch-tutorial |
| Determine allele frequencies | amAlleleFreq print.amAlleleFreq |
| Clustering of multilocus genotypes | amCluster amCSV.amCluster amHTML.amCluster summary.amCluster |
| Produce cascading style sheet (CSS) for HTML | amCSSForHTML |
| Prepare a dataset for use with allelematch | amDataset print.amDataset |
| Data sets to support the tutorials in the supplementary documentation and examples in the manual | amExample1 amExample2 amExample3 amExample4 amExample5 amExampleData |
| Produce a dissimilarity matrix for pairs of multilocus genotypes | amMatrix |
| Pairwise matching of multilocus genotypes | amCSV.amPairwise amHTML.amPairwise amPairwise summary.amPairwise |
| Identification of unique genotypes | amCSV.amUnique amHTML.amUnique amUnique summary.amUnique |
| Determine optimal parameter values for the identification of unique genotypes | amUniqueProfile |
