Package: MMD 1.0.0
MMD: Minimal Multilocus Distance (MMD) for Source Attribution and Loci Selection
The aim of the package is two-fold: (i) To implement the MMD method for attribution of individuals to sources using the Hamming distance between multilocus genotypes. (ii) To select informative genetic markers based on information theory concepts (entropy, mutual information and redundancy). The package implements the functions introduced by Perez-Reche, F. J., Rotariu, O., Lopes, B. S., Forbes, K. J. and Strachan, N. J. C. Mining whole genome sequence data to efficiently attribute individuals to source populations. Scientific Reports 10, 12124 (2020) <doi:10.1038/s41598-020-68740-6>. See more details and examples in the README file.
Authors:
MMD_1.0.0.tar.gz
MMD_1.0.0.zip(r-4.5)MMD_1.0.0.zip(r-4.4)MMD_1.0.0.zip(r-4.3)
MMD_1.0.0.tgz(r-4.4-any)MMD_1.0.0.tgz(r-4.3-any)
MMD_1.0.0.tar.gz(r-4.5-noble)MMD_1.0.0.tar.gz(r-4.4-noble)
MMD_1.0.0.tgz(r-4.4-emscripten)MMD_1.0.0.tgz(r-4.3-emscripten)
MMD.pdf |MMD.html✨
MMD/json (API)
| # Install 'MMD' in R: |
| install.packages('MMD', repos = c('https://fjpreche.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:f083921bc2. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 22 2024 |
| R-4.5-win | NOTE | Aug 22 2024 |
| R-4.5-linux | NOTE | Aug 22 2024 |
| R-4.4-win | NOTE | Aug 22 2024 |
| R-4.4-mac | NOTE | Aug 22 2024 |
| R-4.3-win | OK | Aug 22 2024 |
| R-4.3-mac | OK | Aug 22 2024 |
Exports:MMD_attrMMD_EntropyMMD_Rn
Dependencies:BHbigmemorybigmemory.sriclasse1071MASSplyrproxyRcppuuid
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Attribution of individuals to sources using the MMD method | MMD_attr |
| Loci entropies to measure allele diversity | MMD_Entropy |
| Loci redundancy in sequences | MMD_Rn |
