Package: stockR 1.0.76
Scott D. Foster
stockR: Identifying Stocks in Genetic Data
Provides a mixture model for clustering individuals (or sampling groups) into stocks based on their genetic profile. Here, sampling groups are individuals that are sure to come from the same stock (e.g. breeding adults or larvae). The mixture (log-)likelihood is maximised using the EM-algorithm after finding good starting values via a K-means clustering of the genetic data. Details can be found in: Foster, S. D.; Feutry, P.; Grewe, P. M.; Berry, O.; Hui, F. K. C. & Davies (2020) <doi:10.1111/1755-0998.12920>.
Authors:
stockR_1.0.76.tar.gz
stockR_1.0.76.tar.gz(r-4.5-noble)stockR_1.0.76.tar.gz(r-4.4-noble)
stockR_1.0.76.tgz(r-4.4-emscripten)stockR_1.0.76.tgz(r-4.3-emscripten)
stockR.pdf |stockR.html✨
stockR/json (API)
NEWS
| # Install 'stockR' in R: |
| install.packages('stockR', repos = c('https://cran.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 2 years agofrom:3c49ef6248. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 07 2024 |
| R-4.5-linux-x86_64 | OK | Dec 07 2024 |
Exports:calcFstplot.stockBOOT.objectsim.stock.datastockBOOTstockSTRUCTURE
Dependencies:gtoolsRColorBrewerRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Fst statistics for frequency data | calcFst |
| Plots results of a stockR analysis (a barplot-like representation) | plot.stockBOOT.object |
| Simulates SNP data according to stockSTRUCTURE model | sim.stock.data |
| Calculates bootstrap estimates of stockSTRUCTURE model | stockBOOT |
| Finds stock structure for sampling groups of animals | stockSTRUCTURE |