Package: StAMPP 1.6.3.9000
StAMPP: Statistical Analysis of Mixed Ploidy Populations
Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi:10.1111/1755-0998.12129> for the appropriate citation and user manual. Thank you in advance.
Authors:
StAMPP_1.6.3.9000.tar.gz
StAMPP_1.6.3.9000.zip(r-4.5)StAMPP_1.6.3.9000.zip(r-4.4)StAMPP_1.6.3.9000.zip(r-4.3)
StAMPP_1.6.3.9000.tgz(r-4.4-any)StAMPP_1.6.3.9000.tgz(r-4.3-any)
StAMPP_1.6.3.9000.tar.gz(r-4.5-noble)StAMPP_1.6.3.9000.tar.gz(r-4.4-noble)
StAMPP_1.6.3.9000.tgz(r-4.4-emscripten)StAMPP_1.6.3.9000.tgz(r-4.3-emscripten)
StAMPP.pdf |StAMPP.html✨
StAMPP/json (API)
NEWS
| # Install 'StAMPP' in R: |
| install.packages('StAMPP', repos = c('https://lpembleton.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lpembleton/stampp/issues
- potato - Example genotype input format
- potato.mini - Smaller example genotype input format
Last updated 2 years agofrom:1fecdb79a0. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-win | NOTE | Oct 27 2024 |
| R-4.5-linux | NOTE | Oct 27 2024 |
| R-4.4-win | NOTE | Oct 27 2024 |
| R-4.4-mac | NOTE | Oct 27 2024 |
| R-4.3-win | OK | Oct 27 2024 |
| R-4.3-mac | OK | Oct 27 2024 |
Exports:stampp2genlightstamppAmovastamppConvertstamppFststamppGmatrixstamppNeisDstamppPhylip
Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercodetoolscolorspacecommonmarkcpp11crayondigestdoParalleldplyrfansifarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehtmltoolshttpuvigraphisobanditeratorsjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepegaspermutepillarpixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Example genotype input format | potato |
| Smaller example genotype input format | potato.mini |
| Convert StAMPP genotype data to genlight object | stampp2genlight |
| Analysis of Molecular Variance | stamppAmova |
| Import and Convert | stamppConvert |
| Fst Computation | stamppFst |
| Genomic Relationship Calculation | stamppGmatrix |
| Genetic Distance Calculation | stamppNeisD |
| Export to Phylip Format | stamppPhylip |
