Package: pedmut 0.8.0
Magnus Dehli Vigeland
pedmut: Mutation Models for Pedigree Likelihood Computations
A collection of functions for modelling mutations in pedigrees with marker data, as used e.g. in likelihood computations with microsatellite data. Implemented models include equal, proportional and stepwise models, as well as random models for experimental work, and custom models allowing the user to apply any valid mutation matrix. Allele lumping is done following the lumpability criteria of Kemeny and Snell (1976), ISBN:0387901922.
Authors:
pedmut_0.8.0.tar.gz
pedmut_0.8.0.zip(r-4.5)pedmut_0.8.0.zip(r-4.4)pedmut_0.8.0.zip(r-4.3)
pedmut_0.8.0.tgz(r-4.5-any)pedmut_0.8.0.tgz(r-4.4-any)pedmut_0.8.0.tgz(r-4.3-any)
pedmut_0.8.0.tar.gz(r-4.5-noble)pedmut_0.8.0.tar.gz(r-4.4-noble)
pedmut_0.8.0.tgz(r-4.4-emscripten)pedmut_0.8.0.tgz(r-4.3-emscripten)
pedmut.pdf |pedmut.html✨
pedmut/json (API)
NEWS
| # Install 'pedmut' in R: |
| install.packages('pedmut', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magnusdv/pedmut/issues
Last updated 11 hours agofrom:1ffe5e827d. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Apr 01 2025 |
| R-4.5-win | OK | Apr 01 2025 |
| R-4.5-mac | OK | Apr 01 2025 |
| R-4.5-linux | OK | Apr 01 2025 |
| R-4.4-win | OK | Apr 01 2025 |
| R-4.4-mac | OK | Apr 01 2025 |
| R-4.4-linux | OK | Apr 01 2025 |
| R-4.3-win | OK | Apr 01 2025 |
| R-4.3-mac | OK | Apr 01 2025 |
Exports:adjustRatealwaysLumpablefindStationarygetParamsisBoundedisLumpableisMutationMatrixisMutationModelisReversibleisStationarylumpedMatrixlumpedModelmakeReversiblemutationMatrixmutationModelmutRatesexEqualstabilizestepwiseReversiblevalidateMutationMatrixvalidateMutationModel
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adjust the overall mutation rate of a model | adjustRate |
| Find the stationary frequency distribution | findStationary |
| Get model parameters | getParams |
| Test for mutation matrix/model | isMutationMatrix isMutationModel |
| Combine alleles in a mutation matrix | lumpedMatrix lumpedModel |
| Transformations to reversibility | makeReversible |
| Upper limits for overall mutation rate for the stepwise reversible model. | maxRate |
| Mutation model properties | alwaysLumpable isBounded isLumpable isReversible isStationary model_properties |
| Mutation matrix | mutationMatrix validateMutationMatrix |
| Mutation models | mutationModel sexEqual validateMutationModel |
| Overall mutation rate | mutRate |
| Stabilization of mutation matrix | stabilize |
| Dawid's reversible stepwise model | stepwiseReversible |