Package: corHMM 2.10
corHMM: Hidden Markov Models of Character Evolution
Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Authors:
corHMM_2.10.tar.gz
corHMM_2.10.zip(r-4.5)corHMM_2.10.zip(r-4.4)corHMM_2.10.zip(r-4.3)
corHMM_2.10.tgz(r-4.4-any)corHMM_2.10.tgz(r-4.3-any)
corHMM_2.10.tar.gz(r-4.5-noble)corHMM_2.10.tar.gz(r-4.4-noble)
corHMM_2.10.tgz(r-4.4-emscripten)corHMM_2.10.tgz(r-4.3-emscripten)
corHMM.pdf |corHMM.html✨
corHMM/json (API)
# Install 'corHMM' in R: |
install.packages('corHMM', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thej022214/corhmm/issues
- primates - Example datasets
- primates.paint - Example datasets
- rayDISC.example - Example datasets
Last updated 13 days agofrom:5fac8b1158. Checks:ERROR: 1 WARNING: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | FAIL | Aug 26 2024 |
R-4.5-win | WARNING | Aug 26 2024 |
R-4.5-linux | WARNING | Aug 26 2024 |
R-4.4-win | WARNING | Aug 26 2024 |
R-4.4-mac | WARNING | Aug 26 2024 |
R-4.3-win | WARNING | Aug 26 2024 |
R-4.3-mac | WARNING | Aug 26 2024 |
Exports:ancRECONancRECON_sliceComputeCIConvertPhangornReconstructionscorDISCcorHMMdev.raydiscdropStateMatParsequateStateMatParsfitCorrelationTestgetFullMatgetRateCatMatgetStateMat4DatmakeSimmapplotMKmodelplotRECONrayDISCsimMarkov
Dependencies:apecliclusterGenerationcodacodetoolscolorspacecombinatcorpcorcpp11DEoptimdigestdoParallelexpmfansifarverfastmatchforeachgenericsGenSAggplot2ggseqlogogluegmpgridExtragtableigraphisobanditeratorslabelinglatticelhslifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellnlmenloptrnnetnumDerivoptimParallelphangornphytoolspillarpkgconfigquadprogR6RColorBrewerRcpprlangRmpfrscalesscatterplot3dtibbleutf8vctrsviridisviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Ancestral state reconstruction | ancRECON |
Ancestral state reconstruction for a particular time | ancRECON_slice |
Compute confidence around rate estimates | ComputeCI |
Convert phangorn reconstruction to a vector | ConvertPhangornReconstructions |
Correlated evolution binary traits | corDISC |
Hidden Rates Model | corHMM |
Example datasets | primates primates.paint rayDISC.example |
Test for correlation | fitCorrelationTest |
Combines several rate class index matrices | dropStateMatPars equateStateMatPars getFullMat getRateCatMat |
Produce an index matrix and legend from a dataset | getStateMat4Dat |
Simulate a character history | makeSimmap |
Plot Batch Profile Likelihoods | plot_batch_profile_lik |
Plot a Markov model | plotMKmodel |
Plot ancestral state reconstructions | plotRECON |
Evolution of categorical traits | dev.raydisc rayDISC |
Simulate a character on the tree | simMarkov |