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:Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Jeffrey Oliver [aut], James Boyko [aut]

corHMM_2.10.tar.gz
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corHMM.pdf |corHMM.html✨
corHMM/json (API)

# Install 'corHMM' in R:

install.packages('corHMM', repos = c('https://thej022214.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thej022214/corhmm/issues

Datasets:

primates - Example datasets
primates.paint - Example datasets
rayDISC.example - Example datasets

On CRAN:

9.48 score 12 stars 2 packages 422 scripts 731 downloads 20 mentions 24 exports 61 dependencies

Last updated 20 days agofrom:7a8939a482. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 17 2025
R-4.5-win	OK	Feb 17 2025
R-4.5-mac	OK	Feb 17 2025
R-4.5-linux	OK	Feb 17 2025
R-4.4-win	OK	Feb 17 2025
R-4.4-mac	OK	Feb 17 2025
R-4.3-win	OK	Feb 17 2025
R-4.3-mac	OK	Feb 17 2025

Exports:ancRECON ancRECON_slice ComputeCI ConvertPhangornReconstructions corDISC corHMM corHMMDredge corHMMDredgeBase dev.raydisc dropStateMatPars equateStateMatPars fitCorrelationTest get_batch_profile_lik getFullMat getModelTable getRateCatMat getStateMat4Dat kFoldCrossValidation makeSimmap plot_batch_profile_lik plotMKmodel plotRECON rayDISC simMarkov

Dependencies:ape cli clusterGeneration coda codetools colorspace combinat corpcor cpp11 DEoptim digest doParallel expm fansi farver fastmatch foreach generics GenSA ggplot2 glue gmp gridExtra gtable igraph isoband iterators labeling lattice lhs lifecycle magrittr maps MASS Matrix mgcv mnormt munsell nlme nloptr nnet numDeriv optimParallel phangorn phytools pillar pkgconfig quadprog R6 RColorBrewer Rcpp rlang Rmpfr scales scatterplot3d tibble utf8 vctrs viridis viridisLite withr

corHMM 2.1: Generalized hidden Markov models

James D. Boyko and Jeremy M. Beaulieu

Rendered fromcorHMMv2.1-vignette.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-08-26
Started: 2020-06-15

Citation

Development and contributors

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
Automatic search for optimal discrete character model with regularization with Penalization Options	corHMMDredge
Hidden Rates Model with regularization with Penalization Options	corHMMDredgeBase
Example datasets	primates primates.paint rayDISC.example
Test for correlation	fitCorrelationTest
Perform Batch Profile Likelihood Analysis for Multiple Parameters	get_batch_profile_lik
Print Method for corhmm.kfold Class Objects	getCVTable
Combines several rate class index matrices	dropStateMatPars equateStateMatPars getFullMat getRateCatMat
Summarize Model Statistics for a List of corHMM Objects	getModelTable
Produce an index matrix and legend from a dataset	getStateMat4Dat
Perform K-Fold Cross-Validation for corHMM Models	kFoldCrossValidation
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
The Probability of a Tip State Being Homologous	tipHomology