Package: corHMM 2.10

Jeremy Beaulieu

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://phylotastic.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:

18 exports 11 stars 4.05 score 62 dependencies 2 dependents 20 mentions 392 scripts 718 downloads

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:ancRECON ancRECON_slice ComputeCI ConvertPhangornReconstructions corDISC corHMM dev.raydisc dropStateMatPars equateStateMatPars fitCorrelationTest getFullMat getRateCatMat getStateMat4Dat makeSimmap 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 ggseqlogo 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

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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
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