{ "_id": "6a1fcbf4b401979e7343291a", "Package": "corHMM", "Version": "2.10.4", "Date": "2026-05-14", "Title": "Hidden Markov Models of Character Evolution", "Authors@R": "c(person(\"Jeremy\", \"Beaulieu\", role=c(\"aut\", \"cre\"),\nemail = \"jmbeauli@uark.edu\"),\nperson(\"Brian\", \"O'Meara\", role=c(\"aut\")),\nperson(\"Jeffrey\", \"Oliver\", role=c(\"aut\")),\nperson(\"James\", \"Boyko\", role=c(\"aut\")),\nperson(\"Haoyu\", \"Ji\", role=c(\"ctb\")),\nperson(\"Ben\", \"Bolker\", role=c(\"ctb\")))", "Maintainer": "Jeremy Beaulieu ", "Description": "Fits hidden Markov models of discrete character evolution\nwhich allow different transition rate classes on different\nportions of a phylogeny. 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"page": "ConvertPhangornReconstructions", "title": "Convert phangorn reconstruction to a vector", "topics": [ "ConvertPhangornReconstructions" ] }, { "page": "corDISC", "title": "Correlated evolution binary traits", "topics": [ "corDISC" ] }, { "page": "corHMM", "title": "Hidden Rates Model", "topics": [ "corHMM" ] }, { "page": "corHMMDredge", "title": "Automatic Discovery of Optimal Discrete Character Models via Simulated Annealing", "topics": [ "corHMMDredge" ] }, { "page": "corHMMDredgeBase", "title": "Fit a Single Penalized Hidden Markov Model", "topics": [ "corHMMDredgeBase" ] }, { "page": "dent_likelihood", "title": "Dents the likelihood surface This takes any values that are better (lower) than the desired negative log likelihood and reflects them across the best_neglnL + delta line, \"denting\" the likelihood surface.", "topics": [ "dent_likelihood" ] }, { "page": "dent_propose", "title": "Propose new values This proposes new values using a normal distribution centered on the 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If any proposed values are outside the bounds, it will propose again.", "topics": [ "dent_propose" ] }, { "page": "dent_walk", "title": "Sample points from along a ridge This \"dents\" the likelihood surface by reflecting points better than a threshold back across the threshold (think of taking a hollow plastic model of a mountain and punching the top so it's a volcano). It then uses essentially a Metropolis-Hastings walk to wander around the new rim. It adjusts the proposal width so that it samples points around the desired likelihood. This is better than using the curvature at the maximum likelihood estimate since it can actually sample points in case the assumptions of the curvature method do not hold. It is better than varying one parameter at a time while holding others constant because that could miss ridges: if I am fitting 5=x+y, and get a point estimate of (3,2), the reality is that there are an infinite range of values of x and y that will sum to 5, but if I hold x constant it looks like y is estimated very precisely. Of course, one could just fully embrace the Metropolis-Hastings lifestyle and use a full Bayesian approach.", "topics": [ "dent_walk" ] }, { "page": "primates", "title": "Example datasets", "topics": [ "primates", "primates.paint", "rayDISC.example" ] }, { "page": "fitCorrelationTest", "title": "Test for correlation", "topics": [ "fitCorrelationTest" ] }, { "page": "get_batch_profile_lik", "title": "Perform Batch Profile Likelihood Analysis for Multiple Parameters", "topics": [ "get_batch_profile_lik" ] }, { "page": "getCVTable", "title": "Print Method for corhmm.kfold Class Objects", "topics": [ "getCVTable" ] }, { "page": "getFullMat", "title": "Combines several rate class index matrices", "topics": [ "dropStateMatPars", "equateStateMatPars", "getFullMat", "getRateCatMat" ] }, { "page": "getModelTable", "title": "Summarize Model Statistics for a List of corHMM Objects", "topics": [ "getModelTable" ] }, { "page": "getRateMat4Dat", "title": "Produce an index matrix and legend from a dataset", "topics": [ "getStateMat4Dat" ] }, { "page": "kFoldCrossValidation", "title": "Perform K-Fold Cross-Validation for corHMM Models", "topics": [ "kFoldCrossValidation" ] }, { "page": "makeSimmap", "title": "Simulate a character history", "topics": [ "makeSimmap" ] }, { "page": "plot_batch_profile_lik", "title": "Plot Batch Profile Likelihoods", "topics": [ "plot_batch_profile_lik" ] }, { "page": "plot_transition_summary", "title": "Plot Summary Statistics of Stochastic Character Map Transitions", "topics": [ "plot_transition_summary" ] }, { "page": "plot.dentist", "title": "Plot the dented samples This will show the univariate plots of the parameter values versus the likelihood as well as bivariate plots of pairs of parameters to look for ridges.", "topics": [ "plot.dentist" ] }, { "page": "plotDredgeTrace", "title": "Plot the Trace of a corHMMDredge Simulated Annealing Search", "topics": [ "plotDredgeTrace" ] }, { "page": "plotMKmodel", "title": "Plot a Markov model", "topics": [ "plotMKmodel" ] }, { "page": "plotRECON", "title": "Plot ancestral state reconstructions", "topics": [ "plotRECON" ] }, { "page": "print.dentist", "title": "Print dentist print summary of output from dent_walk", "topics": [ "print.dentist" ] }, { "page": "rayDISC", "title": "Evolution of categorical traits", "topics": [ "dev.raydisc", "rayDISC" ] }, { "page": "simMarkov", "title": "Simulate a character on the tree", "topics": [ "simMarkov" ] }, { "page": "summarize_simmaps", "title": "Summarize Transition Information from Stochastic Character Maps", "topics": [ "summarize_single_simmap", "summarize_transition_stats" ] }, { "page": "summary.dentist", "title": "Summarize dentist Display summary of output from dent_walk", "topics": [ "summary.dentist" ] }, { "page": "tipHomology", "title": "The Probability of a Tip State Being Homologous", "topics": [ "tipHomology" ] } ], "_rundeps": [ "ape", "backports", "checkmate", "cli", "clusterGeneration", "coda", "codetools", "combinat", "corpcor", "cpp11", "DEoptim", "digest", "doParallel", "expm", "farver", "foreach", "future", "future.apply", "generics", "GenSA", "ggplot2", "globals", "glue", "gmp", "gridExtra", "gtable", "igraph", "isoband", "iterators", "labeling", "lattice", "lhs", "lifecycle", "listenv", "magrittr", "maps", "MASS", "Matrix", "mnormt", "nlme", "nloptr", "nnet", "numDeriv", "optimParallel", "osqp", "parallelly", "phangorn", "phytools", "pkgconfig", "progressr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "rlang", "Rmpfr", "RTMB", "S7", "scales", "scatterplot3d", "TMB", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "corHMMv2.1-vignette.Rmd", "filename": "corHMMv2.1-vignette.pdf", "title": "corHMM 2.1: Generalized hidden Markov models", "author": "James D. 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Beaulieu", "engine": "knitr::rmarkdown", "headings": [ "Section 1: Default use of corHMM", "1.1: No hidden rate categories", "1.2: A trait with any number of states and any number of hidden rate categories", "1.3: Estimating \"tip fog\"", "Section 2: How to make and interpret custom models", "2.1: Creating and using custom rate matrices", "2.1.1: One rate category", "2.1.2: Any number of rate categories", "2.2: Biological examples", "2.2.1: Ordered habitat change", "2.2.2: The precursor model", "2.2.3: Ontological relationship of multiple characters", "Section 3: Estimating models when node states are fixed", "3.1: Fixing a single node", "3.2: Estimating rates under a parsimony reconstruction", "3.3: Fixing nodes when the model contains hidden states", "References" ], "created": "2020-06-15 17:27:50", "modified": "2026-03-06 15:01:19", "commits": 14 } ], "_score": 9.596845506981152, "_indexed": false, "_nocasepkg": "corhmm", "_universes": [ "phylotastic" ], "_indexurl": "https://thej022214.r-universe.dev/corHMM", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.10.4", "date": "2026-06-03T06:37:02.000Z", "distro": "noble", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "dadb514acf1c1d39b735ee0ea3de3e3d2986622fd2c5d327e43f8482ad448c20", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" }, { "r": "4.6.0", "os": "linux", "version": "2.10.4", "date": "2026-06-03T06:36:56.000Z", "distro": "noble", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "6aa7dbda5e3e0c24344e0f4e81748d36878a5af03741ada3f883a10af44b6f3b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" }, { "r": "4.5.3", "os": "mac", "version": "2.10.4", "date": "2026-06-03T06:35:58.000Z", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "647a0171c688ef7447424272bb43f03463530c98c03f98749bd8a94390fcac6f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" }, { "r": "4.6.0", "os": "mac", "version": "2.10.4", "date": "2026-06-03T06:36:16.000Z", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "a0549ee177679396209cd69d1b2d0e0399dc9deaab391eabb9c3bb9c9482aa15", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" }, { "r": "4.7.0", "os": "win", "version": "2.10.4", "date": "2026-06-03T06:35:34.000Z", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "1a6d797b379168fe88ee608241d6516606b07fd35ea90ca37f03a9839f398965", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" }, { "r": "4.5.3", "os": "win", "version": "2.10.4", "date": "2026-06-03T06:35:42.000Z", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "ddab2821d86ab5a6e81fa9b7b6a18514699fb4c3f59fe38e43fa1f6cd0ebcb99", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" }, { "r": "4.6.0", "os": "win", "version": "2.10.4", "date": "2026-06-03T06:35:33.000Z", "commit": "ddadab2f62bd0bc569f2e20eba9f7073d8bdc07d", "fileid": "bb5bb6c0c424244600fa5ad635195f1bfada31a0a2654cce30de5adb127d0a62", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841489027" } ] }