Package: ratematrix 1.2.4

Daniel Caetano

ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix

The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.

Authors:Daniel Caetano [aut, cre], Luke Harmon [aut]

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ratematrix.pdf |ratematrix.html✨
ratematrix/json (API)

# Install 'ratematrix' in R:
install.packages('ratematrix', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/caetanods/ratematrix/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • anoles - Data and phylogenetic tree for Anolis lizards
  • centrarchidae - Data and phylogenetic tree for Centrarchidae fishes

On CRAN:

22 exports 9 stars 1.46 score 83 dependencies 18 scripts 213 downloads

Last updated 2 years agofrom:c136d5880f. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 05 2024
R-4.5-win-x86_64NOTESep 05 2024
R-4.5-linux-x86_64NOTESep 05 2024
R-4.4-win-x86_64NOTESep 05 2024
R-4.4-mac-x86_64NOTESep 05 2024
R-4.4-mac-aarch64NOTESep 05 2024
R-4.3-win-x86_64NOTESep 05 2024
R-4.3-mac-x86_64NOTESep 05 2024
R-4.3-mac-aarch64NOTESep 05 2024

Exports:checkConvergencecomputeESScontinueMCMCestimateTimeMCMCextractCorrelationfastSimmapgetStartPointFromPosteriorlikelihoodFunctionlogAnalyzermakePriormergePosteriormergeSimmapplotPriorplotRatematrixplotRootValueratematrixJointMCMCratematrixMCMCreadMCMCreadMCMC_MksamplePriorsimRatematrixtestRatematrix

Dependencies:apebitbit64clicliprclusterGenerationcodacodetoolscolorspacecombinatcorpcorcpp11crayonDEoptimdeSolvedigestdoParalleldotCall64ellipseexpmfansifarverfastmatchforeachfuturefuture.applygeigergenericsggplot2ggseqlogoglassoFastglobalsgluegtablehmsigraphisobanditeratorslabelinglatticelifecyclelistenvmagrittrmapsMASSMatrixmgcvmnormtmunsellmvMORPHmvtnormncbitnlmenumDerivoptimParallelparallellypbmcapplyphangornphylolmphytoolspillarpkgconfigprettyunitsprogressquadprogR6RColorBrewerRcppRcppArmadilloreadrrlangscalesscatterplot3dspamsubplextibbletidyselecttzdbutf8vctrsviridisLitevroomwithr

Introduction to using the 'ratematrix' package

Daniel S. Caetano

Rendered fromIntro_on_the_package.Rmdusingknitr::knitron Sep 05 2024.

Last update: 2020-02-26
Started: 2018-10-29

Set custom starting point with 'ratematrix'

Daniel S. Caetano

Rendered fromSet_custom_starting_point.Rmdusingknitr::knitron Sep 05 2024.

Last update: 2022-06-02
Started: 2017-06-27

Using prior distributions with 'ratematrix'

Daniel S. Caetano

Rendered fromMaking_prior_on_ratematrix.Rmdusingknitr::knitron Sep 05 2024.

Last update: 2019-05-06
Started: 2017-03-29

Readme and manuals

Help Manual

Help pageTopics
Data and phylogenetic tree for Anolis lizardsanoles
Data and phylogenetic tree for Centrarchidae fishescentrarchidae
Performs convergence testscheckConvergence
Compute the ESS for the MCMC samplescomputeESS
Continue unfinished MCMC chain or add more generationscontinueMCMC
Time estimate to complete a MCMC chainestimateTimeMCMC
Extract the posterior distribution of evolutionary correlationextractCorrelation
Fast implementation of stochastic mapping.fastSimmap
Extract sample from MCMC to use as starting point for another MCMCgetStartPointFromPosterior
Likelihood function for the multivariate Brownian motion modellikelihoodFunction
Make analysis of the log file of the MCMC chainlogAnalyzer
Generate prior distributions for the multivariate Brownian motion modelmakePrior
Merge posterior distributionsmergePosterior
Merge two or more regimes of a 'simmap' treemergeSimmap
Plot the prior distribution used in the MCMC analysisplotPrior
Plot the distribution of evolutionary rate matricesplotRatematrix
Plot posterior distribution of root values for the traitsplotRootValue
Print method for the "ratematrix_multi_chain" class.print.ratematrix_multi_chain
Print method for the "ratematrix_multi_mcmc" class.print.ratematrix_multi_mcmc
Print method for the "ratematrix_prior_function" class.print.ratematrix_prior_function
Print method for the "ratematrix_prior_sample" class.print.ratematrix_prior_sample
Print method for the "ratematrix_single_chain" class.print.ratematrix_single_chain
Print method for the "ratematrix_single_mcmc" class.print.ratematrix_single_mcmc
ratematrix.ratematrix
Estimate the evolutionary rate matrix together with the regimes using Markov-chain Monte CarloratematrixJointMCMC
Estimate the evolutionary rate matrix using Markov-chain Monte CarloratematrixMCMC
Read the MCMC output filesreadMCMC
Read output files of MCMC for the predictor regimes.readMCMC_Mk
Take samples from the prior distributionsamplePrior
Simulates multivariate trait evolution using a Brownian motion modelsimRatematrix
Test for difference between evolutionary rate matrix estimatestestRatematrix