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ratematrix
View on CRAN: Click
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Download and install ratematrix package within the R console
Install from CRAN:
install.packages("ratematrix")
Install from Github:
library("remotes")
install_github("cran/ratematrix")
Install by package version:
library("remotes")
install_version("ratematrix", "1.2.4")
Attach the package and use:
library("ratematrix")
Maintained by
Daniel Caetano
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-06-10
Latest Update: 2022-06-03
Description:
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.
How to cite:
Daniel Caetano (2018). ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix. R package version 1.2.4, https://cran.r-project.org/web/packages/ratematrix
Previous versions and publish date:
Other packages that cited ratematrix R package
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Other R packages that ratematrix depends,
imports, suggests or enhances
Functions, R codes and Examples using
the ratematrix R package
Some associated functions: anoles . centrarchidae . checkConvergence . computeESS . continueMCMC . estimateTimeMCMC . extractCorrelation . fastSimmap . getStartPointFromPosterior . likelihoodFunction . logAnalyzer . makePrior . mergePosterior . mergeSimmap . plotPrior . plotRatematrix . plotRootValue . print.ratematrix_multi_chain . print.ratematrix_multi_mcmc . print.ratematrix_prior_function . print.ratematrix_prior_sample . print.ratematrix_single_chain . print.ratematrix_single_mcmc . ratematrix . ratematrixJointMCMC . ratematrixMCMC . readMCMC . readMCMC_Mk . samplePrior . simRatematrix . testRatematrix .
Some associated R codes: RcppExports.R . calcNodeToNode.R . calcNodeToTip.R . calcNodeToTipNode.R . checkConvergence.R . checkHPD.R . checkHeidelTest.R . check_phy_list.R . computeESS.R . continueMCMC.R . dataset_anoles.R . dataset_centrarchidae.R . estimateTimeMCMC.R . extractCorrelation.R . fastSimmap.R . getEllipseMatrix.R . getStartPointFromPosterior.R . hastingsDensity.R . likelihoodFunction.R . logAnalyzer.R . logDensityIWish.R . logDensityMvNorm.R . logLikNode.R . logLikPrunningMCMC.R . logLikSingleRegime.R . makeDataTips.R . makePrior.R . makePriorIWish.R . makePropIWish.R . makePropMean.R . makePropMeanForMult.R . makePropMeanForMultList.R . makePropMeanList.R . makePropMultSigma.R . makePropMultSigmaList.R . makePropSingleSigma.R . makePropSingleSigmaList.R . mergePosterior.R . mergeSimmap.R . multRegimeJointMCMC.R . multRegimeMCMC.R . multiplierProposal.R . mvLogLik.R . plotPrior.R . plotRatematrix.R . plotRootValue.R . print.ratematrix_multi_chain.R . print.ratematrix_multi_mcmc.R . print.ratematrix_prior_function.R . print.ratematrix_prior_sample.R . print.ratematrix_single_chain.R . print.ratematrix_single_mcmc.R . priorDensityVcvBarnard.R . ratematrix-package.R . ratematrixJointMCMC.R . ratematrixMCMC.R . readMCMC.R . readMultRegimeMCMC.R . readSingleRegimeMCMC.R . riwish.R . samplePrior.R . samplePriorSeparationLimits.R . sampleTreeClade.R . simRatematrix.R . singleRegimeMCMC.R . slideWindow.R . slideWindowPositive.R . testRatematrix.R . writeToFile.R . writeToMultFile.R . Full ratematrix package functions and examples
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