Package: ratematrix 1.2.4
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.
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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')) |
Bug tracker:https://github.com/caetanods/ratematrix/issues
- anoles - Data and phylogenetic tree for Anolis lizards
- centrarchidae - Data and phylogenetic tree for Centrarchidae fishes
Last updated 2 years agofrom:c136d5880f. Checks:OK: 1 NOTE: 8. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 05 2024 |
R-4.5-win-x86_64 | NOTE | Sep 05 2024 |
R-4.5-linux-x86_64 | NOTE | Sep 05 2024 |
R-4.4-win-x86_64 | NOTE | Sep 05 2024 |
R-4.4-mac-x86_64 | NOTE | Sep 05 2024 |
R-4.4-mac-aarch64 | NOTE | Sep 05 2024 |
R-4.3-win-x86_64 | NOTE | Sep 05 2024 |
R-4.3-mac-x86_64 | NOTE | Sep 05 2024 |
R-4.3-mac-aarch64 | NOTE | Sep 05 2024 |
Exports:checkConvergencecomputeESScontinueMCMCestimateTimeMCMCextractCorrelationfastSimmapgetStartPointFromPosteriorlikelihoodFunctionlogAnalyzermakePriormergePosteriormergeSimmapplotPriorplotRatematrixplotRootValueratematrixJointMCMCratematrixMCMCreadMCMCreadMCMC_MksamplePriorsimRatematrixtestRatematrix
Dependencies:apebitbit64clicliprclusterGenerationcodacodetoolscolorspacecombinatcorpcorcpp11crayonDEoptimdeSolvedigestdoParalleldotCall64ellipseexpmfansifarverfastmatchforeachfuturefuture.applygeigergenericsggplot2ggseqlogoglassoFastglobalsgluegtablehmsigraphisobanditeratorslabelinglatticelifecyclelistenvmagrittrmapsMASSMatrixmgcvmnormtmunsellmvMORPHmvtnormncbitnlmenumDerivoptimParallelparallellypbmcapplyphangornphylolmphytoolspillarpkgconfigprettyunitsprogressquadprogR6RColorBrewerRcppRcppArmadilloreadrrlangscalesscatterplot3dspamsubplextibbletidyselecttzdbutf8vctrsviridisLitevroomwithr
Introduction to using the 'ratematrix' package
Rendered fromIntro_on_the_package.Rmd
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on Sep 05 2024.Last update: 2020-02-26
Started: 2018-10-29
Set custom starting point with 'ratematrix'
Rendered fromSet_custom_starting_point.Rmd
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on Sep 05 2024.Last update: 2022-06-02
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Using prior distributions with 'ratematrix'
Rendered fromMaking_prior_on_ratematrix.Rmd
usingknitr::knitr
on Sep 05 2024.Last update: 2019-05-06
Started: 2017-03-29