This package is considered a duplicate. The official version of this package is found at:https://caetanods.r-universe.dev/ratematrix

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]

ratematrix_1.2.4.tar.gz
ratematrix_1.2.4.tar.gz(r-4.5-noble)ratematrix_1.2.4.tar.gz(r-4.4-noble)
ratematrix_1.2.4.tgz(r-4.4-emscripten)ratematrix_1.2.4.tgz(r-4.3-emscripten)
ratematrix.pdf |ratematrix.html✨
ratematrix/json (API)

# Install 'ratematrix' in R:

install.packages('ratematrix', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

openblas cpp openmp

2.95 score 1 packages 18 scripts 185 downloads 22 exports 72 dependencies

Last updated 3 years agofrom:cf0cf60269. Checks:OK: 1 NOTE: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Dec 12 2024
R-4.5-linux-x86_64	NOTE	Dec 12 2024

Exports:checkConvergence computeESS continueMCMC estimateTimeMCMC extractCorrelation fastSimmap getStartPointFromPosterior likelihoodFunction logAnalyzer makePrior mergePosterior mergeSimmap plotPrior plotRatematrix plotRootValue ratematrixJointMCMC ratematrixMCMC readMCMC readMCMC_Mk samplePrior simRatematrix testRatematrix

Dependencies:ape bit bit64 cli clipr clusterGeneration coda codetools colorspace combinat corpcor cpp11 crayon DEoptim deSolve digest doParallel dotCall64 ellipse expm fansi fastmatch foreach future future.apply geiger generics glassoFast globals glue hms igraph iterators lattice lifecycle listenv magrittr maps MASS Matrix mnormt mvMORPH mvtnorm ncbit nlme numDeriv optimParallel parallelly pbmcapply phangorn phylolm phytools pillar pkgconfig prettyunits progress quadprog R6 Rcpp RcppArmadillo readr rlang scatterplot3d spam subplex tibble tidyselect tzdb utf8 vctrs vroom withr

Introduction to using the 'ratematrix' package

Daniel S. Caetano

Rendered fromIntro_on_the_package.Rmdusingknitr::knitron Dec 12 2024.

Last update: 2020-02-26
Started: 2018-10-30

Set custom starting point with 'ratematrix'

Daniel S. Caetano

Rendered fromSet_custom_starting_point.Rmdusingknitr::knitron Dec 12 2024.

Last update: 2022-06-03
Started: 2018-06-10

Using prior distributions with 'ratematrix'

Daniel S. Caetano

Rendered fromMaking_prior_on_ratematrix.Rmdusingknitr::knitron Dec 12 2024.

Last update: 2019-05-06
Started: 2018-06-10

Help page	Topics
Data and phylogenetic tree for Anolis lizards	anoles
Data and phylogenetic tree for Centrarchidae fishes	centrarchidae
Performs convergence tests	checkConvergence
Compute the ESS for the MCMC samples	computeESS
Continue unfinished MCMC chain or add more generations	continueMCMC
Time estimate to complete a MCMC chain	estimateTimeMCMC
Extract the posterior distribution of evolutionary correlation	extractCorrelation
Fast implementation of stochastic mapping.	fastSimmap
Extract sample from MCMC to use as starting point for another MCMC	getStartPointFromPosterior
Likelihood function for the multivariate Brownian motion model	likelihoodFunction
Make analysis of the log file of the MCMC chain	logAnalyzer
Generate prior distributions for the multivariate Brownian motion model	makePrior
Merge posterior distributions	mergePosterior
Merge two or more regimes of a 'simmap' tree	mergeSimmap
Plot the prior distribution used in the MCMC analysis	plotPrior
Plot the distribution of evolutionary rate matrices	plotRatematrix
Plot posterior distribution of root values for the traits	plotRootValue
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 Carlo	ratematrixJointMCMC
Estimate the evolutionary rate matrix using Markov-chain Monte Carlo	ratematrixMCMC
Read the MCMC output files	readMCMC
Read output files of MCMC for the predictor regimes.	readMCMC_Mk
Take samples from the prior distribution	samplePrior
Simulates multivariate trait evolution using a Brownian motion model	simRatematrix
Test for difference between evolutionary rate matrix estimates	testRatematrix

Package: ratematrix 1.2.4

ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix

Introduction to using the 'ratematrix' package

Set custom starting point with 'ratematrix'

Using prior distributions with 'ratematrix'

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)