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Package: mcmc3r 0.6.0

Sandra Alvarez-Carretero

mcmc3r: Tools to work with MCMCtree and BPP

Tools to work with MCMCtree, a program for Bayesian inference of species divergence times.

Authors:Sandra Alvarez-Carretero [aut, cre]

mcmc3r_0.6.0.tar.gz
mcmc3r_0.6.0.zip(r-4.7)mcmc3r_0.6.0.zip(r-4.6)mcmc3r_0.6.0.zip(r-4.5)
mcmc3r_0.6.0.tgz(r-4.6-any)mcmc3r_0.6.0.tgz(r-4.5-any)
mcmc3r_0.6.0.tar.gz(r-4.7-any)mcmc3r_0.6.0.tar.gz(r-4.6-any)
mcmc3r_0.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mcmc3r/json (API)

# Install 'mcmc3r' in R:

install.packages('mcmc3r', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dosreislab/mcmc3r/issues

Datasets:

A - A matrix
C - 29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysis
C.arr.unal - 29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysis
C.mat.unal - 29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysis
C.PS - Object of class procSym output by Morpho after PA
carnivores - Carnivores dataset
carnivores19x29.raw - 29 3D landmarks from the skulls of 19 carnivoran specimens
hominids - A BPP A00 MCMC sample for an hominid phylogeny
microcebus - A BPP A00 MCMC sample for a mouse lemur phylogeny
R.sh - Estimated shrinkage correlation matrix
sim.R - Correlation matrix for simulations
sim.tree - Simulated 8-species tree
V - 29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysis
V.arr.unal - 29 3D landmarks from the skulls of 21 Vulpes vulpes specimens before Procrustes analysis
V.mat.unal - 29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysis
V.PS.nov1 - Object of class array output by Morpho after PA
var.foxes - Vector with the population variance of Vulpes vulpes
vulpes21x29.raw - 29 3D landmarks from the skulls of 21 Vulpes vulpes specimens

On CRAN:

4.76 score 7 stars 11 scripts 32 exports 7 dependencies

Last updated from:f6a8f78bc5. Checks:7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	NOTE	131
source / vignettes	OK	171
linux-release-x86_64	NOTE	125
macos-release-arm64	NOTE	111
macos-oldrel-arm64	NOTE	84
windows-devel	NOTE	106
windows-release	NOTE	100
windows-oldrel	NOTE	88
wasm-release	OK	114

Exports:array2matrix bayes.factors block.boot ctlMCMCtree dB dBD dL dU gauss.quad gauss.quad.boot lmk_imp lnL.app make.beta make.bfctlf matrix2array mcmc.sum mcmc2anc mcmc2densitree mcmc2multiphylo pB pL proc2MCMCtree pU qB qL qU sim.morpho sim.pop stepping.stones stepping.stones.boot treeMCMCtree write.morpho

Dependencies:ape coda corpcor digest lattice nlme Rcpp

Total-evidence dating of carnivores integrating molecular and morphometric data

Rendered fromReproduce_Carnivora_analysis.Rmdusingknitr::rmarkdown

Last update: 2025-01-04
Started: 2018-10-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A matrix	A
Convert an array into a matrix	array2matrix
Calculate Bayes factors and posterior model probabilities	bayes.factors
Generate block bootstrap replicates of sampled power likelihoods	block.boot
29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysis	C
29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysis	C.arr.unal
29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysis	C.mat.unal
Object of class procSym output by Morpho after PA	C.PS
Calibration densities	calibrations dB dL dU pB pL pU qB qL qU
Carnivores dataset	carnivores
29 3D landmarks from the skulls of 19 carnivoran specimens	carnivores19x29.raw
Generating the control file to run MCMCtree when using morphological data	ctlMCMCtree
Birth-death process with species sampling	dBD
Estimate marginal likelihood by thermodynamic integration	gauss.quad
A BPP A00 MCMC sample for an hominid phylogeny	hominids
Import various landmark files for different specimens at once	lmk_imp
Calculate the approximate log-likelihood	lnL.app
Estimate marginal likelihood from bootstrap replicates	gauss.quad.boot logL.boot stepping.stones.boot
Make beta values for marginal likelihood calculation	make.beta
Prepare mcmctree or bpp control files for marginal likelihood calculation	make.bfctlf
Convert a matrix into an array	matrix2array
Calculate summaries from an MCMC run	mcmc.sum
Ancestral character reconstruction from an MCMC sample	mcmc2anc
Plot a densi-tree from an MCMC sample	mcmc2densitree
Convert an MCMC sample from MCMCTree or BPP to a list of trees	mcmc2multiphylo
A BPP A00 MCMC sample for a mouse lemur phylogeny	microcebus
Procrustes alignment output in MCMCtree format for Bayesian inference	proc2MCMCtree
Estimated shrinkage correlation matrix	R.sh
Simulate a continuous morphological alignment	sim.morpho
Simulate a population matrix	sim.pop
Correlation matrix for simulations	sim.R
Simulated 8-species tree	sim.tree
Estimate marginal likelihood by stepping stones	stepping.stones
Generating a tree file in MCMCtree format when using morphological data	treeMCMCtree
29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysis	V
29 3D landmarks from the skulls of 21 Vulpes vulpes specimens before Procrustes analysis	V.arr.unal
29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysis	V.mat.unal
Object of class array output by Morpho after PA	V.PS.nov1
Vector with the population variance of Vulpes vulpes	var.foxes
29 3D landmarks from the skulls of 21 Vulpes vulpes specimens	vulpes21x29.raw
Generate a file with a morphological alignment for MCMCtree	write.morpho