Package: mcmc3r 0.5.7

Sandra Alvarez-Carretero

mcmc3r: Tools to work with MCMCtree

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

Authors:Sandra Alvarez-Carretero [aut, cre]

mcmc3r_0.5.7.tar.gz
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mcmc3r.pdf |mcmc3r.html✨
mcmc3r/json (API)

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

Peer review:

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.PS - Object of class procSym output by Morpho after PA
  • 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
  • R.sh - Estimated shrinkage correlation matrix
  • V - 29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysis
  • V.PS.nov1 - Object of class array output by Morpho after PA
  • 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
  • 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
  • sim.R - Correlation matrix for simulations
  • sim.tree - Simulated 8-species tree
  • 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:

4.30 score 5 stars 8 scripts 27 exports 7 dependencies

Last updated 2 months agofrom:af4fa9af83. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-winNOTEDec 10 2024
R-4.5-linuxNOTEDec 10 2024
R-4.4-winNOTEDec 10 2024
R-4.4-macNOTEDec 10 2024
R-4.3-winNOTEDec 10 2024
R-4.3-macNOTEDec 10 2024

Exports:array2matrixbayes.factorsblock.bootctlMCMCtreedBdBDdLdUgauss.quadgauss.quad.bootlmk_impmake.betamake.bfctlfmatrix2arraymcmc.summcmc2ancmcmc2densitreemcmc2multiphylopLproc2MCMCtreeqLsim.morphosim.popstepping.stonesstepping.stones.boottreeMCMCtreewrite.morpho

Dependencies:apecodacorpcordigestlatticenlmeRcpp

Total-evidence dating of carnivores integrating molecular and morphometric data

Sandra Álvarez-Carretero and Mario dos Reis

Rendered fromReproduce_Carnivora_analysis.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-03-28
Started: 2018-10-14

Readme and manuals

Help Manual

Help pageTopics
A matrixA
Convert an array into a matrixarray2matrix
Calculate Bayes factors and posterior model probabilitiesbayes.factors
Generate block bootstrap replicates of sampled power likelihoodsblock.boot
29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysisC
29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysisC.arr.unal
29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysisC.mat.unal
Object of class procSym output by Morpho after PAC.PS
Calibration densitiescalibrations dB dL dU pL qL
Carnivores datasetcarnivores
29 3D landmarks from the skulls of 19 carnivoran specimenscarnivores19x29.raw
Generating the control file to run MCMCtree when using morphological datactlMCMCtree
Birth-death process with species samplingdBD
Estimate marginal likelihood by thermodynamic integrationgauss.quad
A BPP A00 MCMC sample for an hominid phylogenyhominids
Import various landmark files for different specimens at oncelmk_imp
Estimate marginal likelihood from bootstrap replicatesgauss.quad.boot logL.boot stepping.stones.boot
Make beta values for marginal likelihood calculationmake.beta
Prepare mcmctree or bpp control files for marginal likelihood calculationmake.bfctlf
Convert a matrix into an arraymatrix2array
Calculate summaries from an MCMC runmcmc.sum
Ancestral character reconstruction from an MCMC samplemcmc2anc
Plot a densi-tree from an MCMC samplemcmc2densitree
Convert an MCMC sample from MCMCTree or BPP to a list of treesmcmc2multiphylo
A BPP A00 MCMC sample for a mouse lemur phylogenymicrocebus
Procrustes alignment output in MCMCtree format for Bayesian inferenceproc2MCMCtree
Estimated shrinkage correlation matrixR.sh
Simulate a continuous morphological alignmentsim.morpho
Simulate a population matrixsim.pop
Correlation matrix for simulationssim.R
Simulated 8-species treesim.tree
Estimate marginal likelihood by stepping stonesstepping.stones
Generating a tree file in MCMCtree format when using morphological datatreeMCMCtree
29 3D landmarks from the skulls of 19 carnivoran specimens after Procrustes analysisV
29 3D landmarks from the skulls of 21 Vulpes vulpes specimens before Procrustes analysisV.arr.unal
29 3D landmarks from the skulls of 19 carnivoran specimens before Procrustes analysisV.mat.unal
Object of class array output by Morpho after PAV.PS.nov1
Vector with the population variance of Vulpes vulpesvar.foxes
29 3D landmarks from the skulls of 21 Vulpes vulpes specimensvulpes21x29.raw
Generate a file with a morphological alignment for MCMCtreewrite.morpho