Package: bppr 0.6.3
bppr: An R package for BPP
Functions to work with the multi-species coalescent program BPP, for example, functions to calibrate BPP trees to geological time.
Authors:
bppr_0.6.3.tar.gz
bppr_0.6.3.zip(r-4.5)bppr_0.6.3.zip(r-4.4)bppr_0.6.3.zip(r-4.3)
bppr_0.6.3.tgz(r-4.4-any)bppr_0.6.3.tgz(r-4.3-any)
bppr_0.6.3.tar.gz(r-4.5-noble)bppr_0.6.3.tar.gz(r-4.4-noble)
bppr_0.6.3.tgz(r-4.4-emscripten)bppr_0.6.3.tgz(r-4.3-emscripten)
bppr.pdf |bppr.html✨
bppr/json (API)
# Install 'bppr' in R: |
install.packages('bppr', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dosreislab/bppr/issues
Datasets:
- hominids - A BPP A00 MCMC sample for an hominid phylogeny
- microcebus - A BPP A00 MCMC sample for a mouse lemur phylogeny
Last updated 1 years agofrom:7c2928bd1c. Checks:OK: 1 WARNING: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 26 2024 |
R-4.5-win | WARNING | Aug 26 2024 |
R-4.5-linux | WARNING | Aug 26 2024 |
R-4.4-win | WARNING | Aug 26 2024 |
R-4.4-mac | WARNING | Aug 26 2024 |
R-4.3-win | WARNING | Aug 26 2024 |
R-4.3-mac | WARNING | Aug 26 2024 |
Exports:bayes.factorsdslnormgauss.quadmake.betamake.bfctlfmcmc.summarymcmc2densitreemcmc2multiphylomsc2time.rmsc2time.tpslnormqslnormrslnormstepping.stones
Dependencies:
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Calculate Bayes factors and posterior model probabilities | bayes.factors |
Estimate marginal likelihood by thermodynamic integration | gauss.quad |
A BPP A00 MCMC sample for an hominid phylogeny | hominids |
Make beta values for marginal likelihood calculation | make.beta |
Prepare mcmctree or bpp control files for marginal likelihood calculation | make.bfctlf |
MCMC summary | mcmc.summary |
Plot a densi-tree from an MCMC sample | mcmc2densitree |
Convert an MCMC sample from BPP or MCMCTree to a list of trees | mcmc2multiphylo |
A BPP A00 MCMC sample for a mouse lemur phylogeny | microcebus |
Time-calibrate a multi-species phylogeny | msc2time msc2time.r msc2time.t |
The Shifted Log-normal Distribution | dslnorm pslnorm qslnorm rslnorm ShiftedLognormal |
Estimate marginal likelihood by stepping stones | stepping.stones |