Package: pcmabc 1.1.3
Krzysztof Bartoszek
pcmabc: Approximate Bayesian Computations for Phylogenetic Comparative Methods
Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data. See K. Bartoszek, P. Lio' (2019) <doi:10.5506/APhysPolBSupp.12.25>. The suggested geiger package can be obtained from CRAN's archive <https://cran.r-project.org/src/contrib/Archive/geiger/>, suggested to take latest version. Otherwise its required code is present in the pcmabc package. The suggested distory package can be obtained from CRAN's archive <https://cran.r-project.org/src/contrib/Archive/distory/>, suggested to take latest version.
Authors:
pcmabc_1.1.3.tar.gz
pcmabc_1.1.3.tar.gz(r-4.7-any)pcmabc_1.1.3.tar.gz(r-4.6-any)
pcmabc_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pcmabc/json (API)
| # Install 'pcmabc' in R: |
| install.packages('pcmabc', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:8f1a7972b6. Checks:2 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 145 | ||
| source / vignettes | OK | 216 | ||
| linux-release-x86_64 | NOTE | 165 | ||
| wasm-release | OK | 140 |
Exports:draw_phylprocget_phylogenetic_samplePCM_ABCsimulate_phenotype_on_treesimulate_phylprocsimulate_sde_on_branch
Dependencies:abindapebootcalculusclicodacpp11cubaturedata.tabledigestexpmfarverfastmatchgenericsggplot2glassoFastgluegtableigraphisobandlabelinglatticelifecyclemagrittrMatrixmatrixcalcmvSLOUCHmvtnormnlmeouchPCMBasephangornpkgconfigquadprogR6RColorBrewerRcppRcppArmadillorlangS7scalesstatmodsubplexvctrsviridisLitewithrxtableyuimazoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Approximate Bayesian Computations for Phylogenetic Comparative Methods | pcmabc-package pcmabc |
| Plots the trajectory of the stochastic process that evolved on the phylogeny. | draw_phylproc |
| Retrieve contemporary sample | get_phylogenetic_sample |
| ABC estimation for PCMs | PCM_ABC |
| Simulate a stochastic process on top of a phylogeny. | simulate_phenotype_on_tree |
| Simultaneously simulate a phylogeny and a trait evolving on it. | simulate_phylproc |
| Simulate a stochastic differential equation on a branch. using the 'yuima' | simulate_sde_on_branch |