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-4.5-noble)pcmabc_1.1.3.tar.gz(r-4.4-noble)
pcmabc_1.1.3.tgz(r-4.4-emscripten)pcmabc_1.1.3.tgz(r-4.3-emscripten)
pcmabc.pdf |pcmabc.html✨
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 2 years agofrom:8f1a7972b6. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-linux | NOTE | Aug 28 2024 |
Exports:draw_phylprocget_phylogenetic_samplePCM_ABCsimulate_phenotype_on_treesimulate_phylprocsimulate_sde_on_branch
Dependencies:abindapebootcalculusclicodacolorspacecpp11cubaturedata.tabledigestexpmfansifarverfastmatchgenericsggplot2glassoFastgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmgcvmunsellmvSLOUCHmvtnormnlmeouchPCMBasephangornpillarpkgconfigquadprogR6RColorBrewerRcppRcppArmadillorlangscalesstatmodsubplextibbleutf8vctrsviridisLitewithrxtableyuimazoo
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 |