Package: paleobuddy 1.1.0
Bruno do Rosario Petrucci
paleobuddy: Simulating Diversification Dynamics
Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.
Authors:
paleobuddy_1.1.0.tar.gz
paleobuddy_1.1.0.tar.gz(r-4.5-noble)paleobuddy_1.1.0.tar.gz(r-4.4-noble)
paleobuddy_1.1.0.tgz(r-4.4-emscripten)paleobuddy_1.1.0.tgz(r-4.3-emscripten)
paleobuddy.pdf |paleobuddy.html✨
paleobuddy/json (API)
NEWS
| # Install 'paleobuddy' in R: |
| install.packages('paleobuddy', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/brpetrucci/paleobuddy/issues
Last updated 1 months agofrom:9ba6b8e53c. Checks:3 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 07 2025 |
| R-4.5-linux | OK | Mar 07 2025 |
| R-4.4-linux | OK | Mar 07 2025 |
Exports:bd.simbd.sim.traitsbin.occurrencesbinnerdraw.simfind.lineagesis.simmake.phylomake.ratephylo.to.simrexp.varsample.cladesample.clade.traitssim.countstraits.summaryvar.rate.div
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| General rate Birth-Death simulation | bd.sim |
| MuSSE simulation | bd.sim.traits |
| Bin true occurrences into geologic intervals | bin.occurrences |
| Bin occurrences in geologic intervals | binner |
| Jurassic CO2 data | co2 |
| Draw a sim object | draw.sim |
| Separate a paleobuddy simulation into monophyletic clades | find.lineages |
| Phylogeny generating | make.phylo |
| Create a flexible rate for birth-death or sampling simulations | make.rate |
| paleobuddy: Simulating diversification dynamics | paleobuddy-package paleobuddy |
| Converting a phylogeny in a paleobuddy object | phylo.to.sim |
| General rate exponential and Weibull waiting times | rexp.var |
| General rate fossil sampling | sample.clade |
| Trait-dependent fossil sampling | sample.clade.traits |
| Details, generics, and methods for the 'sim' class | head.sim is.sim plot.sim print.sim sim sim.counts summary.sim tail.sim |
| Cenozoic temperature data | temp |
| Summarizing trait data | traits.summary |
| Expected diversity for general exponential rates | var.rate.div |
