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:Bruno do Rosario Petrucci [aut, cre], Matheus Januario [aut], Tiago Quental [aut]

paleobuddy_1.1.0.tar.gz
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paleobuddy_1.1.0.tgz(r-4.5-any)paleobuddy_1.1.0.tgz(r-4.4-any)paleobuddy_1.1.0.tgz(r-4.3-any)
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://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/brpetrucci/paleobuddy/issues

Datasets:
  • co2 - Jurassic CO2 data
  • temp - Cenozoic temperature data

On CRAN:

Conda:

evolutionmacroevolutionpaleobiologypaleontologyphylogenetics

4.95 score 6 stars 4 scripts 343 downloads 16 exports 0 dependencies

Last updated 1 months agofrom:47e7730ca3. Checks:8 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 27 2025
R-4.5-winOKFeb 27 2025
R-4.5-macOKFeb 27 2025
R-4.5-linuxOKFeb 27 2025
R-4.4-winOKFeb 27 2025
R-4.4-macOKFeb 27 2025
R-4.3-winOKFeb 27 2025
R-4.3-macOKFeb 27 2025

Exports:bd.simbd.sim.traitsbin.occurrencesbinnerdraw.simfind.lineagesis.simmake.phylomake.ratephylo.to.simrexp.varsample.cladesample.clade.traitssim.countstraits.summaryvar.rate.div

Dependencies:

Paleobuddy overview

Rendered fromoverview.Rmdusingknitr::rmarkdownon Feb 27 2025.

Last update: 2023-10-17
Started: 2020-07-17