deepSTRAPP: Test for Differences in Diversification Rates over Time

Employ time-calibrated phylogenies and trait/range data to test for differences in diversification rates over evolutionary time. Extend the STRAPP test from BAMMtools::traitDependentBAMM() to any time step along phylogenies. See inst/COPYRIGHTS for details on third-party code.

Version: 1.0.0
Depends: R (≥ 4.4)
Imports: ape (≥ 5.8.0), BAMMtools (≥ 2.1.12), cladoRcpp (≥ 0.15.1), coda (≥ 0.19-4.1), cowplot (≥ 1.1.3), dplyr (≥ 1.1.4), dunn.test (≥ 1.3.6), geiger (≥ 2.0.11), ggplot2 (≥ 3.5.0), methods (≥ 4.4.2), phytools (≥ 2.0.0), plyr (≥ 1.8.9), purrr (≥ 1.0.2), qpdf (≥ 1.4.1), RColorBrewer (≥ 1.1-3), Rcpp (≥ 1.0.14), scales (≥ 1.3.0), stringr (≥ 1.5.1), tidyr (≥ 1.3.1)
LinkingTo: Rcpp
Suggests: knitr, maps (≥ 3.4.2), parallel (≥ 4.4.2), BioGeoBEARS (≥ 1.1.3), rmarkdown
Published: 2026-01-19
DOI: 10.32614/CRAN.package.deepSTRAPP (may not be active yet)
Author: Maël Doré ORCID iD [aut, cre, cph], Dan Rabosky [ctb], Mike Grundler [ctb], Huateng Huang [ctb], Pascal Title [ctb], Liam Revell [ctb], Nicholas J. Matzke [ctb]
Maintainer: Maël Doré <mael.dore at gmail.com>
BugReports: https://github.com/MaelDore/deepSTRAPP/issues
License: MIT + file LICENSE
Copyright: see file COPYRIGHTS
URL: https://github.com/MaelDore/deepSTRAPP, https://maeldore.github.io/deepSTRAPP/
NeedsCompilation: yes
Additional_repositories: https://maeldore.github.io/drat
Citation: deepSTRAPP citation info
Materials: README, NEWS
CRAN checks: deepSTRAPP results

Documentation:

Reference manual: deepSTRAPP.html , deepSTRAPP.pdf
Vignettes: Cut phylogenies (source, R code)
deepSTRAPP: All tutorials (source, R code)
deepSTRAPP: Biogeographic range data (source, R code)
deepSTRAPP: Categorical trait data (source, R code)
deepSTRAPP: Continuous trait data (source, R code)
Explore STRAPP test options (source, R code)
Main tutorial (source, R code)
Model biogeographic range evolution (source, R code)
Model categorical trait evolution (source, R code)
Model continuous trait evolution (source, R code)
Model diversification dynamics (source, R code)
Plot rates through time (source, R code)

Downloads:

Package source: deepSTRAPP_1.0.0.tar.gz
Windows binaries: r-devel: deepSTRAPP_1.0.0.zip, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): deepSTRAPP_1.0.0.tgz, r-oldrel (arm64): deepSTRAPP_1.0.0.tgz, r-release (x86_64): deepSTRAPP_1.0.0.tgz, r-oldrel (x86_64): not available

Linking:

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