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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:

Please use the canonical form https://CRAN.R-project.org/package=deepSTRAPP to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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