Package: deepSTRAPP 1.0.0

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.

Authors:Maël Doré [aut, cre, cph], Dan Rabosky [ctb], Mike Grundler [ctb], Huateng Huang [ctb], Pascal Title [ctb], Liam Revell [ctb], Nicholas J. Matzke [ctb]

deepSTRAPP_1.0.0.tar.gz
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deepSTRAPP_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
deepSTRAPP/json (API)
NEWS

# Install 'deepSTRAPP' in R:
install.packages('deepSTRAPP', repos = c('https://maeldore.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/maeldore/deepstrapp/issues

Pkgdown/docs site:https://maeldore.github.io

Datasets:

On CRAN:

Conda:

6.61 score 1 stars 32 scripts 204 downloads 30 exports 76 dependencies

Last updated from:6f897d53fb. Checks:13 OK. Indexed: yes.

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source / vignettesOK331
linux-release-arm64OK293
linux-release-x86_64OK283
macos-release-arm64OK251
macos-release-x86_64OK350
macos-oldrel-arm64OK187
macos-oldrel-x86_64OK423
windows-develOK1101
windows-releaseOK1123
windows-oldrelOK1044
wasm-releaseOK189

Exports:BSM_to_phytools_simmapcompute_STRAPP_test_for_focal_timecut_contMap_for_focal_timecut_densityMap_for_focal_timecut_densityMaps_for_focal_timecut_phylo_for_focal_timeextract_diversification_data_melted_df_for_focal_timeextract_most_likely_ranges_from_densityMaps_for_focal_timeextract_most_likely_states_from_densityMaps_for_focal_timeextract_most_likely_trait_values_for_focal_timeextract_most_likely_trait_values_from_contMap_for_focal_timeis_dev_versionplot_BAMM_ratesplot_contMapplot_densityMaps_overlayplot_histogram_STRAPP_test_for_focal_timeplot_histograms_STRAPP_tests_over_timeplot_rates_through_timeplot_rates_vs_trait_data_for_focal_timeplot_rates_vs_trait_data_over_timeplot_STRAPP_pvalues_over_timeplot_traits_vs_rates_on_phylogeny_for_focal_timeplot_traits_vs_rates_on_phylogeny_over_timeprepare_diversification_dataprepare_trait_datarun_deepSTRAPP_for_focal_timerun_deepSTRAPP_over_timeselect_best_model_from_BioGeoBEARSselect_best_trait_model_from_geigerupdate_rates_and_regimes_for_focal_time

Dependencies:apeaskpassBAMMtoolsbitopscaToolscladoRcppcliclusterGenerationcodacodetoolscolorspacecombinatcowplotcpp11curlDEoptimdeSolvedigestdoParalleldplyrdunn.testexpmfarverfastmatchforeachgeigergenericsggplot2gluegplotsgtablegtoolsigraphisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigplyrpurrrqpdfquadprogR6RColorBrewerRcppRcppArmadillorlangS7scalesscatterplot3dstringistringrsubplexsystibbletidyrtidyselectutf8vctrsviridisLitewithr

Cut phylogenies

Maël Doré

Rendered fromcut_phylogenies.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-01-13
Started: 2025-08-15

deepSTRAPP: All tutorials

Maël Doré

Rendered fromdeepSTRAPP.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2025-10-17
Started: 2025-08-15

deepSTRAPP: Biogeographic range data

Maël Doré

Rendered fromdeepSTRAPP_biogeographic_data.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-01-13
Started: 2025-08-15

deepSTRAPP: Categorical trait data

Maël Doré

Rendered fromdeepSTRAPP_categorical_data.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-01-13
Started: 2025-08-15

deepSTRAPP: Continuous trait data

Maël Doré

Rendered fromdeepSTRAPP_continuous_data.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-01-13
Started: 2025-08-15

Explore STRAPP test options

Rendered fromexplore_STRAPP_test_types.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2025-12-22
Started: 2025-08-15

Main tutorial

Maël Doré

Rendered frommain_tutorial.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-01-13
Started: 2025-09-01

Model biogeographic range evolution

Maël Doré

Rendered frommodel_biogeographic_range_evolution.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2026-01-13
Started: 2025-08-15

Model categorical trait evolution

Maël Doré

Rendered frommodel_categorical_trait_evolution.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2025-12-29
Started: 2025-08-15

Model continuous trait evolution

Maël Doré

Rendered frommodel_continuous_trait_evolution.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2025-12-29
Started: 2025-09-18

Model diversification dynamics

Maël Doré

Rendered frommodel_diversification_dynamics.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2025-12-29
Started: 2025-08-15

Plot rates through time

Rendered fromplot_rates_through_time.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2025-12-29
Started: 2025-08-15

Readme and manuals

Help Manual

Help pageTopics
Template file for BAMM diversification analysesBAMM_template_diversification
Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) formatBSMs_to_phytools_simmaps BSM_to_phytools_simmap
Compute STRAPP to test for a relationship between diversification rates and trait datacompute_STRAPP_test_for_focal_time
Cut the phylogeny and continuous trait mapping for a given focal time in the pastcut_contMap_for_focal_time
Cut the phylogeny and posterior probability mapping of a categorical trait for a given focal time in the pastcut_densityMap_for_focal_time
Cut phylogenies and posterior probability mapping of each state for a given focal time in the pastcut_densityMaps_for_focal_time
Cut the phylogeny for a given time in the pastcut_phylo_for_focal_time
Data summarizing the evolution of geographic ranges in eelseel_biogeo_data
Data summarizing the evolution of feeding habits in eels using a 3-level factor as categorical traiteel_cat_3lvl_data
Extract diversification data from a BAMM_objectextract_diversification_data_melted_df_for_focal_time
Extract biogeographic range data mapped on a phylogeny at a given time in the pastextract_most_likely_ranges_from_densityMaps_for_focal_time
Extract categorical trait data mapped on a phylogeny at a given time in the pastextract_most_likely_states_from_densityMaps_for_focal_time
Extract trait data mapped on a phylogeny at a given time in the pastextract_most_likely_trait_values_for_focal_time
Extract continuous trait data mapped on a phylogeny at a given time in the pastextract_most_likely_trait_values_from_contMap_for_focal_time
Check whether deepSTRAPP is a development versionis_dev_version
Phylogeny and body mass data for extant and extinct mammals families/genera from Slater, 2013mammals
Plot diversification rates and regime shifts from BAMM on phylogenyplot_BAMM_rates
Plot continuous trait evolution on the treeplot_contMap
Plot posterior probabilities of states/ranges on phylogeny from densityMapsplot_densityMaps_overlay
Plot histogram of STRAPP test statistics to assess resultsplot_histogram_STRAPP_test_for_focal_time
Plot multiple histograms of STRAPP test statistics over time-stepsplot_histograms_STRAPP_tests_over_time
Plot evolution of diversification rates in relation to trait values over timeplot_rates_through_time
Plot rates vs. trait data for a given focal timeplot_rates_vs_trait_data_for_focal_time
Plot rates vs. trait data over time-stepsplot_rates_vs_trait_data_over_time
Plot evolution of p-values of STRAPP tests over timeplot_STRAPP_pvalues_over_time
Plot trait/range evolution vs. diversification rates and regime shifts on phylogenyplot_traits_vs_rates_on_phylogeny_for_focal_time
Plot multiple mapped phylogenies of trait/range evolution vs. diversification rates and regime shifts over time-stepsplot_traits_vs_rates_on_phylogeny_over_time
Dataset providing biogeographic range data for extant ponerine antsPonerinae_binary_range_table
Data summarizing the evolution of geographic ranges in Ponerinae ants using an old ill-calibrated phylogeny for illustrative purposesPonerinae_biogeo_data_old_calib
Data summarizing the evolution of fake size data in Ponerinae ants using a 2-level factor as categorical traitPonerinae_cat_2lvl_data_old_calib
Data summarizing the evolution of fake habitat data in Ponerinae ants using a 3-level factor as categorical traitPonerinae_cat_3lvl_data_old_calib
Data summarizing the evolution of a fake continuous trait in Ponerinae ants extracted for 10 MyaPonerinae_trait_cont_tip_data_10My
Dataset providing fake trait data for extant ponerine ants for illustrative purposesPonerinae_trait_tip_data
Dataset providing the extensive time-calibrated phylogeny of extant ponerine antsPonerinae_tree
Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants using an old calibration for illustrative purposesPonerinae_tree_old_calib
Run a full BAMM (Bayesian Analysis of Macroevolutionary Mixtures) workflowprepare_diversification_data
Map trait evolution on a time-calibrated phylogenyprepare_trait_data
Run deepSTRAPP to test for a relationship between diversification rates and trait data at a given focal timerun_deepSTRAPP_for_focal_time
Run deepSTRAPP to test for a relationship between diversification rates and trait data over multiple time stepsrun_deepSTRAPP_over_time
Compare model fits with AICc and Akaike's weightsselect_best_model_from_BioGeoBEARS
Compare trait evolutionary model fits with AICc and Akaike's weightsselect_best_trait_model_from_geiger
Update diversification rates/regimes mapped on a phylogeny up to a given time in the pastupdate_rates_and_regimes_for_focal_time
Dataset summarizing 1000 posterior samples of BAMM for extant whaleswhale_BAMM_object