Package: deepSTRAPP 1.1.1

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_1.1.1.tar.gz
deepSTRAPP_1.1.1.zip(r-4.7-x86_64)deepSTRAPP_1.1.1.zip(r-4.7-arm64)deepSTRAPP_1.1.1.zip(r-4.6-x86_64)deepSTRAPP_1.1.1.zip(r-4.6-arm64)deepSTRAPP_1.1.1.zip(r-4.5-x86_64)
deepSTRAPP_1.1.1.tgz(r-4.6-x86_64)deepSTRAPP_1.1.1.tgz(r-4.6-arm64)deepSTRAPP_1.1.1.tgz(r-4.5-x86_64)deepSTRAPP_1.1.1.tgz(r-4.5-arm64)
deepSTRAPP_1.1.1.tar.gz(r-4.7-arm64)deepSTRAPP_1.1.1.tar.gz(r-4.7-x86_64)deepSTRAPP_1.1.1.tar.gz(r-4.6-arm64)deepSTRAPP_1.1.1.tar.gz(r-4.6-x86_64)
deepSTRAPP_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
deepSTRAPP/json (API)

# 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:

6.98 score 2 stars 34 scripts 394 downloads 39 exports 76 dependencies

Last updated from:048beb26ea. Checks:14 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK213
linux-devel-x86_64OK318
source / vignettesOK613
linux-release-arm64OK240
linux-release-x86_64OK279
macos-release-arm64FAIL61
macos-release-x86_64OK401
macos-oldrel-arm64OK218
macos-oldrel-x86_64OK539
windows-devel-arm64OK373
windows-devel-x86_64OK1199
windows-release-arm64OK349
windows-release-x86_64OK1162
windows-oldrel-x86_64OK1087
wasm-releaseOK166

Exports:aggregate_contMapsbuild_BAMM_objectcompute_STRAPP_test_for_focal_timeconvert_BSM_to_simmapconvert_BSMs_to_simmapsconvert_contsimmap_to_contMapsconvert_simmaps_to_densityMapscut_contMap_for_focal_timecut_contMaps_for_focal_timecut_densityMap_for_focal_timecut_densityMaps_for_focal_timecut_phylo_for_focal_timecut_simmap_for_focal_timecut_simmaps_for_focal_timeextract_all_trait_values_for_focal_timeextract_diversification_data_melted_df_for_focal_timeextract_most_likely_trait_values_for_focal_timeextract_trait_data_melted_df_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_dataprune_BAMM_objectrun_deepSTRAPP_for_focal_timerun_deepSTRAPP_over_timeselect_best_model_from_BioGeoBEARSselect_best_trait_model_from_geigersubset_BAMM_objectupdate_rates_and_regimes_for_focal_time

Dependencies:apeaskpassBAMMtoolsbitopscaToolscladoRcppcliclusterGenerationcodacodetoolscolorspacecombinatcowplotcpp11curlDEoptimdeSolvedigestdoParalleldplyrdunn.testexpmfarverfastmatchforeachgeigergenericsggplot2gluegplotsgtablegtoolsigraphisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigplyrpurrrqpdfquadprogR6RColorBrewerRcppRcppArmadillorlangS7scalesscatterplot3dstringistringrsubplexsystibbletidyrtidyselectutf8vctrsviridisLitewithr

Cut phylogenies
Rendered fromcut_phylogenies.Rmdusingknitr::rmarkdown

Last update: 2026-10-21
Started: 2025-08-15

deepSTRAPP: Biogeographic range data
Rendered fromdeepSTRAPP_biogeographic_data.Rmdusingknitr::rmarkdown

Last update: 2026-10-21
Started: 2025-08-15

deepSTRAPP: Categorical trait data
Rendered fromdeepSTRAPP_categorical_data.Rmdusingknitr::rmarkdown

Last update: 2026-10-21
Started: 2025-08-15

deepSTRAPP: Continuous trait data
Rendered fromdeepSTRAPP_continuous_data.Rmdusingknitr::rmarkdown

Last update: 2026-10-21
Started: 2025-08-15

Main tutorial
Rendered frommain_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-10-21
Started: 2025-09-01

Import external analyses
Plot pre-rendered graph
Rendered fromimport_external_analyses.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-08-24

Model continuous trait evolution
Rendered frommodel_continuous_trait_evolution.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2025-09-18

Model diversification dynamics
Rendered frommodel_diversification_dynamics.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2025-08-15

Explore STRAPP test options
Rendered fromexplore_STRAPP_test_types.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2025-08-15

Handle uncertainty
Rendered fromhandle_uncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2026-08-24

Model biogeographic range evolution
Rendered frommodel_biogeographic_range_evolution.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2025-08-15

Model categorical trait evolution
Rendered frommodel_categorical_trait_evolution.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2025-08-15

Plot rates through time
Rendered fromplot_rates_through_time.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2025-08-15

deepSTRAPP: All tutorials
Main tutorial | Quick-to-run example | Advanced uses / tutorials | 1/ Full deepSTRAPP workflows on different types of data | 2/ Explore options for trait evolution | 3/ Explore options for BAMM | 4/ Explore the STRAPP test options | 5/ Plot rates through time (RTT) | 6/ Handle uncertainty | 7/ Import external analyses | 8/ Cut phylogenies
Rendered fromdeepSTRAPP.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2025-08-15

Readme and manuals

Help Manual

Help pageTopics
Aggregate a list of contMaps into a unique mean/median contMapaggregate_contMaps
Template file for BAMM diversification analysesBAMM_template_diversification
Build a BAMM object for a deepSTRAPP runbuild_BAMM_object
Compute STRAPP to test for a relationship between diversification rates and trait datacompute_STRAPP_test_for_focal_time
Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) formatconvert_BSMs_to_simmaps convert_BSM_to_simmap
Convert a contsimmap object into a list of contMapsconvert_contsimmap_to_contMaps
Convert simmaps into densityMaps suitable for deepSTRAPPconvert_simmaps_to_densityMaps
Cut the phylogeny and continuous trait mapping for a given focal time in the pastcut_contMap_for_focal_time
Cut the phylogenies and continuous trait mappings of a list of contMaps for a given focal time in the pastcut_contMaps_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
Cut the phylogeny and categorical trait/range mapping for a given focal time in the pastcut_simmap_for_focal_time
Cut the phylogenies and categorical trait/range mappings of a list of simmaps for a given focal time in the pastcut_simmaps_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 all trait data from stochastic maps at a given time in the pastextract_all_trait_values_for_focal_time
Extract diversification data from a BAMM_objectextract_diversification_data_melted_df_for_focal_time
Extract most likely trait data mapped on a phylogeny at a given time in the pastextract_most_likely_trait_values_for_focal_time
Extract trait data from a trait_data objectextract_trait_data_melted_df_for_focal_time
Phylogeny and body mass data for extant and extinct mammal 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 mean 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
Prune a BAMM object to a subset of tipsprune_BAMM_object
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
Subset a BAMM object before a deepSTRAPP runsubset_BAMM_object
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