deepSTRAPP: All tutorials

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Maël Doré

2026-01-13

Main tutorial

Quick-to-run example

A simple use-case that shows how deepSTRAPP can be used to test for differences in diversification rates between two trait states along evolutionary times is available here and within R: vignette("main_tutorial").

This tutorial presents the main functions in a typical deepSTRAPP workflow.
For more advanced used, please refer to the vignettes/tutorials below.

Advanced uses / tutorials

This vignette points to tutorials detailing how to use the [deepSTRAPP] package beyond the simple use-case presented in the README file and also available here: vignette("main_tutorial").

The following tutorials present more advanced usages of deepSTRAPP. They provide explanations on available arguments and interpretations of results of deepSTRAPP across multiple type of data.

1/ Full deepSTRAPP workflows on different types of data

● 1.1/ Full deepSTRAPP workflow for continuous trait data: vignette("deepSTRAPP_continuous_data").

● 1.2/ Full deepSTRAPP workflow for categorical trait data with 3-levels: vignette("deepSTRAPP_categorical_data").

● 1.3/ Full deepSTRAPP workflow for biogeographic range data: vignette("deepSTRAPP_biogeographic_data").

2/ Explore options for trait evolution

● 2.1/ Model evolution of continuous trait data: vignette("model_continuous_trait_evolution").

● 2.2/ Model evolution of categorical trait data: vignette("model_categorical_trait_evolution").

● 2.3/ Model evolution of biogeographic range data: vignette("model_biogeographic_range_evolution").

3/ Explore options for BAMM

● Model diversification dynamics with BAMM within deepSTRAPP: vignette("model_diversification_dynamics").

4/ Explore the STRAPP test options

● Test different hypotheses: vignette("explore_STRAPP_test_types").

Type of STRAPP tests: two-tailed vs. one-tailed.
Continuous: “negative” or “positive” correlation.
Binary with hypothesis: (A > B) vs. (B > A).
Multinominal: Hypotheses for all post hoc tests.

5/ Plot rates through time (RTT)

● Explore options for plotting diversification rates through time in relation to trait data: vignette("plot_rates_through_time").

6/ Cut phylogenies

● Cut different types of (mapped) phylogenies for a given focal-time: vignette("cut_phylogenies").

time-calibrated phylogenies.
contMap for continuous traits.
densityMap for categorical and biogeographic traits.
BAMM_object for diversification dynamics.

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.