deepSTRAPP: All tutorials"

In deepSTRAPP: Test for Differences in Diversification Rates over Time

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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.
  

deepSTRAPP documentation built on Jan. 20, 2026, 1:06 a.m.