# deepSTRAPP: All tutorials

#### 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.