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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 uses,
please refer to the vignettes/tutorials below.
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 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").
● 2.1/
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").
● Model
diversification dynamics with BAMM within
deepSTRAPP:
vignette("model_diversification_dynamics").
● Test
different hypotheses:
vignette("explore_STRAPP_test_types").
● Explore
options for plotting diversification rates through time
in relation to trait data:
vignette("plot_rates_through_time").
● Handle
uncertainty in trait and rate estimates:
vignette("handle_uncertainty").
Explore the three strategies available: - ‘rates_only’: Only accounts
for diversification-rate uncertainty across BAMM posterior samples. -
‘paired’: Accounts for both diversification-rate and ancestral
trait/range reconstruction uncertainty by pairing BAMM posterior samples
with stochastic maps. - ‘full’: Accounts for both diversification-rate
and ancestral reconstruction uncertainty by evaluating every combination
of BAMM posterior samples and stochastic maps.
● Import
external analyses:
vignette("import_external_analyses").
Import and format results of external analyses of trait-evolution
histories and diversification dynamics, and make them ready-to-use as
inputs for a deepSTRAPP run.
● Cut
different types of (mapped) phylogenies for a given
focal-time: vignette("cut_phylogenies").
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.
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