Test for Differences in Diversification Rates over Time
Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochast...
Compute STRAPP to test for a relationship between diversification rate...
Cut the phylogeny and continuous trait mapping for a given focal time ...
Cut the phylogeny and posterior probability mapping of a categorical t...
Cut phylogenies and posterior probability mapping of each state for a ...
Cut the phylogeny for a given time in the past
Extract diversification data from a BAMM_object
Extract biogeographic range data mapped on a phylogeny at a given time...
Extract categorical trait data mapped on a phylogeny at a given time i...
Extract trait data mapped on a phylogeny at a given time in the past
Extract continuous trait data mapped on a phylogeny at a given time in...
Check whether deepSTRAPP is a development version
Plot diversification rates and regime shifts from BAMM on phylogeny
Plot continuous trait evolution on the tree
Plot posterior probabilities of states/ranges on phylogeny from densit...
Plot histogram of STRAPP test statistics to assess results
Plot multiple histograms of STRAPP test statistics over time-steps
Plot evolution of diversification rates in relation to trait values ov...
Plot rates vs. trait data for a given focal time
Plot rates vs. trait data over time-steps
Plot evolution of p-values of STRAPP tests over time
Plot trait/range evolution vs. diversification rates and regime shifts...
Plot multiple mapped phylogenies of trait/range evolution vs. diversif...
Run a full BAMM (Bayesian Analysis of Macroevolutionary Mixtures) work...
Map trait evolution on a time-calibrated phylogeny
Run deepSTRAPP to test for a relationship between diversification rate...
Run deepSTRAPP to test for a relationship between diversification rate...
Compare model fits with AICc and Akaike's weights
Compare trait evolutionary model fits with AICc and Akaike's weights
Update diversification rates/regimes mapped on a phylogeny up to a giv...
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.
Useful links