Hidden State Speciation and Extinction
Adds sampled fossils to a complete phylogeny
Adds sampled stratigraphic intervals to a complete phylogeny
Combinations for Character-free State Speciation and Extinction Search...
Original Hidden Geographic State Speciation and Extinction
Hidden Geographic State Speciation and Extinction
Compute model weights
Get fossilized birth-death samples
Original Hidden State Speciation and Extinction
Hidden State Speciation and Extinction
Original Four state trait-independent Hidden State Speciation and Exti...
Export likelihood function for the GeoHiSSE model
Export likelihood function for the HiSSE model
Original Ancestral State Estimation based on Marginal Reconstruction
Original Ancestral State Estimation based on Marginal Reconstruction f...
Ancestral State Estimation based on Marginal Reconstruction for the Ge...
Ancestral State Estimation based on Marginal Reconstruction for the Hi...
Ancestral State Estimation based on Marginal Reconstruction for the Mi...
Ancestral State Estimation based on Marginal Reconstruction for the Mu...
Character-free State Speciation and Extinction
Character-free State Speciation and Extinction Searching Greedily
A function for catching bad model fits from MiSSEGreedy
Model average rates at tips and nodes
Multicharacter Hidden State Speciation and Extinction
Plotting function geohisse.states objects
Plotting function hisse.states objects
Plotting function misse.states objects
Plotting function for MiSSEGreedy
Plotting function muhisse.states objects
Process fossilized birth-death sample of lineages
Process fossilized birth-death sample of lineages into stratigraphic i...
Prune Redundant Models
Convert simulated result to a tree
Simulate under a GeoHiSSE model
Simulate under a HiSSE model
Summarize Results of the Greedy Algorithm
Adaptive Sampling of the Likelihood Surface
Adaptive Sampling of the Likelihood Surface under the original GeoHiSS...
Adaptive Sampling of the Likelihood Surface under the new version of G...
Adaptive Sampling of the Likelihood Surface under the new version of H...
Adaptive Sampling of the Likelihood Surface under MiSSE
Adaptive Sampling of the Likelihood Surface under MuHiSSE
Phylogenetic independent contrasts using tip rates
Key to translate GeoHiSSE into ClaSSE
Transition Rate matrix generator
Transition Rate matrix generator for the GeoHiSSE model
Transition Rate matrix generator for the HiSSE model
Transition Rate matrix generator for the MuHiSSE model
Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.