Compute model weights
Character-free State Speciation and Extinction Searching Greedily
Adds sampled fossils to a complete phylogeny
Adds sampled stratigraphic intervals to a complete phylogeny
Hidden Geographic State Speciation and Extinction
Character-free State Speciation and Extinction
Original Hidden Geographic State Speciation and Extinction
Get fossilized birth-death samples
Multicharacter Hidden State Speciation and Extinction
A function for catching bad model fits from MiSSEGreedy
Simulate under a GeoHiSSE model
Hidden State Speciation and Extinction
Prune Redundant Models
Process fossilized birth-death sample of lineages into stratigraphic intervals.
Process fossilized birth-death sample of lineages
Plotting function for MiSSEGreedy
generateMiSSEGreedyCombinations
Combinations for Character-free State Speciation and Extinction Searching Greedily
Summarize Results of the Greedy Algorithm
Phylogenetic independent contrasts using tip rates
TranslateParsMakerGeoHiSSE
Key to translate GeoHiSSE into ClaSSE
Original Hidden State Speciation and Extinction
Original Ancestral State Estimation based on Marginal Reconstruction
Original Four state trait-independent Hidden State Speciation and Extinction
Original Ancestral State Estimation based on Marginal Reconstruction for
the GeoSSE and GeoHiSSE models.
Ancestral State Estimation based on Marginal Reconstruction for
the GeoSSE and GeoHiSSE models.
Export likelihood function for the HiSSE model
Ancestral State Estimation based on Marginal Reconstruction for
the HiSSE model.
Ancestral State Estimation based on Marginal Reconstruction for
the MuSSE and MuHiSSE models.
Ancestral State Estimation based on Marginal Reconstruction for
the MiSSE models.
Export likelihood function for the GeoHiSSE model
Plotting function muhisse.states objects
Adaptive Sampling of the Likelihood Surface
Transition Rate matrix generator for the HiSSE model
Simulate under a HiSSE model
Transition Rate matrix generator for the GeoHiSSE model
Adaptive Sampling of the Likelihood Surface under MiSSE
Plotting function geohisse.states objects
Transition Rate matrix generator for the MuHiSSE model
Plotting function hisse.states objects
Model average rates at tips and nodes
Adaptive Sampling of the Likelihood Surface under the new version of HiSSE
Plotting function misse.states objects
Convert simulated result to a tree
Transition Rate matrix generator
Adaptive Sampling of the Likelihood Surface under MuHiSSE
Adaptive Sampling of the Likelihood Surface under the new version of GeoHiSSE model
Adaptive Sampling of the Likelihood Surface under the original GeoHiSSE model