AddFossilPoints |
Adds sampled fossils to a complete phylogeny |
AddStratIntervals |
Adds sampled stratigraphic intervals to a complete phylogeny |
generateMiSSEGreedyCombinations |
Combinations for Character-free State Speciation and Extinction Searching Greedily |
GeoHiSSE |
Hidden Geographic State Speciation and Extinction |
GeoHiSSE.old |
Original Hidden Geographic State Speciation and Extinction |
GetAICWeights |
Compute model weights |
GetFossils |
Get fossilized birth-death samples |
GetModelAveRates |
Model average rates at tips and nodes |
hisse |
Hidden State Speciation and Extinction |
hisse.null4.old |
Original Four state trait-independent Hidden State Speciation and Extinction |
hisse.old |
Original Hidden State Speciation and Extinction |
makeGeoHiSSELikelihood |
Export likelihood function for the GeoHiSSE model |
makeHiSSELikelihood |
Export likelihood function for the HiSSE model |
MarginRecon.old |
Original Ancestral State Estimation based on Marginal Reconstruction |
MarginReconGeoSSE |
Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. |
MarginReconGeoSSE.old |
Original Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. |
MarginReconHiSSE |
Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model. |
MarginReconMiSSE |
Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models. |
MarginReconMuHiSSE |
Ancestral State Estimation based on Marginal Reconstruction for the MuSSE and MuHiSSE models. |
MiSSE |
Character-free State Speciation and Extinction |
MiSSEGreedy |
Character-free State Speciation and Extinction Searching Greedily |
MiSSENet |
A function for catching bad model fits from MiSSEGreedy |
MuHiSSE |
Multicharacter Hidden State Speciation and Extinction |
ParDrop |
Transition Rate matrix generator |
ParEqual |
Transition Rate matrix generator |
plot.geohisse.states |
Plotting function geohisse.states objects |
plot.hisse.states |
Plotting function hisse.states objects |
plot.misse.states |
Plotting function misse.states objects |
plot.muhisse.states |
Plotting function muhisse.states objects |
PlotMisseSpace |
Plotting function for MiSSEGreedy |
ProcessSimSample |
Process fossilized birth-death sample of lineages |
ProcessSimStrat |
Process fossilized birth-death sample of lineages into stratigraphic intervals. |
PruneRedundantModels |
Prune Redundant Models |
SimToPhylo |
Convert simulated result to a tree |
SimulateGeoHiSSE |
Simulate under a GeoHiSSE model |
SimulateHisse |
Simulate under a HiSSE model |
SummarizeMiSSEGreedy |
Summarize Results of the Greedy Algorithm |
SupportRegion.old |
Adaptive Sampling of the Likelihood Surface |
SupportRegionGeoSSE |
Adaptive Sampling of the Likelihood Surface under the new version of GeoHiSSE model |
SupportRegionGeoSSE.old |
Adaptive Sampling of the Likelihood Surface under the original GeoHiSSE model |
SupportRegionHiSSE |
Adaptive Sampling of the Likelihood Surface under the new version of HiSSE |
SupportRegionMiSSE |
Adaptive Sampling of the Likelihood Surface under MiSSE |
SupportRegionMuHiSSE |
Adaptive Sampling of the Likelihood Surface under MuHiSSE |
TipCorrelation |
Phylogenetic independent contrasts using tip rates |
TranslateParsMakerGeoHiSSE |
Key to translate GeoHiSSE into ClaSSE |
TransMatMaker.old |
Transition Rate matrix generator |
TransMatMakerGeoHiSSE |
Transition Rate matrix generator for the GeoHiSSE model |
TransMatMakerGeoHiSSE.old |
Transition Rate matrix generator for the GeoHiSSE model |
TransMatMakerHiSSE |
Transition Rate matrix generator for the HiSSE model |
TransMatMakerMuHiSSE |
Transition Rate matrix generator for the MuHiSSE model |