hisse v1.9.5
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Hidden State Speciation and Extinction
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>.
Functions in hisse
| Name | Description | |
| GeoHiSSE | Hidden Geographic State Speciation and Extinction | |
| TranslateParsMakerGeoHiSSE | Key to translate GeoHiSSE into ClaSSE | |
| MuHiSSE | Multicharacter Hidden State Speciation and Extinction | |
| fGeoHiSSE | fast Hidden Geographic State Speciation and Extinction | |
| Compute Model Weights | Compute model weights | |
| BisseToHisse | BisseToHisse | |
| MiSSE | Character-free State Speciation and Extinction | |
| SimulateGeoHiSSE | Simulate under a GeoHiSSE model | |
| hisse | Hidden State Speciation and Extinction | |
| MiSSEGreedy | Character-free State Speciation and Extinction searching greedily | |
| MarginReconMiSSE | Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models. | |
| plot.geohisse.states | Plotting function geohisse.states objects | |
| Model averaged rates | Model average rates at tips and nodes | |
| MarginRecon | Ancestral State Estimation based on Marginal Reconstruction | |
| MarginReconGeoSSE | Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. | |
| Model averaged equilibrium frequencies | Model average equlibrium frequencies | |
| MarginReconfGeoSSE | fast Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. | |
| MarginReconMuHiSSE | Ancestral State Estimation based on Marginal Reconstruction for the MuSSE and MuHiSSE models. | |
| TransMatMaker | Transition Rate matrix generator | |
| SupportRegionMuHiSSE | Adaptive Sampling of the Likelihood Surface under MuHiSSE | |
| hisse.null4 | Four state trait-independent Hidden State Speciation and Extinction | |
| SimulateHisse | Simulate under a HiSSE model | |
| SupportRegion | Adaptive Sampling of the Likelihood Surface | |
| makeHiSSELikelihood | Export likelihood function for the HiSSE model | |
| SupportRegionGeoSSE | Adaptive Sampling of the Likelihood Surface under GeoSSE | |
| SupportRegionMiSSE | Adaptive Sampling of the Likelihood Surface under MiSSE | |
| plot.muhisse.states | Plotting function muhisse.states objects | |
| TransMatMakerGeoHiSSE | Transition Rate matrix generator for the GeoHiSSE model | |
| TransMatMakerMuHiSSE | Transition Rate matrix generator for the MuHiSSE model | |
| SimToPhylo | Convert simulated result to a tree | |
| plot.hisse.states | Plotting function hisse.states objects | |
| plot.misse.states | Plotting function geohisse.states objects | |
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Vignettes of hisse
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Details
| Date | 2019-07-09 |
| License | GPL (>= 2) |
| VignetteBuilder | knitr |
| RoxygenNote | 6.1.1 |
| NeedsCompilation | yes |
| Packaged | 2019-07-11 18:06:14 UTC; jmbeauli |
| Repository | CRAN |
| Date/Publication | 2019-07-11 21:43:12 UTC |
| depends | ape , deSolve , GenSA , nloptr , subplex |
| imports | data.table , diversitree , methods , parallel , phytools , plotrix |
| suggests | knitr , testthat |
| Contributors | Brian O'Meara, Daniel Caetano |
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