Several Examined and Concealed States-Dependent Speciation and
Extinction
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Documentation for package ‘secsse’ version 2.1.7
Help Pages
| cla_id_paramPos | Parameter structure setting for cla_secsse |
| cla_secsse_loglik | Likelihood for SecSSE model |
| cla_secsse_ml | Maximum likehood estimation for (SecSSE) |
| cla_secsse_ml_func_def_pars | Maximum likehood estimation for (SecSSE) with parameter as complex functions. Cladogenetic version |
| event_times | Event times of a (possibly non-ultrametric) phylogenetic tree |
| example_phy_GeoSSE | A phylogeny with traits at the tips |
| id_paramPos | Parameter structure setting |
| phy | A phylogeny with traits at the tips |
| phylo_Vign | A phylogenetic reconstuction to run the vignette |
| prepare_full_lambdas | Prepares the entire set of lambda matrices for cla_secsse. |
| q_doubletrans | Basic Qmatrix |
| secsse_loglik | Likelihood for SecSSE model |
| secsse_ml | Maximum likehood estimation for (SecSSE) |
| secsse_ml_func_def_pars | Maximum likehood estimation for (SecSSE) with parameter as complex functions. |
| sortingtraits | Data checking and trait sorting |
| traitinfo | A table with trait info to run the vignette |