Several Examined and Concealed States-Dependent Speciation and
Extinction
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Documentation for package ‘secsse’ version 2.6.0
Help Pages
| cla_id_paramPos | Parameter structure setting for cla_secsse |
| cla_secsse_eval | Likelihood for SecSSE model, using Rcpp |
| cla_secsse_loglik | Likelihood for SecSSE model, using Rcpp |
| 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 |
| create_default_lambda_list | helper function to create a default lambda list |
| create_default_q_list | helper function to create a default q_matrix list |
| create_lambda_matrices | helper function to automatically create lambda matrices, based on input |
| create_mus | function to generate generic mus vector |
| create_transition_matrix | helper function to neatly setup a Q matrix, without transitions to concealed states (only observed transitions shown) |
| event_times | Event times of a (possibly non-ultrametric) phylogenetic tree |
| example_phy_GeoSSE | A phylogeny with traits at the tips |
| expand_q_matrix | function to expand an existing q_matrix to a number of concealed states |
| extract_par_vals | function to extract parameter values out of the result of a maximum likelihood inference run. |
| fill_in | helper function to enter parameter value on their right place |
| id_paramPos | Parameter structure setting |
| phy | A phylogeny with traits at the tips |
| phylo_Vign | A phylogenetic reconstuction to run the vignette |
| plot_state_exact | function to plot the local probability along the tree, including the branches |
| plot_state_exact_cla | function to plot the local probability along the tree, including the branches, for the CLA model. |
| prepare_full_lambdas | Prepares the entire set of lambda matrices for cla_secsse. |
| q_doubletrans | Basic Qmatrix |
| secsse_loglik | Likelihood for SecSSE model |
| secsse_loglik_eval | 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. |
| secsse_sim | Function to simulate a tree, conditional on observing all states. |
| sortingtraits | Data checking and trait sorting |
| traitinfo | A table with trait info to run the vignette |