Man pages for secsse
Several Examined and Concealed States-Dependent Speciation and Extinction
| cla_id_paramPos | Parameter structure setting for cla_secsse It sets the... |
| cla_secsse_loglik | Likelihood for SecSSE model, using Rcpp Loglikelihood... |
| cla_secsse_ml | Maximum likehood estimation for (SecSSE) |
| cla_secsse_ml_func_def_pars | Maximum likehood estimation for (SecSSE) with parameter as... |
| create_default_lambda_transition_matrix | Helper function to create a default lambda list |
| create_default_shift_matrix | Helper function to create a default 'shift_matrix' list |
| create_lambda_list | Helper function to automatically create lambda matrices,... |
| create_mu_vector | Generate mus vector |
| create_q_matrix | Helper function to neatly setup a Q matrix, without... |
| default_params_doc | Default parameter documentation |
| 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... |
| extract_par_vals | Extract parameter values out of the result of a maximum... |
| fill_in | Helper function to enter parameter value on their right place |
| id_paramPos | Parameter structure setting Sets the parameters (speciation,... |
| phylo_vignette | A phylogenetic reconstuction to run the vignette |
| plot_idparslist | function to visualize the structure of the idparslist |
| plot_state_exact | Plot the local probability along a tree |
| prepare_full_lambdas | Prepares the entire set of lambda matrices for cla_secsse. It... |
| q_doubletrans | Basic Qmatrix Sets a Q matrix where double transitions are... |
| secsse_loglik | Likelihood for SecSSE model Loglikelihood calculation for the... |
| secsse_loglik_eval | Likelihood for SecSSE model Logikelihood calculation for the... |
| secsse_ml | Maximum likehood estimation for (SecSSE) |
| secsse_ml_func_def_pars | Maximum likehood estimation for (SecSSE) complex functions as... |
| secsse-package | secsse: Several Examined and Concealed States-Dependent... |
| secsse_sim | Function to simulate a tree, conditional on observing all... |
| secsse_single_branch_loglik | Likelihood for SecSSE model Loglikelihood calculation for the... |
| sortingtraits | Data checking and trait sorting In preparation for likelihood... |
| traits | A table with trait info to run the vignette |
