API for secsse
Several Examined and Concealed States-Dependent Speciation and Extinction
| Global functions | |
|---|---|
| build_initStates_time | Source code |
| build_states | Source code |
| calc_ll_cpp | Source code |
| calc_ll_single_branch_cpp | Source code |
| calc_mus | Source code |
| check_input | Source code |
| check_ml_conditions | Source code |
| check_root_state_weight | Source code |
| check_traits | Source code |
| check_tree | Source code |
| cla_id_paramPos | Man page Source code |
| cla_secsse_loglik | Man page Source code |
| cla_secsse_ml | Man page Source code |
| cla_secsse_ml_func_def_pars | Man page Source code |
| collect_branches | Source code |
| collect_node_bars | Source code |
| condition | Source code |
| condition_root_edge | Source code |
| construct_row | Source code |
| construct_row_q | Source code |
| convert_transition_list | Source code |
| convert_transition_list_q | Source code |
| create_default_lambda_transition_matrix | Man page Source code |
| create_default_shift_matrix | Man page Source code |
| create_lambda_list | Man page Source code |
| create_mu_vector | Man page Source code |
| create_q_matrix | Man page Source code |
| create_q_matrix_int | Source code |
| create_states | Source code |
| ct_condition_cpp | Source code |
| default_params_doc | Man page Source code |
| eval_cpp | Source code |
| event_times | Man page Source code |
| example_phy_GeoSSE | Man page |
| expand_q_matrix | Man page Source code |
| extract_answ | Source code |
| extract_data | Source code |
| extract_par_vals | Man page Source code |
| fill_in | Man page Source code |
| generate_phy | Source code |
| get_rates | Source code |
| get_state_names | Source code |
| get_trait_states | Source code |
| get_weight_states | Source code |
| id_paramPos | Man page Source code |
| make_ggplot | Source code |
| master_loglik | Source code |
| master_ml | Source code |
| multi_loglik | Source code |
| penalty | Source code |
| phylo_vignette | Man page |
| plot_idparslist | Man page Source code |
| plot_state_exact | Man page Source code |
| prepare_full_lambdas | Man page Source code |
| print_init_ll | Source code |
| q_doubletrans | Man page Source code |
| replace_matrix | Source code |
| secsse | Man page |
| secsse-package | Man page |
| secsse_loglik | Man page Source code |
| secsse_loglik_choosepar | Source code |
| secsse_loglik_eval | Man page Source code |
| secsse_ml | Man page Source code |
| secsse_ml_func_def_pars | Man page Source code |
| secsse_sim | Man page Source code |
| secsse_sim_cpp | Source code |
| secsse_single_branch_loglik | Man page Source code |
| secsse_transform_parameters | Source code |
| set_and_check_structure_func | Source code |
| sortingtraits | Man page Source code |
| traits | Man page |
| transf_funcdefpar | Source code |
| transform_params_cla | Source code |
| transform_params_normal | Source code |
| update_complete_tree | Source code |
| update_values_transform | Source code |
| update_values_transform_cla | Source code |
