Man pages for richelbilderbeek/splendid
Likelihood model for diversification processes with single lineage rate shifts
| cat2 | cat2 |
| check_input | Check input |
| create_data_file_name | Create data file name |
| create_results_file_name | Create results file name |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| get_conds | Sim Conditionings |
| get_function_names | Get function names |
| get_logliks | Loglik functions |
| get_model_name | Cut word "loglik" from a name |
| get_model_names | Check if provided models make sense |
| get_n_0s | Starting species |
| get_param_names | Get the names of the parameters used in the model |
| get_pkg_name | Get package name |
| get_sim_conds | Conditioning functions |
| l_2_brts | Convert l_0 to brts |
| lik_cond_0 | Lik conditioning 0 |
| lik_cond_1 | Lik conditioning 1 |
| lik_cond_2 | Lik conditioning 2 |
| lik_cond_3 | Lik conditioning 3 |
| loglik_dummy | Dummy loglik function |
| main_save_files | Save data and results |
| ml | sls Maximum Likelihood |
| pars_transform_back | Transform parameters back |
| pars_transform_forward | Transform parameters |
| print_info | Print information about simulated data |
| p_transition_matrix | Transition matrix builder |
| sim | Simulate an sls process |
| sim_adapt_l_matrix_size | Increase the size of the l_0 table if needed |
| sim_check_survival | Check if a clade survives untile final_time |
| sim_cond_0 | Sim conditioning 0 |
| sim_cond_1 | Sim conditioning 1 |
| sim_cond_2 | Sim conditioning 2 |
| sim_cond_3 | Sim conditioning 3 |
| sim_cond_check | Check if inputs for conditioning make sense |
| sim_conditioning | Check if the conditioning is fulfilled |
| sim_cut_l_matrix | Cuts the l_0 table only to the useful rows |
| sim_decide_event | Determines the event |
| sim_event | Apply the event to the simulation |
| sim_events | Events |
| sim_get_brts | Extract the branching times from data |
| sim_get_motherclade | Get the motherclade of a given clade |
| sim_get_n_0 | Initialize n for a new clade |
| sim_get_pars | Get parameters |
| sim_get_pool | Get the pool from the l_0 table |
| sim_get_shifts_info | Get shifts' information |
| sim_get_standard_l_2 | Creates the standard l_2 |
| sim_get_t_0 | Initialize t for a new clade |
| sim_initialize_data_new_clade | Initialize data for a new clade |
| sim_read_l_1 | Reads l_1 |
| sim_sample_deltas | Sample deltas for Doob-Gillespie |
| sim_use_event | Update data and time given the event |
| sls_main | Run the full sls routine |
