Man pages for Giappo/sls
Likelihood model for diversification processes with single lineage rate shifts
| cat2 | cat2 |
| combine_ddd | Combine pn |
| combine_ddd_nodiv | Combine pn in the old wrong way |
| combine_pns | Combine pn |
| combine_pns0 | Combine pn (basic) |
| combine_pns_nodiv | Combine pn in the old wrong way |
| create_data_file_name | Create data file name |
| create_results_file_name | Create results file name |
| cut_loglik_from_name | Cut word "loglik" from a name |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| DFT | dft |
| d_t | BISSE's D |
| e_t | BISSE's E |
| get_function_names | Get function names |
| get_model_names | Check if provided models make sense |
| get_param_names | Get the names of the parameters used in the sls model |
| get_pkg_name | Get package name |
| IDFT | Inverse dft |
| loglik_bisse | BISSE loglik |
| loglik_bisse2 | BISSE loglik |
| loglik_bisse_shift | BISSE loglik with shift |
| loglik_bisse_shift2 | BISSE loglik shift |
| loglik_DDD | DDD-likelihood |
| loglik_preshift | Calculates the preshift loglik using convolutions |
| loglik_preshift2 | Calculates the preshift loglik using convolutions |
| loglik_preshift_nodiv | Calculates the preshift loglik using convolutions |
| loglik_preshift_unobs | Calculates the preshift loglik using convolutions |
| loglik_sls_p | P-likelihood |
| loglik_sls_p2 | P-likelihood |
| loglik_sls_p2_nodiv | P-likelihood (with no division) |
| loglik_sls_p_dummy | P-likelihood dummy |
| loglik_sls_p_dummy_nodiv | P-likelihood (with no division) |
| loglik_sls_p_nodiv | P-likelihood (with no division) |
| loglik_sls_q | Q-likelihood |
| loglik_sls_q_nodiv | Q-likelihood |
| main_save_files | Save data and results |
| one_minus_pt | 1 - Pt |
| one_minus_ut | 1 - ut |
| pars_transform_back | Transform parameters back |
| pars_transform_forward | Transform parameters |
| Pc_1shift | sls-conditioning |
| phase_factor | Fourier term |
| pn | Pn |
| pn_bar | Pn accounting for extinctions after the shifts |
| print_info | Print information about simulated data |
| p_t | Pt |
| P_transition_matrix | Transition matrix builder |
| 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_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_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 sls 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_check_input | Check input |
| sls_conds | Conditionings |
| sls_l_2_brts | Convert l_0 to brts |
| sls_loglik_rhs | Builds the right hand side of the ODE set |
| sls_logliks_div | Logliks with division |
| sls_logliks_dummy | Logliks with dummy shift |
| sls_logliks_experiment | Logliks for the experiment |
| sls_logliks_nodiv | Logliks with no division |
| sls_main | Run the full sls routine |
| sls_main_dummy | Run the full sls routine with dummy shift |
| sls_ML | sls Maximum Likelihood |
| sls_ml_dummy | sls Maximum Likelihood |
| sls_n_0s | Starting species |
| sls_sim | Simulate an sls process |
| ut | ut |
