| approximate_brts | Approximate the branching times to a fixed resolution. Events... |
| brts2time_intervals_and_births | Converts branching times to 'time intervals between branching... |
| calculate_condprob | Calculate conditional probability: user mode |
| cat2 | cat2 |
| check_brts | Check 'brts' |
| check_cond | Check 'cond' |
| check_condprob_eq | Check "equation" for conditional probability |
| check_lx | Check lx |
| check_n_0 | Check 'n_0' |
| check_pars | Check mbd pars |
| check_pc | Check conditional probability |
| check_q_vector | Check q_t |
| check_seed | Check 'seed' |
| check_sum_probs | Check the vectors of probability sums computed during... |
| condprob | Calculate conditional probability: loglik mode |
| condprob_dp | Auxilary function for cond_prob_p, computing rhs |
| condprob_dp_absorb | Auxilary function for cond_prob_p, computing rhs |
| condprob_dp_absorb_lambda | Calculates the lambda component of dp |
| condprob_dp_absorb_mu | Calculates the mu component of dp |
| condprob_dp_absorb_rhs | Auxilary function for cond_prob_p, computing rhs |
| condprob_dp_lambda | Calculates the lambda component of dp |
| condprob_dp_mu | Calculates the mu component of dp |
| condprob_dp_nu | Calculates the nu component of dp |
| condprob_dp_rhs | Auxilary function for cond_prob_p, computing rhs |
| condprob_dq | Auxilary function for cond_prob_q, creating rhs |
| condprob_dq_absorb | Auxilary function for cond_prob_q, creating rhs |
| condprob_dq_absorb_lambda | Calculates the lambda component of dq |
| condprob_dq_absorb_mu | Calculates the mu component of dq |
| condprob_dq_absorb_rhs | Auxilary function for cond_prob_q, creating rhs |
| condprob_dq_lambda | Calculates the lambda component of dq |
| condprob_dq_mu | Calculates the mu component of dq |
| condprob_dq_nu | Calculates the nu component of dq |
| condprob_dq_rhs | Auxilary function for cond_prob_q, creating rhs |
| condprob_nee | Conditional probability using Nee et al's approach |
| condprob_nu_matrix_p | Creates vector of parameters for the conditional probability... |
| condprob_nu_matrix_q | Creates vector of parameters for the conditional probability... |
| condprob_p | Conditional probability calculated with the P-approach |
| condprob_parmsvec | Creates vector of parameters for the conditional probability |
| condprob_p_n1_n2 | Conditional probability P(n1, n2) for all the states n1 and... |
| condprob_q | Conditional probability calculated with the Q-approach |
| condprob_q_m1_m2 | Conditional probability Q(m1, m2) for all the states m1 and... |
| condprob_sim | Estimates conditional probability using simulations |
| count_n_mb_events | Count the number of multiple speciation events |
| count_percentage_mb_events | Count the percentage of multiple speciation events |
| create_a | The A matrix |
| create_a_slow | The A matrix |
| create_b | B matrix |
| create_data_file_name | Create data file name |
| create_empty_phylo | Create an empty phylogeny |
| create_n | N matrix |
| create_results_file_name | Create results file name |
| create_singleton_phylo | Create an empty phylogeny |
| cut_loglik_from_name | Cut word "loglik" from a name |
| default_lx | Default value for lx |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| deliver_loglik | Delivers the likelihood at the end of mbd_loglik |
| estimate_n_taxa | Estimate approximately the expected number of taxa |
| evaluate_sim | Establish whether the outcome of the simulation is in... |
| file_path | Like file.path, but cooler |
| get_function_names | Get function names |
| get_info_l_matrix | Extract information from the l-table |
| get_model_names | Check if provided models make sense |
| get_nee_pars | Calculate the Nee et al's equivalent parameters, starting... |
| get_param_names | Get the names of the parameters used in the mbd model |
| get_pars_filename | Create an empty phylogeny |
| get_pkg_name | Get package name |
| hyper_matrix0 | Function to build a matrix, used in creating the A and B... |
| hyper_matrix1 | Function to build a matrix, used in creating the A and B... |
| hyper_matrix2 | Function to build a matrix, used in creating the A and B... |
| initialize_l_matrix | Initialize the l-table |
| initialize_q_t | Initialize the vector q_t for mbd_loglik |
| is_pmb | Test for pure birth in mbd_loglik |
| main_save_files | Save data and results |
| max_lx | Maximum allowed value for lx |
| max_lx_condprob | Maximum allowed value for lx in condprob |
| mbd_condprob_eqs | Eqs for condprob |
| mbd_conds | Conditionings |
| mbd_experiment_logliks | Logliks for the experiment |
| mbd_experiment_pars | Generates parameters for the mbd experiment |
| mbd_integrate | performs integration of the ode |
| mbd_loglik | Calculates the likelihood for a multiple birth-death process |
| mbd_loglik_rhs | Builds the right hand side of the ODE set for multiple birth... |
| mbd_logliks_function | Loglik functions in mbd package |
| mbd_main | Run the full mbd routine |
| mbd_ml | Maximization of the loglikelihood under a multiple... |
| mbd_ode_fortran | Performs the integration of the ode using FORTRAN code |
| mbd_sim | Creates simulated trees under the multiple birth death... |
| mbd_solve | mbd ODE system integrator |
| mbd_solve_methode | mbd ODE system integrator for a specific ode method |
| min_lx_condprob | Minimum allowed value for lx in condprob |
| my_try_catch | My version of tryCatch |
| nee_mean_nt | Average number of species for b-d process. See Kendall 1948a,... |
| nee_stdev_nt | Average number of species for b-d process. See Kendall 1948a,... |
| one_minus_pt | 1 - Pt |
| one_minus_ut | 1 - ut |
| pars_transform_back | Transform parameters back |
| pars_transform_forward | Transform parameters |
| pmb_loglik | Calculate the log-likelihood for a Pure Multiple Birth model |
| pn | Pn |
| print_info | Print information about simulated data |
| p_t | Pt |
| read_results | Read saved results |
| to_string2 | Convert to string |
| ut | ut |
