Man pages for richelbilderbeek/razzo
The Error if Nature is MBD
| calc_n_taxas | Calculate the number of taxa that trees will have when... |
| check_mbd_params | Create mbd parameters |
| check_mbd_paramses | Check all elements in the list of 'mbd_params'. |
| check_misc_params | Check the misc parameters |
| check_project_folder_name | Check if 'project_folder_name' ends with 'razzo_project' and... |
| check_razzo_experiments | Check razzo experiments |
| check_razzo_params | Check if the 'razzo_params' are valid razzo parameters. |
| check_razzo_params_filenames | Check if all filenames in the 'razzo_params' follow the... |
| check_razzo_params_names | Check if the 'razzo_params' is a list with elements that have... |
| check_traces_in_df | Check if all the traces' names are in the names of the data... |
| clean_path | Clean up a path by removing double folder seperators |
| clean_paths | Clean up a paths by removing double folder seperators |
| collect_all_data | Collect all data |
| collect_esses | Collect esses |
| collect_evidences | Collect marginal loglikelihoods |
| collect_mbd_params | Collect mbd parameters |
| collect_nltt_stats | Collect nltt statistics |
| collect_n_mb_species | Collect the number of multiple-born (MB) species |
| collect_n_mutations | Collect number of mutations |
| collect_n_taxa | Collect the number of taxa for analyses. |
| collect_run_times | Collect the times simulations took to run |
| create_fig_1 | Create figure 1 |
| create_file_all_data | Collect all data in one '.csv' file called... |
| create_file_esses | Create the dataframe with the Effective Samples Sizes (ESSes)... |
| create_file_fig_1 | Save nllt figure |
| create_file_marg_liks | Creates file containing marginal loglikelihoods |
| create_file_mbd_params | Collect all MBD parameters of a 'razzo' run and put these in... |
| create_file_nltt_stats | Creates file containing nltt stats |
| create_file_n_mutations | Creates file containing the number of mutations |
| create_file_n_taxa | Creates file containing the number of taxa |
| create_file_run_times | Creates file containing the run times |
| create_mbd_paramses | Create a list of MBD parameters |
| create_mbd_params_table | Create a table of which each row holds a unique MBD parameter... |
| create_misc_params | Create the parameters for one experiment. Run one point of... |
| create_n_mb_species_file | Create the dataframe with number of multiple-born species and... |
| create_parameters_files | Create all parameter files in... |
| create_params_mbd | Create mbd parameters |
| create_params_razzo | Create one set of parameter for one 'razzo' experiment. |
| create_razzo_alignment_params | Create a razzo alignment parameter set that matches the razzo... |
| create_razzo_beast2_options | Create BEAST2 options that follow the razzo naming... |
| create_razzo_cand_experiments | Create the candidate experiments |
| create_razzo_experiments | Creates a 'pir_params' with the 'razzo' setup and naming... |
| create_razzo_gen_experiment | Create a generative experiment that follows the razzo naming... |
| create_razzo_mrca_prior | Create the MRCA prior as used in the article |
| create_razzo_ns_mcmc | Create a nested sampling MCMC that matches the article |
| create_razzo_paramses | Create the parameters for all experiment |
| create_razzo_pir_params | Creates a 'pir_params' with the 'razzo' setup and naming... |
| create_razzo_twinning_params | Create a 'twinning_params' that follows the razzo naming... |
| create_test_mbd_params | Create MBD parameters used in tests |
| create_test_mbd_paramses | Create a set of testing MBD parameters |
| create_test_razzo_experiments | Create a set of testing experiments |
| create_test_razzo_params | Create one set of parameter for one 'razzo' experiment. |
| create_test_razzo_paramses | Create a list of 'razzo_params' to be used in testing |
| create_test_razzo_pir_params | Creates a 'pir_params' with the 'razzo' setup and naming... |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| get_alignment_filename | Get alignment filename |
| get_best_model | Retrieve the best candidates from the data |
| get_data_paths | Get the folder paths of 'razzo' experiments |
| get_errors_filename | Get errors filename |
| get_evidence_filename | Get evidence filename |
| get_generative_model | Retrieve the generative model from the data |
| get_gen_models | Get the names of the supported generative models |
| get_input_filename | Get input filename |
| get_output_log_filename | Get output log filename |
| get_output_state_filename | Get output state filename |
| get_output_trees_filenames | Get output trees filenames |
| get_razzo_crown_age | Get the crown age used in the article |
| get_razzo_dna_alignment_length | Get the razzo DNA alignment length, as used in the article |
| get_razzo_lambdas | Get the 'lambda's used in the MBD process |
| get_razzo_mcmc | Get the MCMC chain used in the article |
| get_razzo_mcmc_chain_length | Get the MCMC chain length used in the article |
| get_razzo_mcmc_store_every | Get the MCMC sampling interval used in the article |
| get_razzo_mus | Get the 'mu's used in the MBD process |
| get_razzo_mutation_rate | Get the razzo mutation rate, as used in the article |
| get_razzo_n_replicates | Specify the number of replicates |
| get_razzo_nus | Get the 'nu's used in the MBD process |
| get_razzo_qs | Get the 'q's used in the MBD process |
| get_results_path | Get paths for the results |
| get_seed_folder_name | Get seed folder name |
| get_tracelog_filename | Get tracelog filename |
| get_tree_filename | Get tree filename |
| get_treelog_filename | Get treelog filename |
| open_parameters_file | Opens a parameter file and parses it |
| pipe | Pipe operator |
| razzo | razzo: the effect of MBD on inference |
| remove_cbs_exps | Remove all experiments that have a CBS tree prior |
| run_razzo | Runs one 'razzo' experiment |
| run_razzo_from_file | Run a razzo experiment from a filename |
| save_razzo_paramses | Save the list of 'razzo_params' to the exected locations |
| update_razzo | Update the 'razzo' dependencies |
