Man pages for TheoPannetier/DDvTDtools
Compare diversity-dependent (DD) and time-dependent (TD) diversification models
| arg_init_k | Accepted values of argument init_k |
| arg_optim | Possible values of argument optim |
| arg_para | Get possible values of argument para |
| arg_sim | Possible values of argument sim |
| assert_DDvTD_wd | Assert that DDvTD is the working directory |
| assert_init_k | Asserts input init parameter is supported |
| assert_optim | Assert the value of 'optim' is a valid model name for... |
| assert_para | Assert the value of 'para' is a valid parameter combination... |
| assert_sim | Assert the value of 'sim' is a valid model name for... |
| check_convergence_optim | Check optimisation results for completeness |
| check_duplicated_rows | Check a results data frame does not have duplicated rows |
| check_incomplete_rows | Check a results data frame for NAs in rows |
| check_init_pars | Check initial parameter values for run_optim |
| check_loglikelihood_exists | Check a results data frame for log-likelihood |
| check_missing_mcs | Check a results data frame for missing rows |
| count_errors_log | Count errors in a log file |
| default_pars2_dd1 | Default DD pars2 argument passed to DDD |
| default_pars2_td4 | Default TD pars2 argument passed to DDD |
| fill_missing_rows | Fill missing results row with default values |
| fix_indexing | Fix indexing of results data frame |
| format_optim_results_row | Assemble a row of results for run_optim output |
| get_brts | Extract a set of branching times from a dataset of simulated... |
| get_default_initpars | Get default initial parameter values for run_optim... |
| get_delta_aic | Computes the AIC difference between DD and TD |
| get_init_k | Get values for argument init_k |
| get_Kprime | Compute K' from la0, mu0, K |
| get_ltt_tbls | Get LTT tables and average LTT for a set of trees |
| get_multi_brts | Extract multiple sets of branching times from a dataset of... |
| get_p_tbl | Compute threshold values and proportions of correct model... |
| get_summary_ltt_tbl | Get lineage-through-time summaries for a set of phylogenetic... |
| join_optim_tbls | Read a pair of 'optim' tables and join them together |
| params_doc | Documentation for main parameters of the model |
| para_to_pars | Translate 'para' argument into parameter values |
| pipe | Pipe operator |
| plot_avg_ltt | Plot average lineage-through-time plots |
| plot_lr | Plot log-LR distribution for DD & TD trees |
| plot_ltt_nested | Plot n distribution inside a ltt plot |
| plot_n_distrib | Plot the distribution of N for DD & TD trees as violin plots |
| read_optim_results | Read results of the model optimisation |
| read_sim | Load a simulated trees dataset |
| read_sim_multiPhylo | Load a simulated dataset as a multiPhylo object |
| results_optim_struct | Structure of the optimisation results data frames |
| run_optim | Run maximum likelihood optimisation of a model on simulated... |
| run_optim_empirical_sims | Run optimisation on trees simulated from empirical... |
| run_optim_from_n | Run maximum likelihood esimation starting from the number of... |
| run_sim | Simulate a set of phylogenetic trees under a time-dependent... |
| set_DDvTD_dir_struct | Set the structure of the DDvTD directory and enter it |
