Man pages for Neves-P/DAISIErobustness
Test the Robustness of DAISIE to Geodynamics and Traits
| all_endemic | Calculates the number of endemic and non-endemics species on... |
| all_endemic_clades | Checks if all island species are endemic clades. Clade are... |
| any_recols | Determines if the island contains any recolonisations that... |
| append_factor_key | Create key to partition results by scenario |
| calc_ed95_for_plots | Calculate ED95 statistic for all parameter sets of a... |
| calc_ed95_param_set | Calculate ED95 statistic for all results in folder |
| calc_error | Calculates error metrics between two simulations |
| calc_error_metrics | Calculates metrics between error and baseline error... |
| calc_max_spec | Obtain the number of species in the largest clade |
| calc_ml | Calculate maximum likelihood value for the rates |
| calc_runtime_ed95_cor | Calculate correlation between ED95 statistics and runtime |
| check_calc_error_metrics_input | Checks calc_error_metrics_input is correct |
| check_create_folders | Checks and create results folder for output |
| continental_cs | Parameter space of the continental clade-specific... |
| continental_di | Parameter space of the continental diversity-independent... |
| continental_iw | Parameter space of the continental island-wide... |
| continental_land_bridge_cs | Parameter space of the continental land-bridge clade-specific... |
| continental_land_bridge_di | Parameter space of the continental land-bridge... |
| continental_land_bridge_iw | Parameter space of the continental land-bridge island-wide... |
| create_output_file_name | Generated name for saving output of 'run_robustness()' |
| DAISIErobustness-package | DAISIErobustness: Test the Robustness of DAISIE to... |
| default_params_doc | Default parameter documentation |
| extract_param_set | Extracts a set of parameters from the parameter space for the... |
| get_runtime_params | Make runtime data frame |
| is_integration_error_log | Checks if log file shows integration error |
| is_novel_sim_outputs | Measures if the input is a valid collection of simulation... |
| is_param_space_name | Checks whether the parameter space name give is one of the... |
| load_param_space | Loads the parameter space into the environment for... |
| ml_constraints | Checks if MLE passed or errored |
| oceanic_ontogeny_cs | Parameter space of the oceanic ontogeny clade-specific... |
| oceanic_ontogeny_di | Parameter space of the oceanic ontogeny diversity-independent... |
| oceanic_ontogeny_iw | Parameter space of the oceanic ontogeny island-wide... |
| oceanic_ontogeny_sea_level_cs | Parameter space of the oceanic ontogeny sea-level... |
| oceanic_ontogeny_sea_level_di | Parameter space of the oceanic ontogeny sea-level... |
| oceanic_ontogeny_sea_level_iw | Parameter space of the oceanic ontogeny sea-level island-wide... |
| oceanic_sea_level_cs | Parameter space of the oceanic sea-level clade-specific... |
| oceanic_sea_level_di | Parameter space of the oceanic sea-level... |
| oceanic_sea_level_iw | Parameter space of the oceanic sea-level island-wide... |
| plot_cor | Runtime vs ED95 correlation plot |
| read_log_file | Read log file lines |
| read_param_set_log | Reads parameter set number written in log file |
| read_param_space_name_log | Reads parameter space name written in log file |
| read_runtime_log | Calculate job elapsed time from log file |
| read_status_log | Calculate job elapsed time from log file |
| run_novel_sim | Runs DAISIE simulation with a novel model |
| run_oceanic_sim | Runs original clade-specific oceanic DAISIE simulation |
| run_robustness | Run robustness analysis pipeline |
| save_output | Save 'run_robustness()' output |
| trait_CES | Parameter space of the trait-dependent analysis |
