Man pages for cvasi
Calibration, Validation, and Simulation of TKTD Models
| Algae-models | Algae models |
| Algae_Simple | Algae model with exponential growth but without additional... |
| Algae_TKTD | Algae model with exponential growth, forcings (P, I) and... |
| Algae_Weber | Algae model with exponential growth and forcings (I, T) |
| americamysis | A DEB abj scenario of Americamysis bahia |
| cache_controls | Cache control simulations |
| calibrate | Fit model parameters to experimental data |
| CalibrationSet | Calibration set |
| DEB_abj | DEB_abj |
| DEB-models | Dynamic Energy Budget (DEB) models |
| DEBtox | DEBtox model |
| dmagna | A DEBtox scenario of Daphnia magna |
| dose_response | Calculate a dose response curve |
| effect | Effect level |
| epx | Effect profiles (EPx values) |
| epx_mtw | Calculate EPx values for a series of moving time window |
| explore_space | Explore parameter space |
| ExposureSeries | Exposure time-series |
| focusd1 | A Lemna_SETAC scenario with variable environment |
| fx | Generic to calculate effects for a particular scenario |
| get_model | Get model name |
| get_tag | Get scenario tag |
| GUTS_RED_IT | GUTS-RED-IT scenario |
| GUTS-RED-models | GUTS-RED models |
| GUTS_RED_SD | GUTS-RED-SD scenario |
| import_exposure_text | Import exposure profiles from text files |
| import_swash | SWASH project exposure profile import |
| import_toxswa | Read TOXSWA exposure profiles from out-files |
| is_DEB | Test if argument is a DEB model |
| is_GUTS | Test if argument is a GUTS model |
| is_Lemna | Test if argument is a Lemna model |
| is_LemnaThreshold | Test if argument is a LemnaThreshold model |
| is_scenario | Test if argument is an effect scenario |
| Lemna-models | Lemna models |
| Lemna_Schmitt | Lemna model (Schmitt et al. 2013) |
| Lemna_SETAC | Lemna model (Klein et al. 2021) |
| lik_profile | Likelihood profiling |
| log_enable | Start and stop logging |
| log_envir | Log R environment properties |
| log_lik | Calculate log likelihood |
| log_msg | Add a log message |
| log_scenarios | Log scenario properties |
| Macrophyte-models | Macrophyte models |
| metsulfuron | Lemna data published by Schmitt (2013) |
| minnow_it | A GUTS-RED-IT scenario of the fathead minnow |
| minnow_sd | A GUTS-RED-SD scenario of the fathead minnow |
| morse | Import 'morse' model parameters |
| Myrio | Myriophyllum model with exponential growth |
| Myrio_log | Myriophyllum model with logistic growth |
| Myriophyllum-models | Myriophyllum models |
| no_exposure | Zero exposure |
| parameter_set | Set of model parameters |
| pipe | Pipe operator |
| pll_debug | Disable parallelization for debugging |
| plot_epx | Plot EPx values |
| plot_lik_profile | Plot likelihood profiles or all profiled parameters |
| plot_param_space | Plot likelihood profiles or all profiled parameters |
| plot_ppc | Creates a PPC plot for a single dataset |
| plot_ppc_combi | Create PPC plot for one or more datasets |
| plot_scenario | Creates a prediction plot for one effect scenario |
| plot_sd | Creates plot of model results (uncertainties optional) |
| pull_metadata | Pull metadata from scenarios |
| Rsubcapitata | An algae scenario |
| Scenarios | Effect scenario classes |
| Schmitt2013 | A Lemna data set with multiple treatment levels |
| sequence | Sequence of scenarios |
| set_bounds | Set boundaries of model parameters |
| set_endpoints | Set effect endpoints |
| set_exposure | Set exposure time-series |
| set_forcings | Set time-dependent parameters |
| set_init | Set initial state |
| set_mode_of_action | Set mode of action |
| set_noexposure | Set zero exposure |
| set_param | Set model parameters |
| set_tag | Set a tag |
| set_times | Set output times |
| set_transfer | Set transfer events |
| set_window | Set window length |
| simulate | Simulate an effect scenario |
| simulate_batch | Batch simulation of several effect scenarios |
| solver | Calls ODE solver for a particular model |
| survival | Survival rate |
| Transferable | Biomass transfer class |
