Man pages for cvasi
Calibration, Validation, and Simulation of TKTD Models
| Algae-models | Algae models |
| Algae_Simple | Simple algae model without environment (Rendal et al. 2023) |
| Algae_TKTD | Algae model variant (Weber et al. 2012) with scaled damage |
| Algae_Weber | Algae model, _SAM-X_ (Weber et al. 2012) |
| americamysis | A DEB abj scenario of Americamysis bahia |
| batch | Batch simulation of multiple exposure levels |
| cache_controls | Cache control simulations |
| calibrate | Fit model parameters to experimental data |
| CalibrationSet | Calibration set |
| ci_from_hessian | Parameter confidence intervals from fit |
| DEB_abj | DEB_abj |
| DEB-models | Dynamic Energy Budget (DEB) models |
| DEBtox | DEBtox model |
| diagnostics | Diagnostics of solvers |
| 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 |
| fit_growth | Fit growth parameters |
| fit_tktd | Fit TK/TD parameters |
| focusd1 | A Lemna_SETAC scenario with variable environment |
| fx | Generic to calculate effects for a particular scenario |
| get_model | Get model name |
| get_param | Get scenario parameters |
| get_tag | Get scenario tag |
| get_times | Get output times |
| GUTS_IT | GUTS-IT scenario |
| GUTS_RED_IT | GUTS-RED-IT scenario |
| GUTS-RED-models | GUTS-RED models |
| GUTS_RED_SD | GUTS-RED-SD scenario |
| GUTS_SD | GUTS-SD scenario |
| import_morse | Import 'morse' model parameters |
| import_swash | SWASH project exposure profile import |
| import_toxswa | Import _TOXSWA_ exposure series |
| is_deb | Test if argument is a DEB scenario |
| is_guts | Test if argument is a GUTS scenario |
| is_lemna | Test if argument is a Lemna scenario |
| is_LemnaThreshold | Test if argument is a LemnaThreshold scenario |
| 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 v1.3 (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 |
| Magma | Magma model (Witt et al., submitted) |
| Magma-class | Magma scenario class |
| metsulfuron | Lemna model fitted to _metsulfuron_ effect data |
| minnow_it | A fitted GUTS-RED-IT scenario of the fathead minnow |
| minnow_sd | A fitted GUTS-RED-SD scenario of the fathead minnow |
| no_exposure | Zero exposure |
| num_info | Print information about numerical solver result |
| parameter_set | Set of model parameters |
| pipe | Pipe operator |
| pll_debug | Disable parallelization for debugging |
| plot | S3 plotting functions |
| plot_epx | Plot EPx values |
| plot.param_space | Plot profiled parameter space |
| 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 |
| ringtest_c | EFSA Ringtest Dataset C |
| ringtest_it | EFSA Ringtest Dataset A SD |
| ringtest_sd | EFSA Ringtest Dataset A SD |
| rsubcapitata | A Weber scenario of algae exposed to isoproturon |
| Scenarios | Effect scenario classes |
| schmitt2013 | A Lemna effect study data set with multiple treatment levels |
| sequence | Sequence of scenarios |
| sequence.extract | Extract and replace elements of a sequence |
| 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 scenario 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 using multiple exposure series |
| solver | Calls ODE solver for a particular model |
| survival | Survival rate |
| td2cs | Create _calisets_ from _tox_data_ |
| tox_data | Prepare ecotox study data for fitting |
| Transferable | Biomass transfer class |
