# Calibration, Validation, and Simulation of TKTD Models

## Documentation for package ‘cvasi’ version 1.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M N P R S T misc

## -- A --

Algae-class | Algae models
Algae-models | Algae models
AlgaeSimple-class | Simple algae model without environment (Rendal et al. 2023)
AlgaeSimpleScenario-class | Simple algae model without environment (Rendal et al. 2023)
AlgaeTKTD-class | Algae model variant (Weber et al. 2012) with scaled damage
AlgaeTKTDScenario-class | Algae model variant (Weber et al. 2012) with scaled damage
AlgaeWeber-class | Algae model, _SAM-X_ (Weber et al. 2012)
AlgaeWeberScenario-class | Algae model, _SAM-X_ (Weber et al. 2012)
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

## -- B --

batch | Batch simulation of multiple exposure levels
Biomass-transfer | Biomass transfer class

## -- C --

cache_controls | Cache control simulations
calibrate | Fit model parameters to experimental data
calibrate-method | Fit model parameters to experimental data
CalibrationSet | Calibration set
CalibrationSet-class | Calibration set
caliset | Calibration set
ci_from_hessian | Parameter confidence intervals from fit

## -- D --

Deb-class | Dynamic Energy Budget (DEB) models
DEB-models | Dynamic Energy Budget (DEB) models
DebAbj-class | DEB_abj
DebDaphnia-class | DEBtox model
DEBtox | DEBtox model
DebTox-class | DEBtox model
DEBtox2019 | DEBtox model
DEB_abj | DEB_abj
DEB_Daphnia | DEBtox model
diagnostics | Diagnostics of solvers
diagnostics.cvasi_simulate | Diagnostics of solvers
diagnostics.default | Diagnostics of solvers
dmagna | A DEBtox scenario of Daphnia magna
dose_response | Calculate a dose response curve

## -- E --

effect | Effect level
effect-method | Effect level
EffectScenario-class | Effect scenario classes
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
ExposureSeries-class | Exposure time-series

## -- F --

fit_growth | Fit growth parameters
fit_growth-method | Fit growth parameters
fit_tktd | Fit TK/TD parameters
fit_tktd-method | Fit TK/TD parameters
focusd1 | A Lemna_SETAC scenario with variable environment
fx | Generic to calculate effects for a particular scenario
fx-method | Generic to calculate effects for a particular scenario

## -- G --

get_model | Get model name
get_model-method | Get model name
get_model_name | Get model name
get_param | Get scenario parameters
get_param-method | Get scenario parameters
get_tag | Get scenario tag
get_tag-method | Get scenario tag
get_times | Get output times
get_times-method | Get output times
Guts-class | GUTS-SD scenario
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
GutsIt-class | GUTS-IT scenario
GutsRedIt-class | GUTS-RED-IT scenario
GutsRedSd-class | GUTS-RED-SD scenario
GutsSd-class | GUTS-SD scenario
GUTS_IT | GUTS-IT scenario
GUTS_RED_IT | GUTS-RED-IT scenario
GUTS_RED_SD | GUTS-RED-SD scenario
GUTS_SD | GUTS-SD scenario

## -- I --

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_deb | Test if argument is a DEB scenario
is_GUTS | Test if argument is a GUTS scenario
is_guts | Test if argument is a GUTS scenario
is_GUTS_IT | Test if argument is a GUTS scenario
is_guts_it | Test if argument is a GUTS scenario
is_GUTS_SD | Test if argument is a GUTS scenario
is_guts_sd | Test if argument is a GUTS scenario
is_Lemna | Test if argument is a Lemna 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

## -- L --

Lemna-class | Lemna models
Lemna-models | Lemna models
LemnaSchmitt-class | Lemna model (Schmitt et al. 2013)
LemnaSchmittScenario-class | Lemna model (Schmitt et al. 2013)
LemnaSetac-class | Lemna model v1.3 (Klein et al. 2021)
LemnaSetacScenario-class | Lemna model v1.3 (Klein et al. 2021)
Lemna_Schmitt | Lemna model (Schmitt et al. 2013)
Lemna_SchmittThold | Lemna model (Schmitt et al. 2013)
Lemna_SETAC | Lemna model v1.3 (Klein et al. 2021)
length-method | Extract and replace elements of a sequence
lik_profile | Likelihood profiling
log_disable | Start and stop logging
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

## -- M --

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
morse | Import 'morse' model parameters
Myrio | Magma model (Witt et al., submitted)
Myrio_log | Magma model (Witt et al., submitted)

## -- N --

NoExposureSeries-class | Exposure time-series
no_exposure | Zero exposure
num_info | Print information about numerical solver result
num_info.cvasi_fit | Print information about numerical solver result
num_info.cvasi_simulate | Print information about numerical solver result
num_info.default | Print information about numerical solver result

## -- P --

ParameterSet-class | Set of model parameters
parameter_set | Set of model parameters
parameter_set-class | Set of model parameters
pll_debug | Disable parallelization for debugging
plot | S3 plotting functions
plot.cvasi_drc | S3 plotting functions
plot.cvasi_simulate | S3 plotting functions
plot.lik_profile | S3 plotting functions
plot.param_space | Plot profiled parameter space
plot_epx | Plot EPx values
plot_lik_profile | S3 plotting functions
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

## -- R --

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

## -- S --

SAM-X | Algae model, _SAM-X_ (Weber et al. 2012)
SamX | Algae model, _SAM-X_ (Weber et al. 2012)
scenario | Effect scenario classes
Scenarios | Effect scenario classes
scenarios | Effect scenario classes
ScenarioSequence-class | Sequence of scenarios
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_bounds-method | Set boundaries of model parameters
set_endpoints | Set effect endpoints
set_exposure | Set exposure time-series
set_exposure-method | Set exposure time-series
set_forcings | Set time-dependent parameters
set_forcings-method | Set time-dependent parameters
set_init | Set initial state
set_init-method | Set initial state
set_moa | Set mode of action
set_mode_of_action | Set mode of action
set_noexposure | Set zero exposure
set_notransfer | Set transfer events
set_nowindow | Set window length
set_param | Set scenario parameters
set_param-method | Set scenario parameters
set_tag | Set a tag
set_times | Set output times
set_times-method | Set output times
set_transfer | Set transfer events
set_transfer-method | Set transfer events
set_window | Set window length
simulate | Simulate an effect scenario
simulate-method | Simulate an effect scenario
simulate_batch | Batch simulation using multiple exposure series
solver | Calls ODE solver for a particular model
solver-method | Calls ODE solver for a particular model
survival | Survival rate

## -- T --

td2cs | Create _calisets_ from _tox_data_
ToxData-class | Prepare ecotox study data for fitting
tox_data | Prepare ecotox study data for fitting
Transferable | Biomass transfer class
Transferable-class | Biomass transfer class

## -- misc --

[-method | Extract and replace elements of a sequence
[[-method | Extract and replace elements of a sequence
[[<--method | Extract and replace elements of a sequence