Calibration, Validation, and Simulation of TKTD Models

Documentation for package ‘cvasi’ version 1.1.3

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-- A --

Algae-class	Algae models
Algae-models	Algae models
AlgaeSimpleScenario-class	Algae model with exponential growth but without additional forcings
AlgaeTKTDScenario-class	Algae model with exponential growth, forcings (P, I) and scaled damage
AlgaeWeberScenario-class	Algae model with exponential growth and forcings (I, T)
Algae_Simple	Algae model with exponential growth but without additional forcings
Algae_TKTD	Algae model with exponential growth, forcings (P, I) and scaled damage
Algae_Weber	Algae model with exponential growth and forcings (I, T)
americamysis	A DEB abj scenario of Americamysis bahia

-- B --

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

-- D --

DEB-models	Dynamic Energy Budget (DEB) models
DebAbj-class	DEB_abj
DebDaphnia-class	DEBtox Daphnia
DebScenario-class	Dynamic Energy Budget (DEB) models
DEB_abj	DEB_abj
DEB_Daphnia	DEBtox Daphnia
dmagna	A DEBtox Daphnia magna scenario
dose_response	Calculate a dose response curve

-- E --

effect	Effect level
EffectScenario-class	Effect scenario classes
epx	Effect profiles (EPx values)
epx_mtw	Calculate EPx values for a series of moving time window
ExposureSeries	Exposure time-series
ExposureSeries-class	Exposure time-series

-- F --

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 --

-- I --

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_GUTS_IT	Test if argument is a GUTS model
is_GUTS_SD	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

-- L --

Lemna-class	Lemna models
Lemna-models	Lemna models
LemnaSchmittScenario-class	Lemna model (Schmitt et al. 2013)
LemnaSetacScenario-class	Lemna model (Klein et al. 2021)
Lemna_Schmitt	Lemna model (Schmitt et al. 2013)
Lemna_SchmittThold	Lemna model (Schmitt et al. 2013)
Lemna_SETAC	Lemna model (Klein et al. 2021)
log_disable	Start and stop logging
log_enable	Start and stop logging
log_envir	Log R environment properties
log_msg	Add a log message
log_scenarios	Log scenario properties

-- M --

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
MyrioExpScenario-class	Myriophyllum model with exponential growth
MyrioLogScenario-class	Myriophyllum model with logistic growth
Myriophyllum-class	Myriophyllum models
Myriophyllum-models	Myriophyllum models
Myrio_log	Myriophyllum model with logistic growth

-- N --

Zero exposure

-- P --

parameter_set	Set of model parameters
parameter_set-class	Set of model parameters
pll_debug	Disable parallelization for debugging
plot_epx	Plot EPx values
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 --

An algae scenario

-- S --

scenario	Effect scenario classes
Scenarios	Effect scenario classes
scenarios	Effect scenario classes
ScenarioSequence-class	Sequence of scenarios
Schmitt2013	A Lemna data set with multiple treatment levels
sequence	Sequence of scenarios
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_param	Set model parameters
set_param-method	Set model parameters
set_tag	Set a tag
set_times	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 of several effect scenarios
solver	Calls ODE solver for a particular model
solver-method	Calls ODE solver for a particular model
survival	Survival rate

-- T --

Transferable	Biomass transfer class
Transferable-class	Biomass transfer class