Calibration, Validation, and Simulation of TKTD Models
Creates a PPC plot for a single dataset
Creates a prediction plot for one effect scenario
Creates plot of model results (uncertainties optional)
Plot profiled parameter space
S3 plotting functions
Pull metadata from scenarios
Effect scenario classes
Print information about numerical solver result
Set of model parameters
Pipe operator
Disable parallelization for debugging
Plot EPx values
Create PPC plot for one or more datasets
Extract and replace elements of a sequence
Set scenario parameters
Set a tag
Set output times
Set transfer events
Set window length
Magma scenario class
Magma model (Witt et al., submitted)
Zero exposure
Set zero exposure
Test if argument is a GUTS scenario
Test if argument is a Lemna scenario
Test if argument is a LemnaThreshold scenario
Test if argument is an effect scenario
Lemna model (Schmitt et al. 2013)
Simple algae model without environment (Rendal et al. 2023)
Algae model variant (Weber et al. 2012) with scaled damage
Algae model, SAM-X (Weber et al. 2012)
Lemna model v1.3 (Klein et al. 2021)
Algae models
Batch simulation of multiple exposure levels
Cache control simulations
Fit model parameters to experimental data
Calibration set
Parameter confidence intervals from fit
DEB_abj
Dynamic Energy Budget (DEB) models
DEBtox model
Diagnostics of solvers
Calculate a dose response curve
Effect level
Calculate EPx values for a series of moving time window
Effect profiles (EPx values)
Explore parameter space
Exposure time-series
Fit growth parameters
Fit TK/TD parameters
Generic to calculate effects for a particular scenario
Get model name
Get scenario parameters
Get scenario tag
Get output times
GUTS-IT scenario
GUTS-RED-IT scenario
GUTS-RED-SD scenario
GUTS-SD scenario
GUTS-RED models
Import morse model parameters
SWASH project exposure profile import
Import TOXSWA exposure series
Test if argument is a DEB scenario
Lemna models
Likelihood profiling
Start and stop logging
Log R environment properties
Calculate log likelihood
Add a log message
Log scenario properties
Macrophyte models
Sequence of scenarios
Set boundaries of model parameters
Set effect endpoints
Set exposure time-series
Set time-dependent parameters
Set initial state
Set mode of action
Batch simulation using multiple exposure series
Simulate an effect scenario
Calls ODE solver for a particular model
Survival rate
Create calisets from tox_data
Prepare ecotox study data for fitting
Biomass transfer class
Eases the use of ecotoxicological effect models. Can simulate common toxicokinetic-toxicodynamic (TK/TD) models such as General Unified Threshold models of Survival (GUTS) and Lemna. It can derive effects and effect profiles (EPx) from scenarios. It supports the use of 'tidyr' workflows employing the pipe symbol. Time-consuming tasks can be parallelized.