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)
CalibrationSet          Calibration set
DEB-models              Dynamic Energy Budget (DEB) models
DEB_abj                 DEB_abj
DEBtox                  DEBtox model
ExposureSeries          Exposure time-series
GUTS-RED-models         GUTS-RED models
GUTS_IT                 GUTS-IT scenario
GUTS_RED_IT             GUTS-RED-IT scenario
GUTS_RED_SD             GUTS-RED-SD scenario
GUTS_SD                 GUTS-SD scenario
Lemna-models            Lemna models
Lemna_SETAC             Lemna model v1.3 (Klein et al. 2021)
Lemna_Schmitt           Lemna model (Schmitt et al. 2013)
Macrophyte-models       Macrophyte models
Magma                   Magma model (Witt et al., submitted)
Magma-class             Magma scenario class
Scenarios               Effect scenario classes
Transferable            Biomass transfer class
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
ci_from_hessian         Parameter confidence intervals from fit
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
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
import_morse            Import 'morse' model parameters
import_swash            SWASH project exposure profile import
import_toxswa           Import _TOXSWA_ exposure series
is_LemnaThreshold       Test if argument is a LemnaThreshold scenario
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_scenario             Test if argument is an effect scenario
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
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
pll_debug               Disable parallelization for debugging
plot                    S3 plotting functions
plot.param_space        Plot profiled parameter space
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
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
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
