NEW
fit_growth() and fit_tktd() ease parameter
fitting to experimental data.tox_data() and td2cs() ease the import of
experimental tox data for parameter fitting purposes.num_info() can be used as a complement to
deSolve’s diagnostics() and will also provide tips
on how to address common issues with numerics. Can be used on the return
value of simulate().MODIFIED
Lemna_Schmitt model:
temp=12°C and rad=15,000
kJ/(m² day) as documented by Schmitt et al. (2012).Lemna_SETAC model:
beta has been updated
from formerly 0.025 to now 0.25. This reflects
changes to the SETAC working group’s report in version 1.2. The old
value originated from typos in former report versions.Algae_Weber model:
C and parameter k
removed. External concentrations are solely defined by the scenario’s
exposure time-series.T_act=23°C and I=100 uE/m²/s
following parameters reported by Weber et al. (2012).Algae_TKTD model:
D and R_0 added to enable
simulation of flow-through conditions, analogous to the
Algae_Weber model.T_act=23°C and I=100 uE/m²/s
following parameters reported by Weber et al. (2012).Magma (alias Myriophyllum) model:
Magma() to
align with the associated publication by Witt et al.Magma(). The growth
model can be selected by setting parameter growth,
e.g. Magma(growth="log").TSL) has been moved to the front.Rsubcapitata:
rsubcapitata.effect() are no longer
limited to a maximum value of 1.0. Instead, effects are
calculated similarly to relative errors, quantifying the
relative difference of endpoints in control and treatment scenarios.
Values greater than one as well as less than zero can occur.const_growth removed from
Algae_Simple() constructor.simulate_batch() now accepts additional parameters
... which are passed through to
simulate().import_morse(): default value of argument
reset_hb set to FALSE, i.e. the GUTS
background mortality rate is no longer set to zero on import by
default.show()
now includes settings of biomass transfers and moving windows.effect() and
epx().DEPRECATED
cache_controls() will raise an
error.simulate_batch() was superseded by
batch(); the function will raise deprecation warning when
called by users.is_LemnaThreshold() will be removed in future
versions.lower and
upper to calibrate(). Instead, use
set_bounds() on the affected scenarios.batch() function to ease the creation of batch
simulations based on a single scenario and multiple exposure
series.plot() which can graphically depict
the return values of cvasi functions such as
simulate() and dose_response().sequence(): argument
breaks can split the sequence elements at the given time
points to ease the creation of sequences.minnow_it and minnow_sw
now feature a non-zero background mortality rate.Algae_Simple and
Lemna_Schmitt set to lsoda to harmonize the
numerical scheme used within a class of models (before,
ode45 was used).solver() functions simplified; the
following parameters no longer need to be accepted:
times, output times are solely defined by the scenario
itselff, approx, and rule: if
default settings of deSolve’s interpolation of forcings series
needs to be adapted, the fcontrol argument has to be
provided by usersimport_toxswa(): now supports scaling of
imported time series, importing selected TOXSWA output
variables, as well as importing selected substance concentrations.import_exposure_text() moved to the
cvasi.ui package.plot_ppc().morse() renamed to import_morse(), the
function now supports loading parameter sets from morse objects
directly, as well as from .RData and .RDS files.import_morse() renamed to a more
canonical standard, i.e. find.IT to find_it,
find.SD to find_sd and so forth. Using the old
parameter names still works but will raise a warning.plot() to depict return
values of functions such as simulate() and
dose_response().Lemna_SETAC() model by Klein et
al. was integrated into the package. This removes package
lemna as a dependency.Lemna_SETAC() were modified to
ease scenario creation and to reflect common study conditions:
0.0012k_photo_fixed=TRUEtemp=12, irradiance (kJ m-2 d-1) irr=15000,
Phosphorus concentratio (mg P L-1) P=0.3, Nitrogen
concentration (mg N L-1) N=0.6. These defaults only take
effect if parameter k_photo_fixed=FALSE.lik_profile() based on
the routines described by Tjalling Jager (doi: 10.1002/ieam.4333) and
implemented in BYOMsurvival() has been deprecated. Survival
probabilities of affected models are now part of the return value of
simulate().DEB_Daphnia() has been superseded by the
more appropriatly named DEBtox(). The former function is
still available, but will show a warning when used.DEBtox() model equations have been updated to
conform with BYOM’s DEBtox 2019 module version
4.7.param.bounds was added to effect scenario
classes to store valid parameter ranges of commonly fitted model
parameters. The information is currently only used in likelihood
profiling.set_bounds() to set or modify parameter
bounds for one or more scenarios or calibration sets.calibrate() must
accept four arguments; the error function will be supplied with all
observed and predicted values in one call. The two additional parameters
represent optional weights and study IDs.calibrate()tag was added to calibration set
classes to store additional metadata such as study IDs. The information
will be passed on to the error function by
calibrate().caliset(). The former CalibrationSet() is
still available, but will show a warning when used.morse removed (temporarily) as suggested package,
because it was archived by CRANplot_scenario()calibrate()
Algae_TKTD() harmonized with
Algae_Simple() model equationsInitial public release