MODIFIED
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cache_controls() will raise an error.simulate_batch() was superseded by batch(); the function will raise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.NEW
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.MODIFIED
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