NEWS.md

cvasi Development version

New batch() function to ease the creation of batch simulations based on a single scenario and multiple exposure series.
New overloads of plot() which can graphically depict the return values of cvasi functions such as simulate() and dose_response().
New parameter for sequence(): argument breaks can split the sequence elements at the given time points to ease the creation of sequences.
Example scenarios minnow_it and minnow_sw now feature a non-zero background mortality rate.
Default solver of Algae_Simple and Lemna_Schmitt set to lsoda to harmonize the numerical scheme used within a class of models (before, ode45 was used).
Parameter list of solver() functions simplified; the following parameters no longer need to be accepted:
- times, output times are solely defined by the exposure scenario itself
- f, 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 users

Improved import_toxswa(): now supports scaling of imported time series, importing selected TOXSWA output variables, as well as importing selected substance concentrations.
Function import_exposure_text() moved to the cvasi.ui package.
Small bugfix in 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.
Parameters to 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.
New overloads for the generic plot() to depict return values of functions such as simulate() and dose_response().
Model equations of the Lemna_SETAC() model by Klein et al. was integrated into the package. This removes package lemna as a dependency.
Scenario defaults of Lemna_SETAC() were modified to ease scenario creation and to reflect common study conditions:
- Initial biomass set to 0.0012
- Parameter default k_photo_fixed=TRUE
- Forcings default to constant non-zero conditions; temperature (°C) temp=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.

New likelihood profiling with lik_profile() based on the routines described by Tjalling Jager (doi: 10.1002/ieam.4333) and implemented in BYOM
The function survival() has been deprecated. Survival probabilities of affected models are now part of the return value of simulate().
The function DEB_Daphnia() has been superseded by the more appropriatly named DEBtox(). The former function is still available, but will show a warning when used.
The DEBtox() model equations have been updated to conform with BYOM's DEBtox 2019 module version 4.7.
New slot 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.
New function set_bounds() to set or modify parameter bounds for one or more scenarios or calibration sets.
Custom error functions supplied to 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.
Verbose output is enabled by default for calibrate()
New slot 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().
The function to create calibration sets has been renamed to caliset(). The former CalibrationSet() is still available, but will show a warning when used.

Links to MOSAIC web page (mosaic.univ-lyon1.fr) had to be removed because server was inaccessible

morse removed (temporarily) as suggested package, because it was archived by CRAN
Model man pages amended

calibrate()
- Function arguments simplified and partly renamed
- Fitting is now more error-tolerant and will not abort if a simulation fails or if it returns invalid values

Initial public release