cvasi Development version

• NEW

  • Log-Likelihood profiling on count-data is now supported.
  • 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:
    • Default values for all forcings are now set to ease the setup of scenarios, with temp=12°C and rad=15,000 kJ/(m² day) as documented by Schmitt et al. (2012).
  • Lemna_SETAC model:
    • The default value of parameter 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:
    • Unused state variable C and parameter k removed. External concentrations are solely defined by the scenario’s exposure time-series.
    • Additional output levels available. Ordering of output levels harmonized with other models.
    • Default values for all forcings are now set to ease the setup of scenarios, with T_act=23°C and I=100 uE/m²/s following parameters reported by Weber et al. (2012).
  • Algae_TKTD model:
    • New parameters D and R_0 added to enable simulation of flow-through conditions, analogous to the Algae_Weber model.
    • Erroneous growth term in external phosphorous differential equation was removed.
    • Additional output levels available. Ordering of output levels harmonized with other models.
    • Default values for all forcings are now set to ease the setup of scenarios, with T_act=23°C and I=100 uE/m²/s following parameters reported by Weber et al. (2012).
  • Magma (alias Myriophyllum) model:
    • The scenario constructor has been renamed to Magma() to align with the associated publication by Witt et al.
    • Both model variants with exponential and logistic growth terms are created with the same constructor, Magma(). The growth model can be selected by setting parameter growth, e.g. Magma(growth="log").
    • The ordering of optional output variables has been modified and total shoot length (TSL) has been moved to the front.
  • Example scenario Rsubcapitata:
    • Renamed to all lower-case name rsubcapitata.
    • Scenario settings modified to correctly reflect conditions of R. subcapitata exposed to isoproturon in reactor A of Weber et al. (2012).
  • The effects calculated by 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.
  • Unused parameter 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.
  • Scenario information on the console provided by show() now includes settings of biomass transfers and moving windows.
  • Scenario sequences are now supported by effect() and epx().

• DEPRECATED

  • Caching of results of control scenarios is now fully handled by the package. Calls to 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.
  • Soft deprecation of passing arguments lower and upper to calibrate(). Instead, use set_bounds() on the affected scenarios.

cvasi 1.4.0

• NEW
  • 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.
• MODIFIED
  • Requirements relaxed for scenarios with simulated biomass transfers:
    • Transfer time points no longer need to be part of the output times.
    • Negative output times are now supported.
  • 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 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

cvasi 1.3.1

• 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.

cvasi 1.2.0

• 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.

cvasi 1.1.3

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

cvasi 1.1.2

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

cvasi 1.1.1

• Various improvements to plotting routines
• New plot_scenario()

cvasi 1.1.0

• 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

cvasi 1.0.1

• Algae_TKTD() harmonized with Algae_Simple() model equations
• Fix for numerical issues in unit tests and vignette on macOS ARM platform
• Minor changes to conform with CRAN requirements

cvasi 0.10.5

Initial public release