solver: Calls ODE solver for a particular model

In cvasi: Calibration, Validation, and Simulation of TKTD Models

Calls ODE solver for a particular model

Description

Please refer to the Modeling Howto vignette on how to implement custom models by overloading the solver function.

Usage

solver(scenario, times, ...)

## S4 method for signature 'ANY'
solver(scenario, times, ...)

## S4 method for signature 'GutsRedSd'
solver(scenario, times, ...)

## S4 method for signature 'GutsRedIt'
solver(scenario, times, ...)

## S4 method for signature 'LemnaSchmittScenario'
solver(scenario, times, ...)

## S4 method for signature 'LemnaSetacScenario'
solver(scenario, times, ...)

## S4 method for signature 'MyrioExpScenario'
solver(scenario, times, ...)

## S4 method for signature 'MyrioLogScenario'
solver(scenario, times, ...)

## S4 method for signature 'DebAbj'
solver(scenario, times, ...)

## S4 method for signature 'AlgaeWeberScenario'
solver(
  scenario,
  times,
  approx = c("linear", "constant"),
  f = 1,
  method = "lsoda",
  hmax = 0.1,
  ...
)

## S4 method for signature 'AlgaeTKTDScenario'
solver(
  scenario,
  times,
  approx = c("linear", "constant"),
  f = 1,
  method = "lsoda",
  hmax = 0.1,
  ...
)

## S4 method for signature 'AlgaeSimpleScenario'
solver(
  scenario,
  times,
  approx = c("linear", "constant"),
  f = 1,
  method = "ode45",
  hmax = 0.01,
  ...
)

## S4 method for signature 'DebTox'
solver(
  scenario,
  times,
  approx = c("linear", "constant"),
  f = 1,
  rule = 2,
  method = "ode45",
  ...
)

## S4 method for signature 'DebDaphnia'
solver(scenario, times, ...)

Arguments

scenario	scenario object
times	numeric vector of output times, overrides any scenario setting
...	additional parameters passed on to deSolve::ode()
approx	string, interpolation method of exposure series, see deSolve::forcings
f	if approx="constant", a number between 0 and 1 inclusive, see deSolve::forcings
method	string, numerical solver used by deSolve::ode()
hmax	numeric, maximum step length in time, see deSolve::ode()
rule	if approx="constant", a number between 0 and 1 inclusive, see deSolve::forcings

Details

Please note that not all solvers support setting the parameters listed here. In addition, some solvers may set reasonable default values for e.g. maximum step length in time, but not all do. Please check the model documentation for details.

Value

data.frame with simulation results

Methods (by class)

• solver(ANY): Default solver, raises an error

• solver(GutsRedSd): Numerically integrates GUTS-RED-SD models

• solver(GutsRedIt): Numerically integrates GUTS-RED-IT models

• solver(LemnaSchmittScenario): Numerically integrates Lemna_Schmitt models

• solver(LemnaSetacScenario): Numerically integrates Lemna_SETAC models

• solver(MyrioExpScenario): Numerically integrates Myrio models

• solver(MyrioLogScenario): Numerically integrates Myrio_log models

• solver(DebAbj): Numerically integrates DEB_abj models

• solver(AlgaeWeberScenario): numerically integrates Algae_Weber models

• solver(AlgaeTKTDScenario): numerically integrates Algae_TKTD models

• solver(AlgaeSimpleScenario): numerically integrates Algae_Simple models

• solver(DebTox): Numerically integrates DEBtox scenarios

• solver(DebDaphnia): (deprecated) Numerically integrates DEBtox_Daphnia scenarios

cvasi documentation built on Sept. 23, 2024, 9:08 a.m.