scenarios: Run a zero-dimensional model, possibly for multiple scenarios

In dkneis/rodeo: A Code Generator for ODE-Based Models

Run a zero-dimensional model, possibly for multiple scenarios

Description

Triggers dynamic simulation(s) of a 0D model for one to many scenarios. The individual scenarios can differ by the initial state or the values of parameters. Optionally produces basic plots.

Arguments

times	Numeric vector defining the times for which the future state of the system is computed.
scenarios	Either NULL or a named list, each element of which defines a scenario to be considered. In the latter case, list elements must be (named) numeric vectors used to update the initial values and parameters provided as defaults in the workbook from which the model was imported. The vectors for the individual scenarios can differ in length but their length could also be consistent across scenarios. If scenarios is set to NULL, only the default scenario will be run. See details and examples.
fortran	Logical. Passed to the respective argument of dynamics.
plot.vars	Logical. Plot the dynamics of all state variables?
plot.pros	Logical. Plot the dynamics of process rates?
leg	Keyword to set the position of the legend (if plots are created).
mar	Numeric vector of length 4 to control figure margins. See the mar tag of par.
...	Possible optional arguments passed to the numerical solver, namely lsoda. Can be used, for example, to limit the maximum step size through the hmax argument if boundary vary on short time scales.

Value

A data frame with at least three columns and one row for each time requested via the times argument. The first column indicates the scenario, the second column holds the time, and further columns hold the values of state variables and process rates.

Note

If the scenarios argument is used to update initial values and / or parameters, the following applies: For each parameter not being included (by name) in the vector for a particular scenario, the default value will be used (as stored in the workbook from which the model was imported). The same is true for the initial values of variables. See the examples below.

Author(s)

David Kneis [e-mail]

See Also

Look at buildFromWorkbook for how to create a suitable model object.

Examples

# build the model
m <- buildFromWorkbook(system.file("models/SEIR.xlsx", package="rodeo"))

# run with defaults
x <- m$scenarios(times=0:30, scenarios=NULL)

# run with updated values 
x <- m$scenarios(times=0:30,
  scenarios=list(default=c(t=1, i=0.2, r=0.4), fast=c(t=1, i=0.5, r=0.1))
)

dkneis/rodeo documentation built on Dec. 11, 2024, 12:20 p.m.