rodeo (version 0.9.2)

scenarios: 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.

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.

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.

Author

David Kneis

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))
)