SOSDesign-class {rsbml} | R Documentation

## SOSDesign

### Description

Specifies the reaction names and their parameter settings for each run in a batch experiment. It extends `matrix`; each column corresponds to a parameter in the model and each row should hold the parameter settings for one run of the experiment.

### Details

It is often desirable to explore the state space of a model by adjusting its initial parameter settings. One could do this by modifying the model itself for each experiment, but this class aims to provide a more convenient and systematic means of running experiments in batch, over a range of parameter settings. The results of the experiment will then contain the output from each run, which may then be compared.

The design is specified as a matrix, and each column in the matrix should correspond to a parameter defined in an SBML model. The column names should identify the parameters. These are not to be confused with the simulation parameters specified in `SOSProtocol`, which control how the simulation is executed. These should be and are designed to be kept constant across the runs.

There are two different types of parameters: global and local (reaction) parameters. Global parameters may correspond to a `Species` quantity, `Compartment` size, or model-level `Parameter` value. These should be identified in the column names by the `id` of the corresponding SBML element. The element in the `reactions` slot for one of these parameters should be the empty string.

The second type of parameter specifies the value of a `Parameter` element within the `KineticLaw` of a reaction. These should be named by the `id` of the `Parameter`. They also should be namespaced by the containing `Reaction` `id`, which is stored in the corresponding element of the `reactions` slot.

### Objects from the Class

Objects can be created by calls of the form `new("SOSDesign", data, nrow, ncol, byrow, dimnames, ...)`. This is the same as initializing a `matrix`.

### Slots

`.Data`:
  Object of class `"matrix"`, holding the parameter settings.
`reactions`:
  Object of class `"character"` of length the number of columns, holding the reaction IDs for parameters local to a reaction (i.e. `KineticLaw` `Parameter`s). For global parameters, the corresponding value should be the empty string.

### Extends

Class `"matrix"`, from data part. Class `"ExperimentDesign"`, directly. Class `"array"`, by class "matrix", distance 2. Class `"structure"`, by class "matrix", distance 3. Class `"vector"`, by class "matrix", distance 4, with explicit coerce.

### Methods

reactions
  `signature(object = "SOSDesign")`: gets the `reactions` slot.
reactions<-
  `signature(object = "SOSDesign")`: sets the `reactions` slot.

### Author(s)

Michael Lawrence

### References

See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.

### See Also

`SOSExperiment`, the container of this class, for configuring and running a simulation.

[Package rsbml version 2.2.1 Index]