addParameters: Adding parameters

In Vessy/sysBio: A package for modeling biological systems

Description

This function allows users to specify values of parameters used in the reaction (if parameters are used). The current sysBio version assumes that parameters, if defined, will remain constant during simulation. Thus, only numerical values can be assigned to parameter values.

Usage

addParameters(x, pName = NA, iVal = "1", overwrite = FALSE)

Arguments

x	model to which the parameter is added (required)
pName	parameter name (required)
iVal	parameter value; if the value is not specified, sysBio will set it to 1
overwrite	a flag that allows changes to the existing parameter (default value FALSE)

Value

This function adds information about parameters into the model (given as a first argument of the function). Parameters information is stored in the list format and contain the following elements:

• parameters$pName - parameter name

• parameters$initVal - parameter value

Examples

exmp <- newModel("This is an example of a new model")
addMAreaction(exmp, react="A = null", "rf", "rb")
addMAreaction(exmp, react="A + B -> 2*AB", "k", name="Forward AB")
addMAreaction(exmp, react="AB -> null", "rAB")

addMAreactRate(exmp, "rf", "fixed", "1")
addMAreactRate(exmp, "rb", "fixed", "0.75")
addMAreactRate(exmp, "k", "fixed", "0.5")
addMAreactRate(exmp, "rAB", "assigned", "p1*A")

addParameters(exmp, "p1", 0.75)
 
# Show info about model reactions and parameters
exmp$reaction
exmp$parameters

Vessy/sysBio documentation built on May 9, 2019, 9:55 p.m.