addMAreactRate: Adding reaction rates

In Vessy/sysBio: A package for modeling biological systems

Description

This function allows users to define reaction rate. Reaction rate can be defined as a fixed numerical value (e.g., r=m1, where m1 represents a constant parameter, m1=0.9, or just as r=0.9) or initial assignments (e.g., r=m1*A, where m1 represents a constant parameter and A represents a species).

Usage

addMAreactRate(x, rr = NA, type = "fixed", val = "1", overwrite = FALSE)

Arguments

x	model to which the reaction rate is added (required)
rr	reaction rate name (required),
type	reaction rate type; currently supported options are fixed and assigned; if the value is not specified, sysBio will set type to fixed
val	reaction rate value; if defined as fixed, the value should be specified as a number. e.g., 0.1; if defined as assigned, the value can be defined in form of an assignment (function), e.g., B or 10*A. If the value is not specified, sysBio will set the value to 1
overwrite	a flag that allows changes to the existing reaction rate (default value FALSE)

Value

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

• rates$rrName - reaction rate name

• rates$rType - reaction rate type

• rates$rVal - reaction rate 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")

 
# Show info about model reactions and rates
exmp$reaction
exmp$rates

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