eqnlist: Generate eqnlist object

Description

The eqnlist object stores an ODE as a list of stoichiometric matrix, rate expressions, state names and compartment volumes.

Translates a reaction network, e.g. defined by a data.frame, into an equation list object.

Usage

eqnlist(smatrix = NULL, states = colnames(smatrix), rates = NULL,
  volumes = NULL, description = NULL)
as.eqnlist(data, volumes)
# S3 method for data.frame
as.eqnlist(data, volumes = NULL)
is.eqnlist(x)

Arguments

smatrix

Matrix of class numeric. The stoichiometric matrix, one row per reaction/process and one column per state.

states

Character vector. Names of the states.

rates

Character vector. The rate expressions.

volumes

Named character, volume parameters for states. Names must be a subset of the states. Values can be either characters, e.g. "V1", or numeric values for the volume. If volumes is not NULL, missing entries are treated as 1.

description

Character vector. Description of the single processes.

data

data.frame with columns Description, Rate, and one colum for each state reflecting the stoichiometric matrix

object of class eqnlist

...

additional arguments to be passed to or from methods.

Value

An object of class eqnlist, basically a list.

Object of class eqnlist

Details

If data is a data.frame, it must contain columns "Description" (character), "Rate" (character), and one column per ODE state with the state names. The state columns correspond to the stoichiometric matrix.

Examples

Run this code

# NOT RUN {
# Generate eqnlist from the constructor
S <- matrix(c(-1, 1, 1, -1), 
            nrow = 2, ncol = 2, 
            dimnames = list(NULL, c("A", "B")))

rates <- c("k1*A", "k2*B")
description <- c("forward", "backward")

f <- eqnlist(smatrix = S, rates = rates, description = description)
print(f)

# Convert to data.frame
fdata <- as.data.frame(f)
print(fdata)

# Generate eqnlist from data.frame and add volume parameter
f <- as.eqnlist(fdata, volumes = c(A = "Vcyt", B = "Vnuc"))
print(f)
print(as.eqnvec(f))
print(as.eqnvec(f, type = "amount"))

# }