eqnlist: Generate eqnlist object

In dkaschek/dMod: Dynamic Modeling and Parameter Estimation in ODE Models

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 class '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
x	object of class eqnlist
...	additional arguments to be passed to or from methods.

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.

Value

An object of class eqnlist, basically a list.

Object of class eqnlist

Examples

# 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"))

dkaschek/dMod documentation built on June 12, 2025, 2:50 a.m.