eqnlist {dMod} | R Documentation |
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 |
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 |
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"))