jacobian: Calculates the Jacobian matrix.

Description Usage Arguments Value See Also Examples

View source: R/model_utility.R

Description

Calculates the Jacobian matrix.

Usage

1
jacobian(s_matrix, concs, deriv_func = deriv_ma)

Arguments

s_matrix

The stochiometric matrix of the model.

concs

The concentrations of the substrates. Must be a named vector with names being the metabolite names as used in rownames(s_matrix).

deriv_func

The function calculating the derivative. Must be of the form func(idx, subs, concs) where idx is the index of the differentiation variable, subs the stoichiometry of the substrates and concs the concentration of substrates. See mass_action for an example.

Value

The Jacobian matrix of dimension n_s x n_r where entry (i,j) denotes the derivative dv[j]/dS[i].

See Also

stoichiometry to calculate the stochiometric matrix.

Examples

1
2
3
4
5
data(eryth)
S <- stoichiometry(eryth)
concs <- runif(nrow(S))
names(concs) <- rownames(S)
J <- jacobian(S, concs)

cdiener/dycone documentation built on Sept. 9, 2018, 1:20 p.m.