jacobian: Calculates the Jacobian matrix.

In cdiener/dycone: dycone - analyze the dynamic landscape of metabolome data

Description

Calculates the Jacobian matrix.

Usage

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

data(eryth)
S <- stoichiometry(eryth)
concs <- runif(nrow(S))
names(concs) <- rownames(S)
J <- jacobian(S, concs)

cdiener/dycone documentation built on May 13, 2019, 2:41 p.m.