Defines functions dBaranyi

Documented in dBaranyi

#' Baranyi growth model
#' Microbial growth model as defined in Baranyi and Roberts (1994). It has
#' been implemented according to the requirements of
#' \code{\link{ode}}. For consistency the function for isothermal growth,
#' calculations are done considering mu is in log10 scale. In other words,
#' it is multiplied by ln(10).
#' @param time numeric vector (length 1) of storage time
#' @param state named numeric vector with two components: Q and N
#' @param pars named numeric vector of model parameters (Nmax and mu_opt)
#' @param env_func named list of functions returning the values of
#' the environmental conditions for time (t)
#' @param sec_models named list of parameters of the secondary model
#' @return A numeric vector of two components according to the requirements of
#' \code{\link{ode}}.
dBaranyi <- function(time, state, pars, env_func, sec_models) {

    pars <- as.list(pars)
    state <- as.list(state)

    alpha <- state$Q/(1 + state$Q)
    beta <- 1 - state$N/pars$Nmax

    gamma <- calculate_gammas(time, env_func, sec_models)
    mu <- pars$mu_opt*prod(gamma)
    mu <- mu*log(10)  # Convert to ln CFU/[t]

    dN <- alpha * mu * beta * state$N 
    dQ <- mu*state$Q

    list(c(dQ = dQ,
           dN = dN))

Try the biogrowth package in your browser

Any scripts or data that you put into this service are public.

biogrowth documentation built on Aug. 23, 2021, 5:07 p.m.