dget_VRE: Calculate changes on state variables over a time interval
In Echinophoria/DEB_output: Dynamic Energy Budget exploration tools

Description Usage Arguments Value Author(s) References Examples

This function calculates the growth and the changes in the 3 state variables during the time period specified by a. When T or f or both are functions, it also integrates as function of temperature ad f considerig their variation during the time interval

1	dget_VRE(a, VRE, pars)

`a`	a vector containing the time point from the start at which the function has to be evaluated. Should be in days.
`VRE`	a 3 vector with the starting values of V (structure volume, cm^3), R (accumulated reproductive buffer, J) and E (energy reserves, J)
`pars`	a list containing: p: a list containing all the DEB parameters for the species. Called by the get_DEB_pars function. Lp = structural length at puberty, for the function to determine when the accumulation of R starts. s_M = acceleration factor. T: a scalar with the temperature in K or a regression model (T = f(a)) to obtain the temperature (in K) at time a for the correction during the integration. f: scaled functional response during a. It can be a scalar between 0 and 1 when food is constant during the integrated period or a function/regression model as a function of time.

VRE

a list with three vectors corresponding to the values of V, R and E at the time points (a) at which the function is evaluated.

Antonio Aguera. Danish Shellfish Center, DTU-aqua, Nykoebing Mors, Denmark

DEBlab, http://http://www.bio.vu.nl/thb/deb/deblab/

Kooijman SALM (2010) Dynamic Energy Budget theory for metabolic organisation, Third edn. Cambridge University Press, Cambridge, 509 pp.

Lika K, Kearney MR, Freitas V et al. (2011) The covariation method for estimating the parameters of the standard Dynamic Energy Budget model I: Philosophy and approach. Journal of Sea Research, 66, 270_277.

Lika K, Kearney MR, Kooijman SALM (2011) The covariation method for estimating the parameters of the standard Dynamic Energy Budget model II: Properties and preliminary patterns. Journal of Sea Research, 66, 278_288.

path <- system.file('data', package='DEB.tools')
name <- file.path(path, 'results_Odontaster_validus.mat')
p <- get_DEB_pars(name)
a <- seq(1,365,1) # to evaluate de changes daily
Lw <- 5 # cm, physical length of the individual to be evaluated.
e <- 0.8 # -, scaled reserves at the start of the evaluation.
ltR <- get_tj(p, e) # calculates key events for the initial conditions.
Lp <- ltR$lp * p$L_m
V <- (Lw*p$del_M)^3  # cm^3, initial structural volume
R <- 0 # onset of gametogenesis no reproductive buffer accumulated yet.
E <- e * p$E_m * V   # J, initial reserve.
VRE_0 <- c(V, R, E)
pars <- list(p, Lp, ltR$s_M, 283, 0.5)
t_VRE <- ode(VRE_0, a, dget_VRE, pars, method='ode45')
t_VRE <- as.data.frame(t_VRE)
names(t_VRE)<-c('Days',"V", "Er","E")