dget_LUH: Structural length, reserves and maturation during embryonic...

In Echinophoria/DEB_output: Dynamic Energy Budget exploration tools

Description

Calculates the development of structure and the changes in reserves and maturity during the embryonic development (before feeding, i.e. birth)

Usage

dget_LUH(a, LUH, p)

Arguments

a	a vector witht the time points were the state variables will be evaluated along the interval integrated
LUH	a 3-vector containing the starting values for the structural length, scaled reserves and scaled maturity of the embryo
p	a list containing all the DEB parameters for the species. Called by the get_DEB_pars function.

Value

LUH	a list with 4-vectors: L, U and H at the time points provided by a

Author(s)

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

References

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.

Examples

path <- system.file('data', package='DEB.tools')
name <- file.path(path, 'results_Odontaster_validus.mat')
p <- get_DEB_pars(name)
f<-1
ltR <- get_tj(p, f)
U_E0 <- get_uE0(p, ltR$lb, f)   # d.cm^2, initial scaled reserve

# daily weight during development before feeding starts
  a <- seq(1, ltR$tb/p$k_M, 1)                    # days, age at birth
  LUH_0 <- c(1e-3, U_E0, 0)                        # initial state vector
  LUH <- ode(LUH_0, a, dget_LUH, p, method='ode45');
  WD <- 1e6 * (p$w_V * p$M_V * LUH[,2]^3 + p$w_E * p$p_Am/ p$mu_E * LUH[,3]) # ug, dry weight
  plot(WD~LUH[,1], type='l', xlab='days since fertilization', ylab='ug dry weight')

Echinophoria/DEB_output documentation built on Nov. 19, 2019, 10:46 p.m.