dget_LUHj: Structural length, reserves and maturation between birth and...

Description Usage Arguments Value Author(s) References Examples

Description

Calculates the development of structure and the changes in reserves and maturity during the larvae development (when feeding, start)

Usage

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dget_LUHj(a, LUH, p, pars)

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 larva

p

a list containing all the DEB parameters for the species. Called by the get_DEB_pars function.

pars

a 2-vector with lb: scaled length at birth and f: scaled functional response for the larva.

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

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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');

# daily change in weight during the larval feeding stage until metamorphosis
  a <- seq(ltR$tb/p$k_M, ltR$tj/p$k_M,1)                    # days, from birth to metamorphosis
  LUH_0 <- LUH[nrow(LUH),2:4]                    # initial state vector (last row of the results obtained for the non-feeding larva)
  pars = c(ltR$lb, f)
  LUHj <- ode(LUH_0, a, dget_LUHj, p=p, pars=pars, method='ode45')

# all togethe
  LUH = rbind(LUH, LUHj)
  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.