Description Usage Arguments Value Author(s) References Examples
Calculates the development of structure and the changes in reserves and maturity during the larvae development (when feeding, start)
1 | dget_LUHj(a, LUH, p, pars)
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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. |
LUH |
a list with 4-vectors: L, U and H at the time points provided by a |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | 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')
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