get_tj: Life cycle key variables for the model "abj"

Description Usage Arguments Value Note Author(s) References See Also Examples

Description

This function calculates values for variables related to key events during the life cycle of the organism (birth, metamorphosis, maturity, growth). This case is restricted to the particular DEB model case 'abj', that considers metabolism acceleration during the larval stage which grows exponentially until reaching a metamorphosis event (see Kooijman, 2010)

Usage

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get_tj(p, f)

Arguments

p

A named list resulting from the importing of DEB parameters using the function get_DEB_pars. Alternatively a vector containing the DEB parameters (g, k, v_Hb, v_Hj and v_Hp (optional)) in the same order. For symbol meaning check code and documentation of get_DEB_pars

f

Scaled functional response at which the variables are to be calculated (see Kooijman 2010 for a definition of f). It is a value between 0 and 1.

Value

This function return a named list containing scaled lengths and ages at the different key stages (birth, metamorphosis, puberty, etc)

lb

scaled length at birth, start of exogenous feeding

lj

scaled length at metamorphosis

li

scaled ultimate length (von Bertalanffy growth parameter)

tb

scaled age at birth, start of exogenous feeding

tj

scaled age at metamorphosis

ti

scaled age at which animal reach li

s_M

acceleration factor, see Kooijman, 2010

rj

scaled growth rate at exponential phase (feeding larvae)

rB

scaled von Bertalanffy growth rate

Additionally if v_Hp is provided

lp

scaled length at puberty (moment when allocation to gonads starts)

tp

scaled age at puberty

Note

Scaled values obtained here can be unscaled for further use. See examples. For further info on temperature corrections see Kooijman 2010 and t_corr

Author(s)

Antonio Aguera. BioMar, ULB, Bruxelles, Belgium

References

Aguera A, Collard M, Jossart Q, Moreau C, Danis B (2015) Parameter Estimations of Dynamic Energy Budget (DEB) Model over the Life History of a Key Antarctic Species: The Antarctic Sea Star Odontaster validus Koehler, 1906 (ed Thuesen E V.). Plos One, 10, e0140078.

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.

See Also

t_corr get_DEB_pars

Examples

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### get the parameters for the species
pars = get_DEB_pars('results_Odontaster_validus.mat')

### get scaled lengths and ages at f=1 (no food limitation)
f = 1
ltr = get_tj(p, f)

### unscaling lengths to structural lengths (see Kooijman 2010 for definition of structural length)
Lb = ltr$lb * pars$L_m        # cm, structural length at birth
Lp = ltr$lb * pars$L_m        # cm, structural length at puberty

### physical lengths
Lwb = Lb / pars$del_Mj        # cm, physical length of the larva at birth (del_Mj because is in larval stage)
Lwp = Lp / pars$del_M         # cm, physical length (in this case arm length or radius, del_M because is a post-metamorphic length)

### unscaling ages and correcting for temperature
ab = ltr$tb / pars$k_M        # d, age at birth for the reference temperature (T_ref in pars) (in days from fertilization)
T_C = t_corr(pars, 285)       # -, correction factor to get pars at 285K
aTb = ab / T_C                # d, age at birth when development occurs at a temperature of 285K.

### unscaling and correcting for temperature intrinsic growth rates rB and rj

RB = ltr$rB * pars$k_M        # 1/d, instrinsic von Bertalanffy growth rate at reference temperature.
rTB = RB * T_C                # 1/d, instrinsic von Bertalanffy growth rate at 285K.
  

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