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

In Echinophoria/DEB: What the Package Does (One Line, Title Case)

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

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

pars <- get_DEB_pars(system.file('data_examples_templates/results_Odontaster_validus.mat', package='DEB'))
f <- 1
ltr <- get_tj(pars, f)
  

Echinophoria/DEB documentation built on March 16, 2021, 5:22 a.m.