get_DEB_pars: Imports Dynamic Energy Budget parameters into R

In Echinophoria/DEB_output: Dynamic Energy Budget exploration tools

Description

This function reads the MatLab *.mat file generated by the DEBtool procedure (DEBlab) and gives a named list with all the DEB parameters Parameters can also be read from a csv file filled as the available template (R-package data). Parameters can be called in R by name following the DEBlab MatLab DEBtool nomenclature or in case of extra parameters the name given to such parameter during the estimation using the MatLab DEBtool. Parameters are fixed and do not depend on food levels, they are given at a reference temperature (T_ref) included in the parameters list. The output also contains a vector t.pars containing the Arrhenius temperature parameters for temperature correction (T_ref,T_A,T_L,T_H,T_AL,T_AH), according to availability of 1,3 or 5 parameters.The function also calculates the matrices eta_O and n_M for the coupling of energy, mass and mineral fluxes. These are also elements of the named list. For a parameter list and their units type "get_DEB_pars"

Usage

get_DEB_pars(file)

Arguments

file	character string with the path and name of the mat file produced by MatLab DEBtools. Generally a file name like "results_Genus_species.mat" or a csv file following the format of the provided template.

Value

p

A list containing all the basic parameters necessary to run DEB model simulations. It also contains auxiliary parameters calculated from the basic parameters. The list contains one vector "t.pars" with all the Arrhenius temperatures and T_ref. One matrix eta_O (mass energy coupler) and another matrix n_M with mineral compounds. They can all be called by their names following the DEBlab DEBtool nomenclature.

Author(s)

Antonio Aguera. Havforskningsinstituttet, Austevoll, Norway

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.

Examples

path <- system.file('data', package='DEB.tools')
name <- file.path(path, 'results_Odontaster_validus.mat')
pars <- get_DEB_pars(name)

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