Bas KooijmanDept theoretical biology

Vrije Universiteit AmsterdamBas@bio.vu.nl

http://www.bio.vu.nl/thb/

Add_my_peta data and parameter collection

Oslo, 2012/02/10

Contents:

• aims• method• collection• examples• patterns in parameter values

Bas KooijmanDept theoretical biology

Vrije Universiteit AmsterdamBas@bio.vu.nl

http://www.bio.vu.nl/thb/

Oslo, 2012/02/10

Add_my_peta data and parameter collection

Aims of add_my_petEstimation of all parameters of standard DEB model • for a large collection of animal species• on the basis of traceable data and software (open source)• fits can be re-done, data can be added

Computation of implied properties, given parameters template: pars_my_pet

Tool in mastering DEB theory (DEB tele course)Stimulation of application DEB theoryCompare species on the basis of parameter values (adaptation)Use patterns in parameter values to improve estimation

Primary parametersstandard DEB model

Data parameters

Covariation method• estimate all parameters simultaneously using all data: single-step-procedure zero & univariate data: > 100 different types

• use pseudo-data: size-corrected parameter values of `typical’ animal size-correction: covariation method motivation: all parameters must be determined & physical realism of values

• estimation criterion: weighted least squares, weight coefficients value-2

max likelihood with constant variation coefficient

• numerical method: simplex local minimum problem

• mark goodness of fit & completeness of data

• template: mydata_my_pet & predict_my_pet

• http://www.bio.vu/nl/thb/deb/deblabLika et al 2011 J. Sea Res, 22: 270-277

Zero-variate dataLife history events: hatching, birth, metamorphosis, puberty, death

Real data: age, length, dry-, wet-weight at life history events max rates: reproduction, respiration, feeding, growth

Modified by food, temperature

Pseudo data:

Uni-variate data

• length, weight, reproduction, respiration, feeding as functions of time, temperature, food

• Incubation time, juvenile period, life span as functions of time, temperature, food

• weight as function of length • egg number as function of weight/length

Add_my_pet: Phyton_regiusw

eigh

t, g

time since birth, d

Data by Bart Laarhoven

Zoom factor0.01: Brachionus plicatilis

138: Balaenoptera musculus

50: Loxodonta africana10: Sparus aurata

1: Pimephalus promelas

0.1: Sagitta hispida

Specific assimilation

Growth efficiency

Cost for structure

Specific somatic maintenance

Low: < 10 J/d.cm3

3 Eunectus 4 Boa 5 Andrias 7 Callorhinus 8 Esox10 Acipenser

High: > 1000 J/d.cm3

1300 Oikopleura1400 daphnids, copepods1450 Caenorhaditis2100 Bosmina2300 Oikopleura8100 Thalia

Rather high: > 200 , < 1000 J/d.cm3

205 Crinia260 Dendrobaena307 Lymnaea370 Crinia380 Leptodora480 Brachionus480 Macropus

490 Geocrinia, 490 Pseudophryne 500 Danio560 Folsomia580 Asplanchna610 Gammarus890 Chydorus

Thalia

Energy conductance

Maturity maintenance rate coeff

Allocation to soma 10.5.2

κ κ κ

pop

grow

th ra

te, d

-1

max

repr

od ra

te, #

d-1

surv

ivor

func

tion

Frequency distribution of κ among species in the add_my_pet collection:

Mean κ = 0.80, but optimum is κ = 0.5

Lika et al 2011 J. Sea Res, 22: 278-288

COMPLETE mark

Each level includes all lower levels

FIT mark

FIT & COMPLETE marks

DEB tele course 2013http://www.bio.vu.nl/thb/deb/

Free of financial costs; Some 108 or 216 h effort investment

Program for 2013: Feb/Mar general theory (5w) April symposium at NIOZ-Texel (NL) (8d +3 d) Target audience: PhD students

We encourage participation in groups who organize local meetings weeklySoftware package DEBtool for Octave/ Matlab freely downloadable

Slides of this presentation are downloadable from http://www.bio.vu.nl/thb/users/bas/lectures/

Cambridge Univ Press 2009

Audience: thank you for your attention