Add_my_pet a data and parameter collection

1. Add_my_peta data and parameter collection Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thb/ Oslo, 2012/02/10

2. Add_my_peta data and parameter collection Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thb/ • Contents: • aims • method • collection • examples • patterns in parameter values Oslo, 2012/02/10

3. Aims of add_my_pet Estimation 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 theory Compare species on the basis of parameter values (adaptation) Use patterns in parameter values to improve estimation

4. Primary parametersstandard DEB model

5. Data parameters

6. 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/deblab Lika et al 2011 J. Sea Res,22: 270-277

7. Zero-variate data Life 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:

8. 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

9. Add_my_pet: Phyton_regius weight, g time since birth, d Data by Bart Laarhoven

10. Zoom factor 0.01: Brachionus plicatilis 0.1: Sagitta hispida 1: Pimephalus promelas 10: Sparus aurata 50: Loxodonta africana 138: Balaenoptera musculus

11. Specific assimilation

12. Growth efficiency

13. Cost for structure

14. Specific somatic maintenance Low: < 10 J/d.cm3 3 Eunectus 4 Boa 5 Andrias 7 Callorhinus 8 Esox 10 Acipenser High: > 1000 J/d.cm3 1300 Oikopleura 1400 daphnids, copepods 1450 Caenorhaditis 2100 Bosmina 2300 Oikopleura 8100 Thalia • Rather high: > 200 , < 1000 J/d.cm3 • 205 Crinia • Dendrobaena • 307 Lymnaea • 370 Crinia • 380 Leptodora • 480 Brachionus • 480 Macropus 490 Geocrinia, 490 Pseudophryne 500 Danio 560 Folsomia 580 Asplanchna 610 Gammarus 890 Chydorus Thalia

15. Energy conductance

16. Maturity maintenance rate coeff

17. Allocation to soma 10.5.2 pop growth rate, d-1 max reprod rate, #d-1 survivor function κ κ κ 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

18. COMPLETE mark Each level includes all lower levels

19. FIT mark

20. FIT & COMPLETE marks

21. DEB tele course 2013 http://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 weekly Software 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