add_my_pet a data and parameter collection
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Add_my_pet a data and parameter collection. Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam [email protected] http://www.bio.vu.nl/thb /. Oslo, 2012/02/10. Add_my_pet a data and parameter collection. Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam - PowerPoint PPT PresentationTRANSCRIPT
Bas KooijmanDept theoretical biology
Vrije Universiteit [email protected]
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 [email protected]
http://www.bio.vu.nl/thb/
Oslo, 2012/02/10
Add_my_peta data and parameter collection
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 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 r
ate,
d-1
max
rep
rod
rate
, #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 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