Weight coefficients

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AmP estimation

Data and completeness
Parameter estimation
Goodness-of-fit: SMSE / MRE
AmP Literature

Practice - essentials

Starting an estimation for a new species
Setting initial parameter values
Setting weight coefficients
Computing implied properties
Submitting to the collection

Practice - extra modules
Code specification
User-defined files: run, mydata, pars_init, predict
Data: Zero-variate, Univariate, Pseudo-data

Typified models
Estimation options

By default, weights are set automatically (read more here). As a general rule, the weight coefficients should quantify how certain you are about the facts. Thus, depending on your data, you have the possibility to overwrite the automatically set weight coefficients. How exactly is specified in the mydata_my_pet template. We provide here guidance for setting weight coefficients when using the the minimization of the loss function as criterium:

  • First estimate parameters with the default setting of weights, then, if necessary, re-weigh particular data points using the previous estimate as starting values.
  • Change weight coefficients by applying a factor to the existing weight coefficients, to ensure the correct (vector) size: e.g. weights.tW = 5 * weights.tW;
  • Avoid application of large factors, since the loss function then hardly depends on other data, that serve the function of determining parameters.
  • Weigh pseudo-data less than real data in the zero-variate data by a factor 10 (or so for loss-function sb).
  • Weigh points that you don't trust with weight coefficient zero.

A typical reason to re-weigh particular data points is to avoid unrealistic parameter estimates; values of the energy conductance larger than 1 cm/d, or maintenance ratios larger than 1, are likely to be unrealistic. Use related species as reference.

The default weight coefficients for the Pseudo-data are listed in the table below:

Code Value Unit Description sb su
v 0.02 cm/d energy conductance 0.1 0.00001
kap 0.8 - allocation fraction to soma 0.1 0.1
kap_R 0.95 - reproduction efficiency 0.1 0.1
p_M 18 J/d.cm^3 volume-specific somatic maintenance costs 0.1 0.00001
k_J 0.002 1/d maturity maintenance rate coefficient 0.1 0.00001
kap_G 0.8 - growth efficiency 20 20

Growth efficiency kap_G (dimensionless) controls the specific costs for structure [E_G] (units J/cm^3), which very much depends on the water-content. The water-content of structure is specified by the chemical parameter d_V (units g/cm^3) and set to a taxon-specific default value, that can be overwritten.