pars_init file

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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

The pars_init file is where one sets the seed parameter set to start the estimation procedure.

File Structure

Simplified flow chart estimation.jpg

In the next subsections we present the structure of the pars_init file following the order of appearance within the file.


In the field model of metaPar we choose the model used by writing its 3 character code. The models that have been given codes are called typified models.


One starts by setting the reference temperature, i. e. the temperature the next parameters are set for. In the add-my-pet collection the reference temperature is 20ºC. The reference temperature is the same for all entries to allow for interspecies comparisons.

Then one sets the core parameters for the typified model of your choice. For each parameter the user sets the following structures:

Parameter associated
par value of the parameter
free fix/free the parameter for the estimation (use respectively 0 or 1)
units units of the parameter (try to always use the standard units)
label label string that will be used for presentation purposes

To make the connection between the model variables/fluxes and the data we want to predict we may need to use some auxiliary parameters. These are set after the core parameters.

Finally the environmental parameters are set. For example parameters related to food or temperature that one might want to estimate

Chemical parameter setting

Using the function addchem, one can set the chemical parameters to standard values. If there is information on chemical properties of the state variables, the chemical parameters can be set independently or overwritten after using addchem.

Parameter packing

A technical section that ensures that the parameters are properly packed to be exchanged between functions.