Troubleshooter for add-my-pet procedure

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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


There are several types of trouble

The software does not work

  • run check_my_pet to see if any error messages appear which can be repaired.
  • typo
  • not used as planned by curators
  • parameter values are outside domain

software does work, but I cannot find a good fit

  • do all numbers relate to your pet, or are some left from the template?
  • check units (do use standard units; write 2 years as 2 * 365.5 days)
  • check W/L^3 (should not change that much)
  • if possible, check if univariate data specifying an age at a given weight or length (e.g. W_p) are on the growth curve
  • check if R_i really corresponds to the mean number of eggs per day for a fully grown individual
  • fix parameters for which the data contain no information(e.g. kap can only be estimated if W_m and R_i are available)

Frequently encountered error messages

We hope you find inspiration in some of the errors and possible solutions listed below.

Error 1

The check function may give the following warning:

The number of parameters in in the pars_init and in the .mat file are not the same

This warning will occur if the number of parameters in pars_init_my pet is altered, and if pars_init_method (in run_my_pet ) is set to read initial estimates from the .mat file.

SUGGESTION: Set pars_init_method equal to 0 or 2.

See Run file

Error 2

Output argument "info" (and maybe others) not assigned during call to "predict_my_pet"

SUGGESTION: info needs to be defined in predict_my_pet. It usually is an output of one of the DEBtool functions called in the file. If it is not, then put info= 1 either at the beginning or the end of the function.

Error 3

Output argument "q" (and maybe others) not assigned during call to "petregr_f".

SUGGESTION: This error occurs if you try and estimate parameters while none of the parameters defined in pars_init_my_pet are free. You need to thus check if the parameters you are trying to estimate are free.

Error 4

In pars_init_Pelagia_noctiluca.m: The seed parameter set did not pass the filter. Check previous warnings

SUGGESTION: This error occurs if you have set parameter values in pars_init_my_pet (or saved parameter values in results_my_pet,mat) that violate parameter filters. Parameter filters are integrated into a simplex method to confine parameter trajectories to the physically allowed part of the parameter space. In addition, users can specify additional parameter filters at the start of the predict file. These filters avoid that the parameters walk outside their logical domain during the estimation procedure, which substantially contribute to the stability of the estimation process. Read more about the structure of the AmP system and filters here