run file

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AmP estimation
Concepts

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

Simplified flow chart estimation.jpg


The run file is where one executes the code and sets all of the options.

Options are set via estim_options In the following table we present the different options that the user can set as well as what each option does.


Options Description
pars_init_method

Parameter initialization method

  • 0 - get initial estimates from automatized computation(does not always work, more research is needed)
  • 1 - read initial estimates from .mat file (for continuation)
  • 2 - read initial estimates from pars_init file(default)
filter
  • 0 - do not use filter [the search will be unrestricted]
  • 1 - use filter (default) [the search will be performed in the volume of the parameter space defined by the boundaries]
loss_function
  • sb - symmetric bounded (default)
  • su - symmetric unbounded
  • re - relative error (original one, no longer in use since the DEB2017 release of DEBtool)
report
  • 1 - prints to screen the step numbers and the corresponding simplex ssq values (default)
  • 0 - does not print to screen the step numbers and the corresponding simplex ssq values
results_output

Results output format

  • 0 - only saves data to .mat (no printing to html or screen and no figures) - use this for (automatic) continuations
  • 1, -1 - no saving to .mat file, prints results to html (1) or screen (-1)
  • 2, -2 - saves to .mat file, prints results to html (2) or screen (-2)
  • 3, -3 - like 2 (or -2), but also prints graphs to .png files (default is 3)
  • 4, -4 - like 3 (or -3), but also prints html with implied traits
  • 5, -5 - like 3 (or -3), but also prints html with implied traits including related species
  • 6 - like 5, but also prints html with population traits

If a customized results file exists, the results output prints results using that file.

pseudodata

Pseudo-data choice for multispecies estimation

  • 0 - put pseudodata together with data for each pet (default)
  • 1 - put pseudodata apart for all pets (only for multispecies estimation)
method
  • 'nm' - use Nelder-Mead method (default)
  • 'no' - do not estimate
max_step_number maximum number of steps
max_fun_evals maximum number of function evaluations

Example of how to set some options : estim_options('max_step_number',5e3)