Simulation plan tutorial

Experimental design matrix

The experimental design matrix has a row for each simulation run and a column for each parameter to be varied. The values of the parameters are represented by integer keys (e.g. -1, 0 and 1, for lower value, normal value and higher value). The matrix is defined in a .txt file, without column or row headers, with the keys separated by semicolons.

Parameter files

There is a parameter file for each parameter to be varied. This specifies the correspondence between the keys and the values of the parameter. The parameter may be a value, a list of values or an expression.

If the experimental design specifies two keys, -1 and 1, for a parameter then the parameter file will look like

Parameter defined by a list

  -1=0.5;0.8;0.9;0.11
  1=0.5;0.11;0.15;0.41

Parameter defined by an expression

  -1=if(condition = true) return 5 ; else return 3 ;
  1=if(condition = true) return 7 ; else return 3 ;

Parameter defined by a single value

  -1=0.8
  1=1.2

Rules

The parameters for rules can also be modified. The parameter file for the rule must define all the values for the public parameters of the rule (see file amp.txt in the sample files <http://www.isis-fish.org/v4/downloads/Exemple_directory.zip>_). For some rules, it may be necessary to define the population, the fishing gear, the zone, etc. targeted by the rule. In this case the name of the object cannot be used and the internal code for the object is required. This is of the form

  fr.ifremer.isisfish.entities.Zone#1169028645767#0.37798185123822536

To determine the code, run a simulation with the rule correctly parameterized. You will find the code in the debug.txt file (in the same directory as the .bat or .sh file used to run ISIS-Fish) against the parameter name at the point where the rule is initialized.

N.B. the syntax in the simulation plan files is strict.

• No spaces
• No semicolon at the end of the line
• No leading + sign for positive keys (+1 is not allowed, use 1)

Sample files

These sample files are for a sensitivity analysis for the parameters describing growth, accessibility, selectivity and closure period for a regulated fishing area.

sample matrix.txt and parametername.txt files

The matrix.txt and parametername.txt files should be placed in single directory, preferably a sub-directory of the directory with the .bat or .sh file used to run ISIS-Fish.

sample simulation plan script

Simulation plan scripts can be written or modified using the script editor. If you do not use the script editor, the sample script should be copied to isis-fish-4\isis-database\simulationplans in your user or home directory. This script sets the values of the parameters to be varied for each simulation using the experimental design.

This script has all the methods for reading the matrix.txt and parametername.txt files. The directory with the matrix.txt and parametername.txt files should be declared in the script (around line 117).

  public String param_directory = "Sample_directory/"

The parameters to be varied, their order in the matrix and the filenames are defined by the declarations in the script around lines 104-108 and 158

  static private final String MATRIX = "matrix";
  ...
  static private final String AMP = "amp";
  Arrays.asList(new String[] { VBGF, CATCHABILITY, SELECTIVITY, AMP }

The script also has code for modifying the parameters in the database (see the API documentation (http://www.isis-fish.org/v4/user/API.html) for the methods that can be used to modify the database).

Sample script

Calibration script

This simulation plan uses a variable step simplex method for calibrating two parameters (the accessibility for large and small fish) to match quarterly landings.