MSE Batch plugin user notes

10 Sept, 2010

Overview

The MSE Batch plugin allows you to run the MSE module in batch mode from a command file. The command file runs the MSE module changing input harvest rule parameters for each iteration and outputting data file.

MSE parameters in the command file

1. Number of MSE simulations
2. End Year
3. Assessment and Implementation error
4. Primary Production forcing functions
5. Primary Production forcing function variation
6. Fleet Control types
7. Harvest rules
   1. Fishing Mortality
   2. Total Allowable Catch
   3. Target Fishing Mortality (hockey stick parameters)

How to run

still to do Load the MSE batch plugin interface from the MSE in the navigation tree Load a command file hit the run button

Command file format

The command file is a CSV (coma separated values) file that contains tags. A tag is a predefined string of text that appears at the start of the line and is used to identify the line as valid input for the MSE module. After the data part of the tag there must be a least one empty entry to mark the end of the valid data. All data that appears after the empty entry will be ignored. For example

Control_File_Version,1.0,,,ignored comments,,,

Lines in the command file that do not contain a recognized tag will be ignored. A command file can any number of lines that are not valid inputs as long as they don't start with a valid tag, these could include comments and user notes. The order that tags appear in the file is not important.

Tags

Control_File_Version

 Control_File_Version,1.0,,

• Version number of the control file 1.0 for the current version. Used to identify parameter that may be in the file.

Model_Name

Model_Name,C:\EwE\Some model.ewemdb,,,

• Full path to a valid EwE model
• Used to check the command file against the currently loaded EwE model. If the models do not match a warning will be issued.

Ecosim_Scenario

Ecosim_Scenario,Scenario1,,

• Name of the Ecosim Scenario that the command file can work with

Run_Type

Run_Type,1,,

• Type harvest rules to set for the current MSE run. For each run of the MSE the harvest rules for the other Run_Type's will be set to zero.
• Valid inputs,
  • 1 Fishing Mortality (Constant_F) sets the fishing mortality rates to a constant value for the run,
  • 2 Total Allowable Catch (Constant_Y) sets the catch to a constant value for the run,
  • 3 Target Fishing Mortality(Hockey stick) sets the
  • 0 Any when this Run_Type option is set the harvest rules for other Run_Types will not be set to zero. This option allows for different types of harvest rules during the same MSE run.

Number_Sims

Number_Sims,50,,

• Number of Ecosim simulation the MSE will run for each iteration. This is the 'Number of trials' parameter on the MSE run form.

Error_CV

Error_CV,0.3,,

• Coefficient of variation for the observation and implementation error for the MSE stock assessment model. This is the equivalent of the Group CV's in the MSE interface.

Output_Directory

Output_Directory,C:\EwE data,,

• Directory where the MSE batch output will be sent. The MSE batch will try to create the directory if it does not already exist.