AGEPRO: auxillaryOutputFlag(stockSummaryFlag) Changes

[efletcherPIFSC]

To give the user more flexibility to output specific "auxiliary files" with AGEPRO calculation engine output files, @JonBrodziak has proposed to add additional options to the [OPTIONS] option StockSummaryFlag (and rename it as AuxillaryOutputFlag)

Note

AGEPRO VERSION 4.2 version format Input files will be phased out, but its compatible with AGEPRO VERSION 4.0.

AGEPRO Model Run Output Files

In AGEPRO-GUI, each AGEPRO Calculation Engine model run is stored as a subdirectory under the system's home's AGEPRO directory. For example:

C:\\Users\\winusername\\Documents\\AGEPRO\\Example3_2024-08-01_13-00-21

In the model run directory contains the bootstrap file (.BSN), AGEPRO model input file (*.INP), Calculation Engine Output File (*.OUT), and Auxiliary files.

File	Description
<AgeproModel>.bsn	Bootstrap File
<AgeproModel>.inp	AGEPRO Model input file
<AgeproModel>.out	AGEPRO Calculation Output File. (Includes Stock Distribution if enabled)
<AgeproModel>.xx1	Auxiliary #​1: Stock Numbers Of Age
<AgeproModel>.xx2	Auxiliary #​2: Recruitment
<AgeproModel>.xx3	Auxiliary #​3: Spawning Stock Biomass
<AgeproModel>.xx4	Auxiliary #​4: Total Stock Biomass (From Jan 1st)
<AgeproModel>.xx5	Auxiliary #​5: Mean Stock Biomass
<AgeproModel>.xx6	Auxiliary #​6: Combined Catch Biomass
<AgeproModel>.xx7	Auxiliary #​7: Landings
<AgeproModel>.xx8	Auxiliary #​8: Discards
<AgeproModel>.xx9	Auxiliary #​9: Fishing Mortality
<AgeproModel>.xx10	Auxiliary #​10: Catch By Fleet

Stock at Size Distribution

Original Behavior (AGEPRO VERSION 4.0)

For AGEPRO VERSION 4.0 input files, Stock at Size Distribution can be added to the output via stockSummaryFlag = 1 . This will append the Stock at Size Distribution to the AGEPRO output file, and include the Stock Numbers of Age Auxiliary File. stockSummaryFlag = 0 discards this to output.

New Behavior (AGEPRO VERSION 4.25)

There are more options to handle Stock at Size Distribution for AGEPRO VERSION 4.25 input files:

• For AGEPRO output without any Stock of Age Distribution data but keep the most of the auxiliary files (#​2-10), set auxiliaryOutputFlag = 0. This is the same functionality used in the AGEPRO VERSION 4.0 format

• To append Stock at Size Distribution to AGEPRO output file and include ALL auxiliary files, use auxiliaryOutputFlag = 1. This will include the Stock Numbers of Age Auxiliary file. This is the same functionality in the AGEPRO VERSION 4.0 format.

• To only generate an AGEPRO output file without Stock at Age Distribution data, set auxiliaryOutputFlag = 2

• To only generate an AGEPRO output file with Stock at Age Distribution data, set auxiliaryOutputFlag = 3

• To append Stock At Age Distribution Data to AGEPRO output, but exclude the Stock Numbers of Age Auxiliary file (Auxiliary files #​2-10 are kept), set auxiliaryOutputFlag = 4.

stockSummaryFlag/auxilllaryOutputFlag Changes

stockSummaryFlag for AGEPRO VERSION 4.0

• stockSummaryFlag allows the user to append the tables of stock size at age distribution summary to the AGEPRO output file and enable the accompanying Stock at Age auxiliary file.

  • Stock of age distribution summary (appended to the AGEPRO output file) MUST have the stock of age auxiliary file.

• There is one stock size at age table per time period in the projection. Each table has rows that are age classes and columns that are percentiles of the distribution of numbers of fish in each age class. There are 10 auxiliary output files.

  If Auxiliary Files are not enabled, AGEPRO (AGEPRO VERSION 4.0) will generate Auxiliary files without any data.

• stockSummaryFlag = 0

  • Stock at Age Distributions NOT (calculated and) appended to AGEPRO Output File

  • Clear/Nullify Stock Numbers of Age Auxiliary File #​1

  • Output Auxiliary Files #​1-10

• stockSummaryFlag = 1

  • Calculate and append stock of age distributions to AGEPRO Output File

  • Output Auxiliary files #​1-10

auxiliaryOutputFlag for AGEPRO VERSION 4.25

• auxiliaryOutputFlag supersedes stockSummaryFlag with more options to control auxiliary file output.

• auxiliaryOutputFlag = 0

  • Stock at Age Distributions NOT calculated and appended to AGEPRO Output File

  • Clear/Nullify Stock Numbers of Age Auxiliary File #​ 1

  • Output Auxiliary Files #​2-10

• auxiliaryOutputFlag = 1

  • Calculated and append Stock at Age Distributions to AGEPRO Output File

  • Output Auxiliary Files #​1-10

• auxiliaryOutputFlag = 2

  • Stock of Age Distributions NOT calculated and appended to AGEPRO Output File

  • Do NOT output any Auxiliary Files

• auxiliaryOutputFlag = 3

  • Calculate and append Stock at Age Distributions to AGEPRO Output File

  • Do NOT output any Auxiliary Files

• auxiliaryOutputFlag = 4

  • Calculate and append Stock at Age Distributions to AGEPRO Output File

  • Clear/Nullify Stock Numbers of Age Auxiliary File #​1

  • Output Auxiliary Files #​2-10