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2.3 VPA2Box
VPA-2BOX is a flexible software tool for analyzing the abundance and mortality of exploited animal populations that is based on the ADAPT framework developed by Parrack (1986) and Gavaris (1988). The primary difference between this package and other versions of ADAPT is the capability of analyzing two different stocks simultaneously, making possible routine quantitative analyses of the effect of sex-specific growth or stock intermixing. In addition, a wide variety of options are provided with respect to the types of data that may be used and the way the parameters are estimated.
To conduct projections PRO-2BOX is used.
Current Entry 4th December, 2018
First Entry April 2002
First ICCAT Reference
PORCH, 1995
Catalogue Committee
Proposer:
Seconder:
Reviewers:
ICCAT Secretariat
VPA-2box Version 4.01
PRO-2box Version 3.0
VPA-2box Version 4.01
PRO-2box Version 3.0
The source code is available here
Clay E. Porch NMFS, Southeast Fisheries Science Center 75 Virginia Beach Drive Miami, FL 33149, USA Clay.Porch@noaa.gov
Copies of the executable code and manual for VPA-2BOX may be distributed without restriction.
The development of VPA-2BOX is ongoing, and the author appreciates comments regarding it, including any suspected bugs. However, no formal technical support is offered.
There is no warranty of any kind. While considerable effort has been made to ensure the program performs as described in the manual (see Appendix 3), the author and the U.S. government cannot be held responsible for any errors therein.
The only file needed for a complete installation is the executable VPA-2BOX.exe. To run the program you can either place the executable in a directory of your choosing and add that directory to your PATH statement as described in the documentation for your operating system and restart or place a copy of VPA-2BOX.exe in the directory where you plan to do the analyses.
The program may be run from the Windows Run dialog, entering the name VPA-2BOX at a DOS prompt, or double clicking on the VPA-2BOX.EXE icon in Windows Explorer. It may also be run in batch mode from the Windows command line, DOS or other shell environments. For example, a .bat file may be written such as the example vpa.bat to the right. The program may be started by double clicking or otherwise calling the batch file. In this example the name of the executable vpa-2box is followed by the name of an ASCII text file that contains the specifications needed to make the run (the user may specify the name and extension).
If the name of the control file is not entered in the command line, the program will prompt the user as shown in the screen capture below. There is no graphical user interface; VPA-2BOX runs only as a console-mode program that takes all input from ASCII text files (described in chapter 3). The screen is used only to enter the name of the control file and to display certain error and advisory messages. Hence, the user must be able to create and edit ASCII text files.
It is also possible to compile VPA-2BOX on linux and mac platforms. An example of code for a batch file, Makefile.bat, that builds the program for mac platforms and places the executable in a directory called “build” is included in the text box below (courtesy of Matthew Supernaw, Southeast Fisheries Science Center). Note that the compiler, in this case gfortran, is specified on the 12th line by FC = gfortran.
See manual for a complete description of Data requirements and Program outputs
A variety of outputs are available in the output diagnostic statistics and derived quantities file.
The programme can aslso conduct retrospective analyses and bootstraps.
GAVARIS , S. 1988. An adaptive framework for the estimation of population size. Can. Atl. Fish. Sci. Adv. Comm. (CAFSAC) Res. Doc. 88/29. 12 pp.
PARRACK , M. L. 1986. A method of analyzing catches and abundance indices from a fishery. ICCAT Coll. Vol. Sci. Pap. 24:209-221.
PORCH , C. E. 1995. A two-area VPA with discrete mixing: Can we discriminate between mixing rates given the present condition of the data? ICCAT Coll. Vol. Sci. Pap. 44(1): 198-208.