Population Analysis Model
Version 3.4.4 (March 2014)
The present version of ADAPT is a completely rewritten implementation of the age structured estimation model first introduced by Gavaris. We have incorporated features introduced by Conser, Mohn, and Restrepo in other versions of the ADAPT code. Population cohorts are estimated by a backward projection method that requires specification of a guess of the number of survivors in the last year and a decision rule for estimating the fishing mortality rate on the oldest age group in all remaining years. Catch is assumed to be measured without error. Backward projection can be based on either solution of the catch equation or by use of Pope’s approximation.
Population estimates are chosen so as to minimize the sum of squares difference between the population abundance and a set of one or more abundance indices. The IMSL implementation of the Levenburg-Marquardt method is used to solve the nonlinear least squares problem. Catchability coefficients are estimated as functions of population estimates and observed indices.
Bootstrapping is used to estimate the precision of all model parameters and all quantities that are functions of model parameters.
The graphical interface allows for model specification, importation of data sets, review of model results, and graphical display of model inputs and outputs. A comprehensive reference manual and context-sensitive help files are included. The calculation engine is written in FORTRAN using International Mathematics and Statistical Library functions for random number generation, optimization, matrix manipulation and sorting.
FACT 1.5 or 1.6 version input files will be automatically converted into the new format. Please refer to the help topic in the VPA application for more details about converting FACT input files.
WHAT files can not be converted directly. Please contact NFT support if you need to convert old WHAT input files.
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Collie, J. S. 1988 . Evaluation of virtual population analysis tuning procedures as applied to Atlantic bluefin tuna. Collect. Vol. Sci. Pap ICCAT, 28: 203-220.
Conser, R. J. and J.E. Powers. 1989. Extensions of the ADAPT VPA tuning method designed to facilitate assessment work on tuna and swordfish stocks. ICCAT Working Doc. scrs/89/43. 15pp.
Gavaris, S. 1988. An Adaptive framework for the estimation of population size. CAFSAC Res. Doc. 88/29. 12pp.
Gavaris, S. 1993. Analytical estimates of reliability for the projected yield from commercial fisheries. Can Spec Pub Fish Aquat Sci 120: 185-191.
Gulland, J. A. 1965. Estimation of mortality rates. Annex. to Arctic Fisheries Working Group Report. ICES CM 1965, doc. No 3. 9pp.
Mohn, R.K. and R. Cook. 1993. Introduction to sequential population analysis. NAFO Sci. Counc. Studies #17 110pp.
Parrack, M. L. 1986. A method of analyzing catches and abundance indices from a fishery. ICCAT Coll. Vol. Sci. Papers 24: 209-221.
Patterson K.R. and G.P. Kirkwood. 1995. Comparative performance of Adapt and Laurec-Shepherd methods for estimating fish population parameters and in stock management. ICES Journal of Marine Science 52 (2): 183-196.
Pope J. G. 1972. An investigation of the accuracy of virtual population analysis using cohort analysis. ICNAF Res. Bull. 9:65-74.
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For recent changes please see the VPA documentation, or contact User Support.
VPA Version 3.0.1 (January 2010)
Improved Graphical Interface
User may estimate a catch multiplier for a specified years range thus accounting indirectly for catch uncertainty
User may perform sensitivity analysis on Natural Mortality over a specified year & age range
Improved retrospective mode capability
User may specify weighting factors on surveys of abundance over a matrix of years and surveys
New Plus Group Calculation Option
New Reference Manual
The Pope's Approximation option has been dropped so you may notice increased run times for bootstrap runs
The Retrospective mode is now run as a set of VPA single run mode cases. This allows users to review the individual constituent runs of each retrospective iteration
VPA Version 2.7.2 (September 2007)
Includes a new plotting feature for retrospective cases.
Users may now view plots of all age classes. Previously, only numbers at recruitment age were plotted.
An auxiliary data file is generated with this data.
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Older Version Changes
VPA Version 2.7 (May 2007)
Fixed a minor bug in the retrospective model estimation.
Fixed a minor bug that cleared the Age Series output plots when the selection for Time Series Plots was set to None Selected.
VPA Version 2.6.1 (May 2007)
Fixed a bug where the stock estimate grid was incorrectly tied together with the age 1 estimate options.
Fixed a bug where the IMSL advanced options were incorrectly displayed in the GUI.
VPA Version 2.6 (April 2007)
Added the ability to combine bootstrapping with retrospective analysis.
Added the ability to create VPA data by taking raw data and changing the way the plus group is defined.
Includes a new grid editing tool with easier data entry and copy/paste abilities.
Ability to save files with spaces in the file name, and use spaces in folder names.
Upgraded version of the plotting package.
VPA Version 2.5.2 (June 2006)
The latest features include running VPA with bootstrapped retrospective
Improved Plot graphics
User may input raw data and then create a VPA input file from a subset of that data both with and without a plus group
Exporting an R object after the model has completed. Object includes complete input & output data
VPA Version 2.3.3 (November 2005)
Change to the retrospective plots. In cases where the user has not made a stock estimate in the terminal year+1 for the first age class and selects to allow that value to remain at zero, the plot will treat this data point as missing and will not attempt to plot a value of zero in the retrospective plot.
VPA Version 2.3.2 (October 2005) adds recruitment to bootstrap plotting.
VPA Version 2.3.1 (April 2005)
Additional plots are now available for comparing surveys of abundance.
A bug was fixed in the advanced features for handling estimation of recruitment stock numbers in the terminal year plus one in retrospective cases. The bug fix assures a consistent age range when using geometric mean or CDF estimates for recruitment stock in terminal year plus one as the retrospective time frame is decremented. This fix was for retrospective model runs only. Other runs were not affected.
A bug fix now allows the auxiliary file output to support time series up to 100 years (increased from 50).
VPA Version 2.2
The graphic interface was re-styled to a multi-document interface with separate forms for input and output. This allows the user to find the needed item with fewer tabs to sort through.
Options were added to allow plots to use default light & dark background color schemes as well as user customized schemes.
A plot collection feature was added that allows users to easily assemble groups of plots into a single document for ease of use in meetings.
An option was added so that users can view text output reports with the text editing software package of their choice or continue to use the viewer that comes with the Toolbox.
The output report now includes a detailed echo of all input data tables
Users may now save incomplete data by choosing to save input files without validation from the File Menu
website last modified May 16, 2016