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.
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.
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.
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
