5.1 Why use Bayesian methods?
The main reason for using a Bayesian approach to stock assessment is that it facilitates
representing and taking fuller account of the uncertainties related to models and
parameter values. In contrast, most decision analyses based on maximum likelihood (or
least squares) estimation involve fixing the values of parameters that may, in actuality,
have an important bearing on the final outcome of the analysis and for which there is
considerable uncertainty. One of the major benefits of the Bayesian approach is the
ability to incorporate prior information. While other stock assessment approaches use
"prior" information by specifying levels or ranges of individual parameters for use in
sensitivity analysis, the Bayesian approach forces the analyst to look at historical data
sets or to canvass expert knowledge to determine what is known about the biological
parameters and processes. Most traditional stock assessment methods do not use any
of the quantitative information that could be gathered from historical experience with
other stocks and, in effect, treat each stock assessment as a new and independent
problem.
In the past, the effects of uncertainty have been evaluated through sensitivity analysis. In
general, this involved changing the value of a single parameter only and rerunning the
entire stock assessment. This limitation to a single parameter was due to time-
constraints and to avoid large amounts of model output. There is clearly a need for
sensitivity analysis for any stock assessment. However, current practice cannot
guarantee that some (reasonably plausible) combination of parameter values does not
give rise to behaviour that would not be expected from the results of sensitivity tests that
involve changing the value of a single parameter only. In addition, it is often difficult to
summarise the management implications of sensitivity tests that exhibit considerable
sensitivity without some form of integration across those tests. In contrast, the Bayesian
approach to stock assessment explicitly allows for weighting across alternative
hypotheses through Bayes Theorem. The use of Bayesian techniques does not
eliminate the need for sensitivity tests. It is still necessary to conduct an extensive
examination of the sensitivity of the stock assessment and decision analysis results to
the choice of the prior distributions, which data sets to include in the assessment which
to ignore, etc. Current stock assessments, both Bayesian and non-Bayesian, tend to
ignore the true range of uncertainty (both model and parameter). In particular, model-
structure uncertainty is usually completely ignored (Sainsbury (1988) is a notable
exception) even though the impact of this source of uncertainty can be more important
than that of uncertainty about the values for the parameters for any one model.
The reasons for not considering the full range of uncertainty were discussed before (see
Section 1.2.1) but briefly these relate to lack of knowledge about which alternative
models to consider, computational constraints and time limitations. Our experience is
that there are rarely difficulties identifying many alternative models. Unfortunately, the
constraints under which most assessments are conducted force the analyst to restrict
the set of alternative models substantially. The implication of ignoring some plausible
models is, of course, that uncertainty is under-estimated (to an unknown extent). The
inability to consider a wide range of models (including models that imply that the
assessment data are not indicative of trends in abundance) would explain some of the
many spectacular assessment failures.
5.2 Overcoming problems with prior distributions
The process of choosing prior distributions can be very time-consuming and frustrating.
Scientists who are experts with the species concerned but who are unaware of Bayesian
techniques (and hence do not have a full understanding of what is meant by a prior
distribution) can provide "prior distributions" which are either inconsistent or far too
precise (Walters and Ludwig, 1994). Although "expert" opinion is currently the dominant
method for determining priors, and is the source of many problems, we believe that prior
distributions will increasingly be determined by analysis of information from synthesis
studies and hence depend less on "expert" opinion (see Section 4.3). The majority of the
problems encountered during the development of Bayesian assessments have resulted
from arguments about the choice of prior distributions. In particular, considerable
difficulties have arisen when attempts have been made to select appropriate
noninformative prior distributions. In contrast, the development of informative priors
tends to be productive with most participants in the stock assessment groups concerned
cooperating even in fairly confrontational assessment situations.
Punt and Hilborn (1997) recommend that whenever a Bayesian assessment is
conducted, considerable care should be taken to document fully the basis for the various
prior distributions. This documentation process must include specifying which models
were considered for inclusion in the analysis and why some of these models were not
included in the final analyses, even though they may be plausible. We have found that
the process of constructing priors increases the participation in the assessment process
of non-modellers (i.e. biologists, industry, and members of the conservation movement).
This increases the confidence that decision makers place in the assessment results
because all of the stakeholders can have input into the assessment.
5.3 The computational demands
It is extremely intensive computationally to apply Bayes Theorem to complex models. It
often takes days of computer time even on reasonably powerful personal computers to
conduct an analysis based on an age-structured model. The algebraic demands of the
methods (e.g. the need for a full understanding of probability theory) have also
discouraged application of the method. However, in order to conduct defensible decision
analyses for assessments based on maximum likelihood estimation, it is usually
necessary to conduct a bootstrap analysis (e.g. Restrepo et al., 1992). Such an analysis,
although not usually as intensive computationally as applying Bayes Theorem, can often
take several hours on a personal computer. Furthermore, even seemingly simple
approaches such as bootstrapping are not without their theoretical traps (e.g. Poole et
al., 1999).
5.4 In conclusion
While no approach to stock assessment can guarantee the "correct" answer, the
Bayesian approach to fisheries stock assessment provides the most theoretically
defensible framework within which probabilistic questions (e.g. is the stock increasing,
what is the impact of a TAC of 10,000 tonnes) can be addressed. The ability to consider
model uncertainty within a single framework, although currently underused, is a major
advantage of Bayesian methods. Finally, the Bayesian approach to fisheries stock
assessment provides a formal framework for incorporating information from other
species and
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