Browsing by Subject "ADAPT-VPA"

Now showing 1 - 8 of 8
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    Open Access
    A statistical model for stock assessment of southern bluefin tuna with temporal changes in selectivity
    (2003) Butterworth, Doug S; Ianelli, J N; Hilborn, R
    Assessment of the status of southern bluefin tuna (SBT) by Australia and Japan has used a method (ADAPT) that imposes a number of structural restrictions, and is similar to methods used for a number of stocks world-wide. A flexible method for assessment of the SBT population is presented that is much less restrictive and has potentially wide applicability. The three key features are: (1) all fitting to data is within the context of maximum likelihood, (2) catch-at-age data are not assumed to be without error (as in existing methods), but rather to be random variables, while age-specific selectivity is allowed to change over time within the bounds of specific structure, and (3) autocorrelation in recruitment processes is considered within the likelihood framework of the model. While the results suggest the stock has been depleted considerably from its virgin biomass, and are generally consistent with previous assessments, they also indicate that it is not as much below the biomass that will produce maximum suitable yield as previously estimated and that the extent of stock rebuilding necessary may not be as large as has been argued. The available data are shown to provide little information on the steepness parameter of the stock-recruitment function, and hence on sustainable catch levels for the stock.
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    Application of ADAPT-VPA to various stock hypotheses for the Antarctic minke whales distributed through IWC management areas IIIE to VIW
    (2006) Mori, M.; Butterworth, Doug S; Kitakado, T.
    This paper focuses primarily on addressing suggestions made during the Ulsan meeting of the Scientific Committee for refinement of the ADAPT-VPA assessments of Antarctic minke whales presented in Mori and Butterworth (2005). The methodology is extended to take account of different selectivities for the Russian and Japanese fleets during the period of commercial whaling, but this has little effect on results. The slopes of catch curves for the research catches have decreased and then stabilised during the course of the JARPA programme. This is indicative of a change in recruitment trends over time, rather than of a very high natural mortality as was amongst the postulates at the time of commercial whaling. ADAPT-VPA assessments are run for the five stock structure hypotheses specified by the Scientific Committee for the minke whales distributed through Areas IIIE to VIW, and for various choices of series of abundance estimates to which to fit the model. These runs generally indicate a trend of increasing recruitment of about 4% pa until the mid-1960s, followed by a trend in total abundance that decreases or is sometimes stable, depending on the abundance estimate series selected for fitting. Results for the Istock (Areas IIIE+IV+VW) are quite sensitive to this selection, but those for the P-stock (Areas VE+VIW) less so. Estimates of natural mortality M are generally in the 0.06 to 0.09 range, with a tendency to be somewhat higher for the P- compared to the I-stock. Fits of the outputs from the ADAPT-VPA to a stock-recruitment model generally require a carrying capacity for minke whales that first increased and then declined during the last century, and suggest MSYR1+ values in the 4-7% range. Possibilities for further work are outlined, including disaggregation of the analysis by sex.
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    Further progress on application of ADAPT-VPA to Antarctic minke whales
    (2007) Mori, Mitsuyo; Butterworth, Doug S; Kitakado, Toshihide
    The ADAPT-VPA assessment methodology originally developed by Butterworth et al. (1999) has been appreciably advanced by taking into account various comments made during a series of IWC-SC meetings and is applied here to abundance estimates (from both IDCR/SOWER and JARPA surveys) as well as catch at age data (both commercial and scientific) for the I and P-stocks of Antarctic minke whales. The improvements to the methodology allow account to be taken of various further aspects, primarily: 1) inter-annual differences in the distribution of the population between different management Areas, 2) a stock-recruitment relationship, 3) the effects of possible ageing-error, and 4) the effects of possible change in age-at-sexual maturity over time as indicated by analyses of readings of transition phases in ear plugs. Furthermore sensitivities to various functional forms for selectivity and natural mortality with age are explored. The general pattern shown by analysis for both stocks is of a minke whale abundance trend that increased over the middle decades of the 20th Century to peak at about 1970, and then stabilized or declined somewhat for the next three decades. The recruitment trend is similar, though with its peak slightly earlier. The annual natural mortality rate, M, is estimated to be 0.056 with a CV of 0.16 for the I-stock, and 0.069 with a CV of 0.15 for the P-stock for the “Reference case” assessments. When only the JARPA abundance estimates are used for tuning, M is estimated as 0.037 and 0.060 for the I- and P-stocks, respectively. The estimation of M is fairly robust to the various assumptions of the model. This analysis is considered preliminary, as conclusions relating to estimates of M and trends in abundance and recruitment obtained using this approach await further revisions of 1) abundance estimates obtained from IDCR and JARPA surveys, and 2) error-models for the catch-at-age data, particularly those obtained from the commercial harvests.
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    Open Access
    On the compatibility of results from ADAPT-VPA and transition-phased-based trends in age-at-maturity for the I-Stock of Antarctic minke whales
    (2007) Butterworth, Doug S; Mori, Mitsuyo
    A counter example is provided to show that inferences of incompatibility between population trends from ADAPT-VPA and independently estimated changes in the age-at-sexual-maturity of Antarctic minke whales over the late 1940s to late 1960s are not robust to plausible variants of the ADAPT-VPA assessment (specifically in this case admitting the possibility of a small negative slope in selectivity at larger ages). Final conclusions on this matter should await fuller investigations on the ability to the ADAPT-VPA estimator to reliably estimate the shape of the time-trend in carrying capacity over this period, upon which inferences of compatibility or otherwise are critically dependent.
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    Progress on application of ADAPT-VPA to minke whales in Areas IV and V given updated information from IDCR/SOWER and JARPA surveys
    (2005) Mori, M; Butterworth, Doug S
    The ADAPT-VPA assessment methodology of Butterworth et al. (1999) is applied to abundance estimates (from both IDCR/SOWER and JARPA surveys) and catch at age data (both commercial and scientific) for Areas IV and V. The methodology is extended to be able to take account of inter-annual differences in the distribution of the population between the two Areas when they are assessed jointly. An important feature of these updated results is that revised JARPA estimates of abundance are shown to be statistically comparable with estimates from the IDCR/SOWER programme (i.e. calibration factor not significantly different from 1). The general pattern shown by results is of a minke whale abundance trend that increased over the middle decades of the 20th Century to peak at about 1970, and then declined for the next three decades. The recruitment trend is similar, though with its peak slightly earlier. The factor to which the results are most sensitive is the value of natural mortality M. The assessments do show retrospective patterns, primarily related to changes in the best estimate of M as time has progressed. This in turn seems linked to the IDCR/SOWER survey trends suggesting higher, and the JARPA survey trends lower estimates of M. For the assessment of the two Areas combined, M is estimated at 0.068 with a CV of 0.12; this compares with CVs of typically 0.35 for the Area-specific assessments of Butterworth et al. (1999), which were based on eight seasons’ fewer data. The paper reflects an account of work in progress, and suggestions are made of areas where further analyses would be desirable.
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    Progress on application of ADAPT-VPA to minke whales in Areas IV and V given updated information from IDCR/SOWER and JARPA surveys
    (2005) Mori, M; Butterworth, Doug S
    The ADAPT-VPA assessment methodology of Butterworth et al. (1999) is applied to abundance estimates (from both IDCR/SOWER and JARPA surveys) and catch at age data (both commercial and scientific) for Areas IV and V. The methodology is extended to be able to take account of inter-annual differences in the distribution of the population between the two Areas when they are assessed jointly. An important feature of these updated results is that revised JARPA estimates of abundance are shown to be statistically comparable with estimates from the IDCR/SOWER programme (i.e. calibration factor not significantly different from 1). The general pattern shown by results is of a minke whale abundance trend that increased over the middle decades of the 20th Century to peak at about 1970, and then declined for the next three decades. The recruitment trend is similar, though with its peak slightly earlier. The factor to which the results are most sensitive is the value of natural mortality M. The assessments do show retrospective patterns, primarily related to changes in the best estimate of M as time has progressed. This in turn seems linked to the IDCR/SOWER survey trends suggesting higher, and the JARPA survey trends lower estimates of M. For the assessment of the two Areas combined, M is estimated at 0.068 with a CV of 0.12; this compares with CVs of typically 0.35 for the Area-specific assessments of Butterworth et al. (1999), which were based on eight seasons’ fewer data. The paper reflects an account of work in progress, and suggestions are made of areas where further analyses would be desirable.
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    Report on an investigation of reasons for differences between outputs from ASPM and ADAPT-VPA assessments of the Gulf of Maine cod stock
    (2005) Butterworth, Doug S; Rademeyer, Rebecca A; Plagányi, Éva E
    The application of ADAPT-VPA and ASPM assessment methods to the same data set for the Gulf of Maine cod stock allows two primary reasons for earlier differences in assessment results from these two approaches to be identified: • the longer period of data which the ASPM method is able to take into account; and • decreasing selectivity at larger ages estimated by the ASPM approach, in contrast to the flat selectivity assumed by the ADAPT-VPA application of Mayo et al. (2002). Arguments are presented that the ASPM approach (with specific details of an application still to be discussed) should be preferred over ADAPT-VPA as the basis for management recommendations for this resource. Since the ASPM assessments consistently indicate the resource status to be appreciably better relative to the MSY biomass, this has important implications for what might constitute appropriate management measures at present.
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    Statistical catch-at-age analysis vs. ADAPT-VPA:the case of Gulf of Maine cod
    (Oxford University Press (OUP), 2008) Butterworth, Doug S; Rademeyer, Rebecca A
    In 2003, given an estimate of a spawning-stock biomass (Bsp) of 27% of the maximum sustainable yield (MSY) level based on an adaptive framework-virtual population analysis (ADAPT-VPA) assessment using data only after 1981, the Gulf of Maine cod (Gadus morhua) stock was deemed “overfished” under the US Magnuson–Stevens Act. However, an alternative statistical catch-at-age assessment (SCAA) at the time, using survey data from 1964, indicated Bsp above . This is investigated, together with other (sometimes conflicting) suggestions made during a number of recent assessment reviews of this stock. The primary reason for the different result is that the ADAPT-VPA assessment imposed asymptotically flat selectivity-at-age when there was strong statistical evidence for dome-shaped selectivity. Once adjusted for this, either assessment method robustly estimates Bsp relatively close to rather than below the “overfished” threshold of 0.5 . SCAA allows the longer series of survey data available to be incorporated, providing a better basis to estimate MSY-related targets and doubling the related precision in some cases. As such targets are important when implementing the Magnuson–Stevens Act, SCAA seems preferable to ADAPT-VPA for assessing this stock. Some broader inferences to be drawn from this comparative process include the need for: (i) careful treatment of the plus-group, especially if selectivity may be dome-shaped; (ii) flexible parameterizations of selectivity-at-age in SCAA to avoid false perceptions of the precision of results; and (iii) care in the use of the Beverton–Holt stock–recruitment function, as it gives inappropriately low estimates of if there is an overall negative trend in the estimates of recruitment plotted against Bsp.