OpenUCT :: Browsing by Author "De Moor, Carryn L"

Browsing by Author "De Moor, Carryn L"

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Alternative hypotheses of two mixing stocks of South African sardine: some projections assuming no future catch
(2014) De Moor, Carryn L
This document shows projections of the sardine 1+ biomasses under a no catch scenario for a number of the alternative hypotheses considered by de Moor et al. (2014). The alternatives are summarised again below for ease of reference, together with details of any changes in the simulation testing framework of de Moor and Butterworth (2013). Projections are shown from the results at the joint posterior mode (even though some of these have not converged, see de Moor et al. (2014)), which thus only incorporate simulated future random error, and from the posterior distributions of a limited number of hypotheses which did converge at the joint posterior mode. Given the limited time available to run MCMC, full convergence diagnostics were not checked for any results presented here. Samples were randomly drawn with resampling from a segment of the chain123 . For simplicity, the average sardine catch weight at age is kept constant at the baseline values for all hypotheses.
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Alternative OMP trade-off curves in response to the request by SAPFIA
(2010) De Moor, Carryn L; Butterworth, Doug S
In preparation for OMP-12, SAPFIA requested trade-off curves to be plotted for three cases where changes to the TAC rules and/or constraints of OMP-08 are considered and asked for a trade-off curve to show the effect of alternative choices of the control parameter β which specifies the proportion of the sardine biomass estimate from the November survey that is recommended as the TAC (subject to other constraints). [The SPFIA requests are reproduced in the Appendix.]
Open Access
An alternative relationship to determine future movement of sardine recruits between the "west" and "south" stocks
(2013) De Moor, Carryn L; Butterworth, Doug S
de Moor and Butterworth (2013a) explored some possible relationships between the proportion of “west” stock recruits moving to the “south” stock and “west” or “south” stock 1+ biomass or recruitment. A relationship based on the ratio of “south” to “west” stock 1+ biomass in the previous November was used for initial testing of Candidate Management Procedures under a two stock sardine hypothesis.
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Application of the ''River Model'' to estimate the impact of fishing on the amount of anchovy available to west coast penguin colonies
(2014) De Moor, Carryn L; Butterworth, Doug S
A simple approach is used to estimate the extent to which the amount of anchovy recruits of the year which would otherwise have been available to penguin colonies off the West Coast has been reduced by historic levels of fishing. Results suggest that over the past decade the extent of this reduction has been a median of 5-6% and at most some 25%.
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Assessing the South African sardine resource: two stocks rather than one?
(National Inquiry Services Centre (NISC), 2015) De Moor, Carryn L; Butterworth, Doug S
Sardine Sardinops sagax distributed off the west and south coasts of South Africa have traditionally been assumed to comprise a single well-mixed stock for assessment and management purposes. New research, however, lends weight to the possibility of two stocks in this region. A precautionary management approach thus needs to consider the impact of management decisions on the hypothesised two individual stocks as well as on the resource as a whole. As a first step in this process, Bayesian assessments of South African sardine are presented, which compare results for the traditional single-stock hypothesis with those that follow from a new two-mixing-stock hypothesis. Recruits from the west stock are assumed to move to and remain part of the south stock in annual pulses of varying size. This movement is estimated to be appreciable, and to take place from a substantially more productive west stock to the south stock. This immigration makes a greater contribution to the south-stock biomass than do years of above-average south-stock recruitment. Importantly, this two-mixing-stock hypothesis is shown to be consistent with the data available. Further alternative sardine stock-structure hypotheses suggested by the most recent data are discussed.
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Assessment of the South African anchovy resource using data from 1984 – 2009: attempts to resolve residual trends
(2010) De Moor, Carryn L; Butterworth, Doug S
Further testing of the proposed baseline anchovy assessment, “A0” from de Moor and Butterworth (2010) is undertaken. It is proposed that the assumption of two stock recruitment “regimes” (pre- and post-2000) be taken forward as a robustness test during OMP testing.
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Assessment of the South African anchovy resource using data from 1984 – 2010: posterior distributions for the two base case hypotheses
(2011) De Moor, Carryn L; Butterworth, Doug S
The operating model (OM) for the South African anchovy resource has been updated from that used to develop OMP-08 given four more years of data and a revised time series of commercial catch. The OM with results at the posterior mode has already been presented (de Moor and Butterworth 2011). The posterior distributions for the two base case hypotheses are similar in many respects except for parameters relating to the stock recruitment relationship.
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Assessment of the South African anchovy resource using data from 1984 – 2010: results at the posterior mode
(2011) De Moor, Carryn L; Butterworth, Doug S
The operating model (OM) for the South African anchovy resource has been updated from that used to develop OMP-08 given four more years of data and a revised time series of commercial catch. A Hockey Stick stock recruitment relationship, and the same median juvenile and adult natural mortality rates as in previous assessments are used. When considering the Beverton Holt, Ricker and Hockey stick stock recruitment relationships, AICc model selection criterion do not show strong support for one relationship over another, yet the carrying capacity at the posterior mode differs considerably between the Hockey Stick and other relationships. Two base case hypotheses are chosen: one estimates random effects about adult natural mortality over time while the other assumes time-invariant annual adult natural mortality. There has been a decrease in recruitment residual standard deviation and in recruitment autocorrelation for this updated OM compared to that used in previous OMs. The impact of this on the appropriate choices of a risk definition and threshold for the new OMP to be developed needs to be considered. The resource abundance remains above the historic average, with a model-estimated 1+ biomass of 2.2-2.4 million tons in November 2010, having provided 8 years of above average recruitment in the past 11 years. The harvest proportion over the past 11 years has not exceeded 0.13.
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Assessment of the South African anchovy resource using data from 1984 – 2010: variability in natural mortality
(2011) De Moor, Carryn L; Butterworth, Doug S
Initial results of the updated assessment of the South African anchovy resource, using data from 1984 to 2010, were presented by de Moor and Butterworth (2011). This work included the use of a random effects model for adult natural mortality with a fixed standard deviation of 0.2 and 0.5. This approach has now been further extended such that annual autocorrelation can be included and the associated parameters can be estimated, rather than fixed. Similar testing on the use of random effects models for juvenile natural mortality has also been undertaken.
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Assessment of the South African anchovy resource using data from 1984-2009
(2010) De Moor, Carryn L; Butterworth, Doug S
The assessment of the South African anchovy resource has been updated given three more years of data and a revised time series of commercial catch. The base case hypothesis has the same juvenile and adult natural mortality rates as previous assessments, but a Beverton Holt stock recruitment relationship is now assumed instead of a hockey stick with fixed inflection point based on the AICc selection criterion. This change has resulted in a large increase in median posterior carrying capacity from previous assessments. There has been a decrease in recruitment residual standard deviation and in recruitment serial autocorrelation with the newer assessments. The impact of this on the appropriate choice of a risk definition and threshold for the new OMP to be developed next year will be considered early in the OMP development phase. The resource abundance remains above average, with a model-estimated 1+ biomass of 3.5 million tons in November 2009, and the resource has produced 8 years of above average recruitment in the past 11 years. The harvest proportion in the past 9 years has not exceeded 0.14.
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Assessment of the South African sardine resource using data from 1984-2010: further work towards a base case single stock hypothesis
(2011) De Moor, Carryn L; Butterworth, Doug S
The sardine assessment is extended to consider three hypotheses for the presence of two (west and east) stocks separated at Cape Agulhas. The first hypothesis of two completely separated stocks is dismissed, as it implies that an unrealistically low proportion of the recruits for the eastern stock are detected in the recruitment survey. The second hypothesis of movement of recruits from west to east stocks, the extent of which varies from year to year, is more successful in terms of matching the data for realistic values of detectability of eastern recruits in the recruitment survey. However the proportion moving from year to year is only weakly correlated with high biomass or recruitment in the western stock that year. The third hypothesis is a variant of the second for which the data are less informative because the “dividing line” between west and east recruits is taken to be unknown. This (in the one of several possible forms implemented thus far) produces similar results to the second hypothesis. It is proposed that because of the limited time available now to complete the OMP revision, and further issues still to be resolved relating to future projections under two stock hypotheses in relation to the distribution of catching, that future work in finalising this OMP process be restricted to the second hypothesis (specifically the variant which assumes movement from 1994 onwards onwards when the recruit survey was extended further eastwards).
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Assessment of the South African sardine resource using data from 1984-2010: further work towards a base case single stock hypothesis
(2011) De Moor, Carryn L; Butterworth, Doug S
Further work towards choosing a base case single sardine stock hypothesis operating model has been undertaken. This work extends that reported in de Moor and Butterworth (2011).
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Assessment of the South African sardine resource using data from 1984-2010: initial results for a two stock hypothesis
(2011) De Moor, Carryn L; Butterworth, Doug S
The sardine assessment is extended to consider three hypotheses for the presence of two (west and east) stocks separated at Cape Agulhas. The first hypothesis of two completely separated stocks is dismissed, as it implies that an unrealistically low proportion of the recruits for the eastern stock are detected in the recruitment survey. The second hypothesis of movement of recruits from west to east stocks, the extent of which varies from year to year, is more successful in terms of matching the data for realistic values of detectability of eastern recruits in the recruitment survey. However the proportion moving from year to year is only weakly correlated with high biomass or recruitment in the western stock that year. The third hypothesis is a variant of the second for which the data are less informative because the “dividing line” between west and east recruits is taken to be unknown. This (in the one of several possible forms implemented thus far) produces similar results to the second hypothesis. It is proposed that because of the limited time available now to complete the OMP revision, and further issues still to be resolved relating to future projections under two stock hypotheses in relation to the distribution of catching, that future work in finalising this OMP process be restricted to the second hypothesis (specifically the variant which assumes movement from 1994 onwards onwards when the recruit survey was extended further eastwards).
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Assessment of the South African sardine resource using data from 1984-2011, with some results for a single stock hypothesis
(MARAM, University of Cape Town, 2012) De Moor, Carryn L; Butterworth, Doug S
Although the base case operating model for the South African sardine resource was updated from the last assessment (Cunningham and Butterworth 2007) to take account of new data collected between 2007 and 2010 (de Moor and Butterworth 2011a), the International Review Panel for the 2011 International Fisheries Stock Assessment Workshop suggested some revisions to this model (Smith et al. 2011) before it is used in the development of a new MP. de Moor and Butterworth (2011a) proposed two base case operating models; one which estimated random effects about adult natural mortality over time while the other assumed constant (time-invariant) adult natural mortality. The inclusion of the random effects was in response to similar changes made to the base case operating models for anchovy (de Moor and Butterworth 2011b). Smith et al. (2011) suggested rather that a base case with constant natural mortality be used.
Open Access
Assessment of the South African sardine resource using data from 1984-2011: further results for a two stock hypothesis
(2013) De Moor, Carryn L; Butterworth, Doug S
As part of the process of updating the assessment of the South African sardine resource, a model of the sardine two mixing-stock hypothesis is being developed. This hypothesis postulates a “west” stock distributed west of Cape Agulhas and a “south” stock distributed south-east of Cape Agulhas with movement from the “west” to the “south” stock in November as recruits age to 1 year olds. de Moor and Butterworth (2012a) presented some initial results for a two mixing-stock model, but cautioned that those results may not yet have fully converged and that the lack of a Hessian prevented MCMC simulation to estimate posterior distributions for key model parameters. Work has continued on this model to try to ascertain in which areas the model may be overparameterised and which “unimportant” parameters can be fixed at their estimated values without influencing results. In this document further results for the model of a two sardine mixing-stock hypothesis are presented. The current fit is improved from that of de Moor and Butterworth (2012a) and a Hessian is estimated by ADMB. The main changes to the model are detailed below. Some ideas for further work are also listed.
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Assessment of the South African sardine resource using data from 1984-2011: initial results for a two stock hypothesis
(2012) De Moor, Carryn L; Butterworth, Doug S
As part of the process of updating the assessment of the South African sardine resource, a sardine two mixing-stock hypothesis is to be tested. This hypothesis postulates a “west” stock distributed west of Cape Agulhas and a “south” stock distributed south-east of Cape Agulhas with movement from the “west” to the “south” stock in November as recruits age to 1 year olds.
Open Access
Assessment of the South African sardine resource using data from 1984-2011: results for a two stock hypothesis at the posterior mode
(2013) De Moor, Carryn L; Butterworth, Doug S
As part of the process of updating the assessment of the South African sardine resource, a model of a sardine two mixing-stock hypothesis has been developed. This hypothesis postulates a “west” stock distributed west of Cape Agulhas and a “south” stock distributed south-east of Cape Agulhas, with movement from the “west” to the “south” stock in November as recruits age to 1 year olds. de Moor and Butterworth (2012a, 2013) presented some initial results for a two mixing-stock model. Work on modelling this hypothesis has continued to try to ascertain in which areas the model may be over-parameterised and which “unimportant” parameters can be fixed at constant values without unduly influencing key results. Further testing of model assumptions has also been undertaken. In this document further results for the model of a two sardine mixing-stock hypothesis are presented and a base case operating model is proposed.
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Can anchovy age structure be estimated from length distribution data collected during surveys?
(National Inquiry Services Centre (NISC), 2013) De Moor, Carryn L; Butterworth, Doug S; Coetzee, J C
Historically, a time-series of proportions-at-age 1 from annual November hydro-acoustic surveys has been used to inform the assessment of, and in particular the choice of appropriate values for juvenile and adult natural mortality for, the South African anchovy Engraulis encrasicolus. However, information from direct ageing is limited and almost two decades old. A new method is developed to estimate the annual proportions of anchovy at age 1 directly from the population length distributions estimated from samples taken during the November surveys. This method involves modelling the annual length distributions of age 1 and age 2+ anchovy. The analysis provides a new time-series of proportions-at-age 1, together with associated standard errors, for input into assessments of the resource. The results also caution against the danger of scientists reading more information into data than is really there.
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Catch to natural predation ratios for sardine and anchovy
(2010) De Moor, Carryn L; Butterworth, Doug S
One approach to place the size of annual fishery catches of sardine and anchovy into perspective is to contrast them with annual losses to natural mortality, which correspond to the amounts consumed by natural predators. This is pursued here using results from the most recent assessments of these two resources (de Moor and Butterworth 2009a,b). The methodology for computing consumption of anchovy is set out in the Appendix; that for sardine is very similar.
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Comparison of sardine November proportion-at-age from different length frequencies and age readers
(2011) De Moor, Carryn L; Butterworth, Doug S
de Moor and Butterworth (2009) recommended that a new method to weight the trawls when calculating the sardine length frequency observed during the November surveys be applied. This new method involved weighting the individual trawls equally for all trawls of sample sizes greater than 40 and down weighting those of smaller sample size. The method used previously weighted the individual trawls by the acoustic weighting associated by that trawl as a proportion of the total acoustic weighting of all trawls. This investigation was initially prompted in 2007 when considering the unusual lack of evidence for strong cohorts in length frequency data and the proportions-at-age which showed a higher proportion of older ages than implied by current estimates of natural mortality. This latter concern remained when the proportions-at-age were recently recalculated using ALKs provided by Deon Durholtz. The proportions-at-age are now compared using ALKs provided by Cynthia Mtengwane and the revised November length frequencies for sardine (Coetzee and Merkle 2011).