Rebuild (aka The “Puntalyzer“)
The rebuilding plans for overfished west coast groundfish resources developed by the Pacific Fishery Management Council, PFMC, include rebuilding analyses. These provide much of the biological information on which the Council can base its decisions regarding the time to rebuild to the biomass at which MSY is achieved, the probability of recovery to this biomass, and the catches expected under the rebuilding plan for different levels of probability.
The Scientific and Statistics Committee of the PFMC has developed guidelines for conducting rebuilding analyses, which have been used as the basis for developing software for this purpose. The attached ZIP file includes an executable file to conduct rebuilding analyses, an example input file, a spreadsheet to display the results, and documentation for the software. The FORTRAN code for the rebuilding analysis is available on request from Andre Punt. Note that all the normal disclaimers apply when using this software.
Ageing Error Estimator
The program “Agemat” is used to compute age-reading error matrices given data on the otoliths (or any form of ageing structure) which have been read multiple times, either by the same age-reader or different age-readers. It can deal with data for which the true age is known, in addition to data for which the true age is unknown. The program can utilize multiple data sets (defined as sets of otoliths read by the same set of readers). The method, as originally published, is described in Punt et al. (2008). An alternative implementation has been developed by Toshi Kitakato and was used to analyse data from an age-reading experiment for Southern Hemisphere minke whales (Kitakado et al., 2010).
This software has been used in several assessments of west coast groundfish stocks.
Kitakado, T, Punt, AE. 2010. Examination of the period/reader effect on the age-determination for the Antartic minke whales and its implications to the statistical catch-at-age analyses. Document SC/62/IA2 presented to the IWC Scientific Committee.
Punt, AE, Smith, DC, KrusicGolub, K, Robertson, S. 2008. Quantifying age-reading error for use in fisheries stock assessments, with application to species in Australia’s Southern and Eastern Scalefish and Shark Fishery. Can. J. Fish. Aquat. Sci. 65:1991-2005.
Size Model Simulator
Size-structured population dynamics models are used to conduct stock assessments primarily for hard-to-age species such as prawns, rock lobsters, and abalone, for which the key data sources are indices of abundance, catch and survey length-frequency information, and tag-recapture data. A Shiny package for size structured models has been developed that describes a simple size-structured population dynamics model and allows users to modify parameters of the model (including those related to growth, natural mortality and selectivity) to examine the impacts on the relative frequency by size class in the population and the catch. The package also allows users to explore the relationships between fishing mortality, spawning biomass and yield and conduct projections. The code that implements the package can be downloaded and run directly from Rstudio, although you may need to download several packages to get it to run.