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FLOSS - FL Operating Model and Sampling Simulator

Builds multi-fleet, multi-species age-structured operating models from life-history parameters, fleet selectivity, relative catchability and a target MSY, driven by shared fleet effort (with optional effort creep), and generates the data such fisheries produce (catch, effort, CPUE, survey indices, length frequencies and biological samples). Designed for training and for trainers who need realistic example datasets with a known truth. Built on FLR ('FLCore', 'FLBRP', 'FLasher', 'FLife') and 'FLRef'.

Last updated

3.62 score 14 scripts

cpueTargeting - Simulators and Tools for CPUE Targeting and Standardization

Multispecies operating models for exploring spatial and vertical targeting and catch-per-unit-effort standardization. Includes the multi-habitat cluster example of Winker et al. (2014), the four-species bathymetric Run 22 model based on the spatial simulator of Thorson et al. (2017) <doi:10.1139/cjfas-2015-0598> and Ono et al. (2015) <doi:10.1016/j.fishres.2015.05.021>, and its extension to a longline tuna fishery with species vertical distributions and hook depth by hooks-between-floats, following the habitat-based approach of Bigelow et al. (2002). Provides a step-by-step toolbox for real catch and effort data: data formatting, cumulative species curves, fleet and catch composition exploration, habitat-based subsetting (Stephens and MacCall 2004), and targeting covariates from the catch composition (principal components with the Optimal Coordinates test, and clustering into fishing tactics).

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3.48 score 1 stars 10 scripts

mmsyFM - Multispecies MSY Fleet Model for Mixed-Fishery Harvest Strategies

Simulates mixed fisheries in which fleet segments (e.g. demersal, pelagic and mixed or small-scale) allocate their fishing days across metiers by expected profit, on top of Schaefer surplus-production stocks with seasonal availability and JABBA-type process error. Finds the multispecies maximum sustainable yield (MMSY) subject to a safeguard for every stock, tunes the fleet to an open-access status quo, and tunes and tests effort- and closure-based harvest strategies with assessment and implementation error, data lags, species complexes and nominal assignment of stocks to fleets.

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3.30 score 6 scripts

JABBA3 - Bayesian State-Space Surplus Production Models in 'RTMB'

The next generation of 'JABBA' (Just Another Bayesian Biomass Assessment), now with hyperdrive. Fits Bayesian state-space surplus production models in 'RTMB' in well under a second, so you can spend less time waiting for chains to converge and more time arguing about priors. Full posteriors are available through 'tmbstan' (NUTS) for those who still like their MCMC. Inputs and outputs follow 'FLR' conventions for use with 'ggplotFL', 'FLRef' and 'mse', and helpers convert classic 'JABBA' inputs so old scripts survive the jump to hyperspace.

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2.00 score 1 stars 6 scripts