3 Work Package 3: Evaluating and testing of long-term management strategies

3.1 Evaluating the utility of a Novel Harvest Control Rule in the management of long-lived sporadically recruiting species through Management Strategy Evaluation

supervisor_account Cian Kelly (UiB), Mikko Heino (UiB), Daniel Howell (IMR)

calendar_today 2019-08-16

The code for the masters thesis work with the above title. Contains a Novel HCR, which reflected an Escapement HCR, was tested on a stock whose dynamics was informed by Greenland halibut (Reinhardtius hippoglossoides). The code is implemented as a modification of the FLBEIA software (https://github.com/flr/FLBEIA).

Download (software): cian-flbeia_alternative.zip

Related identifiers: https://bora.uib.no/bora-xmlui/handle/1956/20734

3.2 Ecological effects and ecosystem shifts caused by mass mortality events on early life stages of fish

supervisor_account Holly Perryman (IMR; https://orcid.org/0000-0001-9341-682X), and Ina Nilson (University of Bergen/IMR)

calendar_today 2019-11-06

The following deposition contains scripts for creating the figures in Olsen et al. (2019). This deposition includes example files for executing the code. The files are inputs and outputs to/from the Norwegian and Barents Seas Atlantis model.

Jupyter notebook: (show) (download)

Download (software): holly-MMEmanuscript477196.R

Related identifiers: https://doi.org/10.3389/fmars.2019.00669

References: Olsen, E., Eide, C.H., Nilsen, I., Perryman, H.A. and Vikebø, F., 2019. Ecological effects and ecosystem shifts caused by mass mortality events on early life stages of fish. Frontiers in Marine Science, 6, p.669.

Keywords: Atlantis; marine ecosystem model; data processing; biomass trends; spider plots

3.3 Atlantis-R interface

supervisor_account Ibrahim Umar (IMR), Holly Perryman (IMR), Rebecca Gorton (CSIRO), Elizabeth A. Fulton (CSIRO)

calendar_today 2019-10-24

The marine ecosystem model Atlantis is structured following the MSE framework, meaning Atlantis simulates both the operating model and the management procedure. This is an advantageous feature for simulating MSE under and ecosystem-based context, however it may be cumbersome to program complicated/specific management procedures into Atlantis. To integrate Atlantis into the REDUS framework, Atlantis was programmed to send/receive data back and forth with the statistical software R. With this new functionality, Atlantis can be treated solely as an operating model while R is used to simulate the management procedure. Thus, management procedures previously programmed in R can now be simulated under an ecosystem-based context within Atlantis.

License: LGPL3 + CSIRO-proprietary

URL (software): https://git.imr.no/REDUS/atlantis-code

Keywords: ecosystem, MSE, simulation, C, marine, box, model, multi-species, biogeochemical, physical

3.4 GadgetR

supervisor_account Ibrahim Umar (IMR), Bjarki Thor Elvarsson (Hafro), James Begley (Hafro), Hoskuldur Bjornsson (Hafro), Gunnar Stefnasson (Hafro), Lorna Taylor (Hafro), Daniel Howell (IMR), Sigurdur Hannesson (Hafro), Narfi Stefansson (Hafro), Hersir Sigurgeirsson (Hafro), Morten Nygard Asnes (IMR), Kristin Froysa (IMR), Audbjorg Jakobsdottir (Hafro), Jon Gudmundsson (Hafro), Gudmundur Einarsson (Hafro), Thordis Linda Thorarinsdottir (Hafro), Kristjana Yr Jonsdottir (Hafro), Mark G. Johnson (US-EPA), Bill Goffe (USM)

calendar_today 2018-06-21

GadgetR is an R library that allows users to create a two-way interface to the simulation function (via a “gadget -s” command line switch) of Hafro’s Globally applicable Area Disaggregated General Ecosystem Toolbox (Gadget) program. To simply put, GadgetR provides users flexibility to explicitly control gadget simulation steps, and inspect and modify (as needed) gadget internal objects (such as recruitment parameters, fleet consumption amount, among others) at any point in time during the simulation. These functionalities are especially useful when you want to use a gadget model as an operating model (single or multi- species) in existing management strategy (MSE) frameworks in R (FLR/mse or FLBEIA). GadgetR ships with the latest Gadget program (version 2.2.00-BETA) and retains all of the original Gadget program functionality.

License: GPL2

URL (software): https://github.com/REDUS-IMR/gadget

Related identifiers: https://redus-imr.github.io/gadget/articles/quickstart.html

Keywords: simulation, optimization, multi-species, stock, gadget ecosystem, R, C++, MSE

3.5 Multi Fleet Deterministic Projection (MFDP)

supervisor_account Ibrahim Umar (IMR)

calendar_today 2020-12-18

Program for the fisheries short-term prediction. Allows for multi-fleet catch constraints and multi-annual prediction. This program is an attempt to re-create the original Multi Fleet Deterministic Projection (MFDP) program for fisheries in R.

License: LGPL3

Jupyter notebook: (show) (download)

URL (software): https://github.com/REDUS-IMR/mfdp

Keywords: mfdp, fisheries, forecast, multi-year, REDUS, IMR

3.6 MSE Framework

supervisor_account Ibrahim Umar (IMR), Daisuke Goto (IMR), Alfonso Perez Rodriguez (IMR)

calendar_today 2019-03-14

FLR-Gadget is a Management Strategy Evaluation (MSE) framework using FLR (The Fisheries Library in R) mse (https://github.com/flr/mse) with an R package of customized Gadget (Globally applicable Area Disaggregated General Ecosystem Toolbox, https://github.com/Hafro/gadget2), GadgetR (https://github.com/REDUS-IMR/gadget), as an operating model (OM). This framework is designed to run single and multi- species MSEs. The OM can be age- or length- based. The framework runs short-cut and full-feedback MSEs. Currently, a4a (Assessment for All, https://github.com/flr/FLa4a) statistical catch-at-age model and SAM (State-space Assessment Model, https://github.com/flr/FLSAM) are implemented as an assessment model.

License: LGPL3

Jupyter notebook: (show) (download)

URL (software): https://github.com/dgoto2/flr-gadget

Keywords: IMR, REDUS, FLR, MSE, multi-species, simulation, framework, R, fisheries, gadget

3.7 mse-bootstrap-gcp

supervisor_account Ibrahim Umar (IMR), Jennifer Devine (IMR), Daisuke Goto (IMR)

calendar_today 2019-02-24

Scripts for running the North Sea Saithe Management Strategy Evaluation (MSE) on Google Cloud Platform (GCP)

License: LGPL3

URL (software): https://github.com/REDUS-IMR/mse-bootstrap-gcp

Keywords: IMR, REDUS, bash, GCP, MSE, North Sea Saithe, simulation, parallel

3.8 North Sea saithe Management Strategy Evaluation (MSE)

supervisor_account Jennifer Devine (IMR), Daisuke Goto (IMR), Ibrahim Umar (IMR), Colin Millar (ICES), Jose De Oliveira (CEFAS), Simon Fischer (CEFAS)

calendar_today 2019-06-17

A management strategy evaluation (MSE) framework for North Sea saithe (Pollachius virens) in Subareas 4, 6 and Division 3.a (North Sea, Rockall and West of Scotland, Skagerrak and Kattegat) developed using the Fisheries Library in R mse package as part of the Workshop on North Sea stocks Management Strategy Evaluation (WKNSMSE).

URL (software): https://github.com/ices-taf/wk_WKNSMSE_pok.27.3a46

Related identifiers: https://doi.org/10.17895/ices.pub.5090

Keywords: mse, saithe, ices, north sea, R, FLR, REDUS, IMR