Flr an open source framework for the evaluation and development of management strategies
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L.T. Kell, I. Mosqueira, P. Grosjean, J-M. Fromentin, D. Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott. FLR: An Open-Source Framework for the Evaluation and Development of Management Strategies. What is FLR?. Fisheries Library in R

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Flr an open source framework for the evaluation and development of management strategies

L.T. Kell, I. Mosqueira, P. Grosjean, J-M. Fromentin, D. Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

FLR: An Open-Source Framework for the Evaluation and Development of Management Strategies


What is flr
What is FLR? Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Fisheries Library in R

  • Provides extensible toolbox for simulating fisheries systems.

  • R – Open Source implementation of S

  • Uses R inbuilt graphical and statistical routines

  • Many user developed packages


What can be flr used for
What can be FLR used for? Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Many different things:

    • development of plausible biological models

    • simulate management procedures (harvest control rules)

    • development of fleet dynamic models

    • include economics (indicators)

    • new additions include compliance model

    • not just stock assessments (XSA, ICA etc.)


Philosophy of flr
Philosophy of FLR Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Open source license (GPL): you can modify a copy of the code, but you must distribute it under the same license.

  • Collaborative: Discussions are open (mailing list), website is editable, external review is encouraged

  • Breaking the barrier between user and developer

  • Improves inter-disciplinary dialogue


Design principles
Design principles Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Object Oriented Programming

  • Different elements of system are treated as “objects”, e.g. stocks, fleets

  • Each object stores data and has functions that act on that data

  • Data stored in five dimensions:

    • User defined (e.g. age or length)

    • Year

    • Unit (e.g. male / female)

    • Season

    • Area

  • Sixth dimension - iteration


Basic classes
Basic classes Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Include:

    • FLBiol – biological operating model

    • FLSR – stock-recruitment model

    • FLFleet – fleet and catch data

    • FLAssess – basic assessment class

  • Objects can be linked together to create simulations – “Lego blocks”

  • Learning curve: trade-off between flexibility and simplicity


Analysis with fleda
Analysis with FLEDA Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott


Evaluating management strategies
Evaluating Management Strategies Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Many sources of uncertainty: data, models, fleet behaviour, stock dynamics, environment etc.

  • Approach developed to simulate each aspect separately, e.g. simulate stock; assessment.

  • Combine simulated components within framework with feedback.

  • Allows for evaluation of robustness of alternative management strategies to underlying uncertainties.

  • Termed “Management Strategy Evaluation”.

  • Accepted approach (IWC, NOAA, NZ, ICES)


Management Strategy Evaluation Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

Hypotheses

Biological

Economic

Fleet behaviour

Stock/Fleet

Dynamics

The “Fishery”

The “Fishery”

The “Fishery”

Alternatives

Measures

Data

Management

Measures

Management


OPERATING MODEL Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

Represents the “true” dynamics of the system against which performance will be measured

MANAGEMENT PROCEDURE

Assess status of stock and set management options depending upon perceived status of fishery stock(s)

MODEL CONDITIONING

Management decision stage

Fleet dynamics

FLFleet

Management procedure

FLHCR

Biological reference points (e.g. MSY)

FLBRP

IMPLEMENTATION MODEL

FLEcon

INITIAL CONDITIONS

SUMMARY STATISTICS

Used to evaluate performance of management procedures against objectives.

Population biology

Assessment procedure

Stock dynamics

FLBiol

OBSERVATION ERROR MODEL

Generation of data on fishery and stocks.

FLOEM

Perceived stock

FLStock

Stock assessment (e.g. VPA)

FLAssess

Stock processes

e.g. Recruitment

FLSR

Auxiliary information

(e.g. tuning indices)

FLIndices

Assessment assumptions


North sea flatfish
North Sea Flatfish Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Under COMMIT and EFIMAS

  • Evaluated EU Management Strategy

  • Two stocks – plaice and sole

  • Three fleets – Dutch, UK, Other

  • Aim of HCR is to reduce F to FMSY

  • Fleets either TAC or effort limited – depending on outcome of HCR

  • Economics also included - indicators


The flr wiki
The FLR Wiki Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

http://flr-project.org


The flr wiki1
The FLR Wiki Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • News and developments

  • Documentation

  • Tutorials and course material

  • Examples

  • Download packages

  • Users and developers can edit content


The flr packages
The FLR packages Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Main package: FLCore

    • Main classes and functions

  • Collection of secondary packages

    • FLAssess

    • FLEDA

  • What’s in a package?

    • R code for all classes, methods and functions

    • Help pages for each of them

    • Examples and datasets

    • Test scripts

  • CVS


The flr initiative
The FLR initiative Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Work funded by a number of EU projects (FEMS, COMMIT, EFIMAS, Fisboat, …)

  • Core team

    • Maintenance & development of main packages

    • 6 month release of official versions

    • Testing of submitted packages


COBECOS requirements Garcia, R. Hillary,  E. Jardim, S. Mardle, M. Pastoors, J. J. Poos, F. Scott and R. Scott

  • Requirement for development of generic code

  • Implement COBECOS theoretical approach on a case-study basis

  • Each case-study has individual requirements

  • Guidance can be provided

  • Use simple relationships versus complex (MSE) – depends on resources, data, linkages to other projects.


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