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
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What is FLR?
• 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
2
What can be FLR used for?
• 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
• 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
4
Design principles
• 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
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Basic classes
• 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
Evaluating Management
Strategies
• 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
Stock/Fleet
Dynamics
The
The
“Fishery”
The
“Fishery”
“Fishery”
Hypotheses
Biological
Economic
Fleet behaviour
Data
Management
Alternatives
Measures
Management
Measures
MODEL
CONDITIONING
OPERATING MODEL
MANAGEMENT PROCEDURE
Represents the “true” dynamics
of the system against which
performance will be measured
Assess status of stock and set management options
depending upon perceived status of fishery stock(s)
Management decision stage
Fleet dynamics
Management
procedure
Biological
reference
points (e.g.
MSY)
FLHCR
FLBRP
Perceived
stock
Stock
assessment
(e.g. VPA)
FLStock
FLAssess
Stock processes
e.g. Recruitment
Auxiliary
information
(e.g. tuning
indices)
Assessment
assumptions
FLSR
FLIndices
INITIAL
CONDITIONS
IMPLEMENTATION
MODEL
FLEcon
FLFleet
SUMMARY
STATISTICS
Used to evaluate
performance of
management
procedures
against
objectives.
Stock dynamics
OBSERVATION
ERROR MODEL
Generation of data
on fishery and
stocks.
FLBiol
FLOEM
Population biology
Assessment procedure
North Sea Flatfish
•
•
•
•
•
•
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
http://flr-project.org
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The FLR Wiki
•
•
•
•
•
•
News and developments
Documentation
Tutorials and course material
Examples
Download packages
Users and developers can edit content
The FLR packages
• 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
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The FLR initiative
• 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
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COBECOS requirements
• 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.