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//Quick link to: [[doc|documentation]], [[pkg:packages]], [[courses:courses]], [[appl|examples]]//
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====== Fisheries Library in R (FLR) ======
{{pic:fishing.gif?150 }} Welcome to the webpage of the FLR project. 

The FLR library is a collection of tools in [[http://www.r-project.org/|R]] that facilitates the construction of bio-economic simulation models  of fisheries and ecological sytems (//[[team:paperflcore|read more]]//). It is a generic toolbox, but is specifically suited for the construction of simulation models for evaluations of fisheries management strategies. The FLR library is under development by the [[team|FLR Team]]. 

{{team:sfms_050.pdf|The FLR paper}}


===== Latest News =====
  * 01 Jan 2009: THIS IS A BACKUP COPY OF THE OLD FLR WIKI. PLEASE VISIT [[http://wiki.flr-project.org]] FOR THE NEW VERSION. THIS CONTENT IS MAINTANED HERE FOR REFERENCE PURPOSES BUT WILL NOT BE UPDATED

  * 09 July 2008: A four day [[courses:IMARES|course on FLR]] was given at IMARES. 
  * 31 March 2008: A four day [[courses:JRC08|course on FLR]] was given at JRC.  
  * 02 January 2008: FLCore 2.0 almost ready. Release candidates are now available.
  * 21 February 2008: [[proj:projects:GHal|FLR used for NAFO Greenland Halibut MSE]] 
  * 25 January 2007: The major FLR packages are now available for R-2.4.1.
  * 25 January 2007: A bugfix release of a number of packages for R-2.3.1 is now available.
  * 11 October 2006: [[courses:allcourses_nov06jan07|A number of courses]] will be held in Nov 2006 and Jan 2007, focusing on FLR as a stock assessment tool
  * 29 June 2006: FLR has been {{ppt:galway_flr_presentation.ppt|presented}} at the [[http://www.ices06sfms.com/|ICES Symposium on Fisheries Management Strategies]]
  * [[news:old|click here]] for older news items.


===== Software / packages =====

{{ pic:flr-relationships.gif?300}} 
FLR is a library that consists of a number of R-packages. 
Each package has its own [[pkg:packages|information page]] on the design of the classes and on the methods that are included. New packages are regularly released and several prototype packages are under development. 

The basic package of FLR is [[pkg:flcore|FLCore]] that contains all the basic classes and methods to 
hold and manipulate the data that is needed in the simulation.  The basic structure in FLCore is the [[pkg:flcore:flquant|FLQuant]]: a 5-dimensional array whereby the first dimension can be set by the users (e.g. age, length, vessel type) and the other dimensions are year, unit (e.g. sex, spawning type), season and area. Different FLQuants have been grouped into classes of FLCore. 

Examples of the basic classes are the [[pkg:flcore:flstock|FLStock]]-object that holds all the information that is 
needed to carry out a stock assessment, and the [[pkg:flcore:flfleet|FLFleet]]-object that holds the information on 
a fishing fleet (see: [[pkg:flcore|FLCore overview]])

The most recent stable version of FLCore is The Golden Jackal, released: 1 February 2007. Packages are available at the repository, by calling install.packages(repos="http://flr-project.org/R"), and through the [[http://sourceforge.net/project/showfiles.php?group_id=108356|sf.net file release system]].

With the new version of R (2.5.0) we have now 2 distributions available. Be carefull with the versions of your packages.

^pkg ^R 2.4.1 ^R 2.5.0^
^FLCore |1.4.3 |1.4.4|
^FLAssess |1.4.1 |1.4.2|
^FLBayes |1.4.1 |1.4.1|
^FLEDA |1.4.2 |1.4.3|
^FLSTF |1.4.2 |NA (check fails)|
^FLXSA |1.4.2 |NA (check fails)|


===== More information? =====

More specific information on FLR can be found on the following pages:
  * [[team:paperflcore|An introduction to FLR]]
  * [[pkg:packages|FLR packages descriptions]]
  * [[http://sourceforge.net/project/showfiles.php?group_id=108356|Downloads]]
  * [[doc|Documentation]]
  * [[http://sourceforge.net/mail/?group_id=108356|Mailing lists]]
  * [[doc:help:faq|Frequently asked questions]]
  * [[courses:courses|Tutorials and courses]] 
  * [[appl|Examples and applications]]
  * [[BRP|Biological Reference Points]] 
  * [[HCR|Harvest Control Rules]]
  * [[MSE|A Generic Management Strategy Evaluation]]
  * [[AD|Automatic Differentiation]]
  * [[proj:projects|Research projects]]
  * [[links:links|Links]]
  * [[doc:biblio|References, bibliography and catalogue of fisheries models ]]
  * [[team:team|FLR team]]
  * [[team:contribute|How to contribute?]]


===== How to use this wiki =====

These webpages are based on a wiki system. A wiki is an open documentation system, where registered users can edit existing content and create new pages (you need to register by clicking __Login__ on the bottom right handside of the page). A page exists with the [[wiki:syntax]] understood by the wiki engine. You can also test wiki writing at the [[wiki:playground]]. Pages with similar content are grouped following namespaces ([[wiki:namespaces|read more]]). Active links are shown in green. Links to pages that do not exist yet are shown in red. 
\\
The content published in this wiki http://flr-project.org/ is licensed under the[[http://creativecommons.org/licenses/by-nc-sa/2.0/|Creative Commons Attribution-NonCommercial-ShareAlike License Version 2.0]].
\\

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**Acknowledgement**
\\
 Various EU funded research-projects are contributing to the FLR platform in the form of R packages. 
The core classes were developed in the FEMS project.\\ 
[[http://www.efimas.org|EFIMAS]], [[http://www.commit-fish.info|COMMIT]] and other project ([[proj:projects|read more]]) are extending the core classes and developing secondary packages for biological and economic modelling. 

All contributions are welcome ([[team:contribute|read more]]).


2005 © [[team:team|FLR team]]
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