Introduction   to FLR FLR Core   TeamIntroductionPhilosophyof FLR         Introduction to FLRWhat isFLR?Design ofFLR      ...
Introduction   to FLR FLR Core                         Outline   TeamIntroductionPhilosophyof FLR               1   Introd...
Introduction   to FLR FLR Core                              Outline   TeamIntroductionPhilosophyof FLR               1   I...
Introduction   to FLR FLR Core                              Outline   TeamIntroductionPhilosophyof FLR               1   I...
Introduction   to FLR FLR Core                              Outline   TeamIntroductionPhilosophyof FLR               1   I...
Introduction   to FLR FLR Core                              Outline   TeamIntroductionPhilosophyof FLR               1   I...
Introduction   to FLR FLR Core                                     Need for FLR   TeamIntroduction               Schnute e...
Introduction   to FLR FLR Core                                          Need for FLR   TeamIntroduction               Schn...
Introduction   to FLR FLR Core                                          Need for FLR   TeamIntroduction               Schn...
Introduction   to FLR FLR Core                                                  Goals   TeamIntroductionPhilosophyof FLRWh...
Introduction   to FLR FLR Core      A brief history of FLR   TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s...
Introduction   to FLR FLR Core                A brief history of FLR   TeamIntroductionPhilosophyof FLRWhat is            ...
Introduction   to FLR FLR Core                A brief history of FLR   TeamIntroductionPhilosophyof FLRWhat is            ...
Introduction   to FLR FLR Core                A brief history of FLR   TeamIntroductionPhilosophyof FLRWhat is            ...
Introduction   to FLR FLR Core                 A brief history of FLR   TeamIntroductionPhilosophyof FLRWhat is           ...
Introduction   to FLR FLR Core                  A brief history of FLR   TeamIntroductionPhilosophyof FLRWhat is          ...
Introduction   to FLR FLR Core      FLR 1.4 - The Golden Jackal   TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRW...
Introduction   to FLR FLR Core                 A brief history of FLR   TeamIntroductionPhilosophyof FLR         2007-2009...
Introduction   to FLR FLR Core                 A brief history of FLR   TeamIntroductionPhilosophyof FLR         2007-2009...
Introduction   to FLR FLR Core      FLR 2.2 - Swordfish Polka   TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat...
Introduction   to FLR FLR Core                              Mission statement   TeamIntroductionPhilosophyof FLRWhat is   ...
Introduction   to FLR FLR Core                              Mission statement   TeamIntroductionPhilosophyof FLRWhat is   ...
Introduction   to FLR FLR Core                              Mission statement   TeamIntroductionPhilosophyof FLRWhat is   ...
Introduction   to FLR FLR Core                              Mission statement   TeamIntroductionPhilosophyof FLRWhat is   ...
Introduction   to FLR FLR Core                                GNU project   Team                                      (htt...
Introduction   to FLR FLR Core                      Collaboration and Open   Team                                         ...
Introduction   to FLR FLR Core                         Development of FLR   TeamIntroductionPhilosophyof FLRWhat isFLR?Des...
Introduction   to FLR FLR Core           Cut the crap, what is FLR?   TeamIntroductionPhilosophyof FLRWhat isFLR?Design of...
Introduction   to FLR FLR Core          ... and where can I get it ?   TeamIntroductionPhilosophyof FLRWhat isFLR?Design o...
Introduction   to FLR FLR Core          Object oriented   Team               programming with S4IntroductionPhilosophyof F...
Introduction   to FLR FLR Core                       Object oriented   Team                            programming with S4...
Introduction   to FLR FLR Core                        Object oriented   Team                             programming with ...
Introduction   to FLR FLR Core                         Object oriented   Team                              programming wit...
Introduction   to FLR FLR Core                         Object oriented   Team                              programming wit...
Introduction   to FLR FLR Core                         Object oriented   Team                              programming wit...
Introduction   to FLR FLR Core                         Object oriented   Team                              programming wit...
Introduction   to FLR FLR Core                         Object oriented   Team                              programming wit...
Introduction   to FLR FLR Core                         Object oriented   Team                              programming wit...
Introduction   to FLR FLR Core      Design principles   TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
Introduction   to FLR FLR Core                           Design principles   TeamIntroductionPhilosophyof FLRWhat is      ...
Introduction   to FLR FLR Core                            Design principles   TeamIntroductionPhilosophyof FLRWhat is     ...
Introduction   to FLR FLR Core                            Design principles   TeamIntroductionPhilosophyof FLRWhat is     ...
Introduction   to FLR FLR Core                            Design principles   TeamIntroductionPhilosophyof FLRWhat is     ...
Introduction   to FLR FLR Core                            Design principles   TeamIntroductionPhilosophyof FLRWhat is     ...
Introduction   to FLR FLR Core                                                       FLR & S4   Team                      ...
Introduction   to FLR FLR Core                                            Packages   Team                   FLR packages d...
Introduction   to FLR FLR Core      MSE - The Lego block   Team                           approachIntroductionPhilosophyof...
Introduction   to FLR FLR Core      What’s next ?   TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
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Intro to FLR

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Intro to FLR

  1. 1. Introduction to FLR FLR Core TeamIntroductionPhilosophyof FLR Introduction to FLRWhat isFLR?Design ofFLR FLR Core TeamWhat’s next? June 22, 2011
  2. 2. Introduction to FLR FLR Core Outline TeamIntroductionPhilosophyof FLR 1 IntroductionWhat isFLR?Design ofFLRWhat’s next?
  3. 3. Introduction to FLR FLR Core Outline TeamIntroductionPhilosophyof FLR 1 IntroductionWhat isFLR?Design ofFLR 2 Philosophy of FLRWhat’s next?
  4. 4. Introduction to FLR FLR Core Outline TeamIntroductionPhilosophyof FLR 1 IntroductionWhat isFLR?Design ofFLR 2 Philosophy of FLRWhat’s next? 3 What is FLR?
  5. 5. Introduction to FLR FLR Core Outline TeamIntroductionPhilosophyof FLR 1 IntroductionWhat isFLR?Design ofFLR 2 Philosophy of FLRWhat’s next? 3 What is FLR? 4 Design of FLR
  6. 6. Introduction to FLR FLR Core Outline TeamIntroductionPhilosophyof FLR 1 IntroductionWhat isFLR?Design ofFLR 2 Philosophy of FLRWhat’s next? 3 What is FLR? 4 Design of FLR 5 What’s next ?
  7. 7. Introduction to FLR FLR Core Need for FLR TeamIntroduction Schnute et al. (2007 and 1998) compared the number ofPhilosophy software tools and languages currently available for stockof FLR assessments with the Babel tower myth:What isFLR?Design ofFLRWhat’s next?
  8. 8. Introduction to FLR FLR Core Need for FLR TeamIntroduction Schnute et al. (2007 and 1998) compared the number ofPhilosophy software tools and languages currently available for stockof FLR assessments with the Babel tower myth:What isFLR?Design of ”After the people of Babel sought to build a tower to heaven, the LordFLR God devised a plan (Genesis 11: 4-7). ’Behold the people is one; andWhat’s next? they all have one language; and this they began to do; and now nothing will be restrained from them, which they have imagined to do.... Let us go down, and there confound their language, that they may not understand one another’s speech.’ Italics highlight the prospects for accomplishment with a common language, if the scientific community could ever agree on one”
  9. 9. Introduction to FLR FLR Core Need for FLR TeamIntroduction Schnute et al. (2007 and 1998) compared the number ofPhilosophy software tools and languages currently available for stockof FLR assessments with the Babel tower myth:What isFLR?Design of ”After the people of Babel sought to build a tower to heaven, the LordFLR God devised a plan (Genesis 11: 4-7). ’Behold the people is one; andWhat’s next? they all have one language; and this they began to do; and now nothing will be restrained from them, which they have imagined to do.... Let us go down, and there confound their language, that they may not understand one another’s speech.’ Italics highlight the prospects for accomplishment with a common language, if the scientific community could ever agree on one” ”The cosmic plan for confounding software languages seems to be working remarkably well among the community of quantitative fishery scientists!”
  10. 10. Introduction to FLR FLR Core Goals TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLR To promote and generalize the use of good quality, openWhat’s next? source, flexible software in all areas of quantitative fisheries research and management advice, with a key focus on Management Strategies Evaluation.
  11. 11. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
  12. 12. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLRWhat is Started by FEMS EU projectFLR?Design ofFLRWhat’s next?
  13. 13. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLRWhat is Started by FEMS EU projectFLR? COMMIT & EFIMAS EU projects provided much of timeDesign ofFLR and sweatWhat’s next?
  14. 14. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLRWhat is Started by FEMS EU projectFLR? COMMIT & EFIMAS EU projects provided much of timeDesign ofFLR and sweatWhat’s next? Presented to ICES WG Methods 2004
  15. 15. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLRWhat is Started by FEMS EU projectFLR? COMMIT & EFIMAS EU projects provided much of timeDesign ofFLR and sweatWhat’s next? Presented to ICES WG Methods 2004 FLCore version 1.0 - December 2005 FLQuant with 5 dimensions, no ” iter” Release often, release early. Bugs galore
  16. 16. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLRWhat is Started by FEMS EU projectFLR? COMMIT & EFIMAS EU projects provided much of timeDesign ofFLR and sweatWhat’s next? Presented to ICES WG Methods 2004 FLCore version 1.0 - December 2005 FLQuant with 5 dimensions, no ” iter” Release often, release early. Bugs galore FLCore version 1.4 - 2007 Stable, full of treats an joy
  17. 17. Introduction to FLR FLR Core FLR 1.4 - The Golden Jackal TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
  18. 18. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLR 2007-2009: The Silk Road to version 2What isFLR? New FLQuant with 6 dimensions: uncertainty in structureDesign of Rewrite of most methodsFLR Extension of methods availableWhat’s next New classes: FLModel? Stronger use of class inheritance Overhaul of man pages Simplification of package map
  19. 19. Introduction to FLR FLR Core A brief history of FLR TeamIntroductionPhilosophyof FLR 2007-2009: The Silk Road to version 2What isFLR? New FLQuant with 6 dimensions: uncertainty in structureDesign of Rewrite of most methodsFLR Extension of methods availableWhat’s next New classes: FLModel? Stronger use of class inheritance Overhaul of man pages Simplification of package map FLCore version 2.0 - January 2009 2.2: actual stable version 2.3: under development
  20. 20. Introduction to FLR FLR Core FLR 2.2 - Swordfish Polka TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
  21. 21. Introduction to FLR FLR Core Mission statement TeamIntroductionPhilosophyof FLRWhat is The FLR project provides a platform for quantitativeFLR? fisheries science based on the R statistical language. TheDesign ofFLR guiding principles of FLR are:What’s next?
  22. 22. Introduction to FLR FLR Core Mission statement TeamIntroductionPhilosophyof FLRWhat is The FLR project provides a platform for quantitativeFLR? fisheries science based on the R statistical language. TheDesign ofFLR guiding principles of FLR are:What’s next openness - through community involvement and the open? source ethos
  23. 23. Introduction to FLR FLR Core Mission statement TeamIntroductionPhilosophyof FLRWhat is The FLR project provides a platform for quantitativeFLR? fisheries science based on the R statistical language. TheDesign ofFLR guiding principles of FLR are:What’s next openness - through community involvement and the open? source ethos flexibility - through a design that does not constrain the user to a given paradigm
  24. 24. Introduction to FLR FLR Core Mission statement TeamIntroductionPhilosophyof FLRWhat is The FLR project provides a platform for quantitativeFLR? fisheries science based on the R statistical language. TheDesign ofFLR guiding principles of FLR are:What’s next openness - through community involvement and the open? source ethos flexibility - through a design that does not constrain the user to a given paradigm extendibility - through the provision of tools that are ready to be personalized and adapted.
  25. 25. Introduction to FLR FLR Core GNU project Team (http://gnu.org)IntroductionPhilosophyof FLRWhat isFLR?Design of ”Free software is a matter of liberty, not price.”FLRWhat’s next? free = free speech free != free beer
  26. 26. Introduction to FLR FLR Core Collaboration and Open Team SourceIntroductionPhilosophyof FLRWhat isFLR?Design of ”I think the real issue about adoption of open source is that nobodyFLR can really ever ’design’ a complex system. That’s simply not howWhat’s next? things work: people aren’t that smart - nobody is. And what open source allows is to not actually ’design’ things, but let them evolve, through lots of different pressures in the market, and having the end result just continually improve” Linus Torvalds
  27. 27. Introduction to FLR FLR Core Development of FLR TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLR FLR is a collaborative development project, where distinctWhat’s next? scientists that constitute the FLR Core Team, aka ”Les miserables” work simultaneously on code, documentation, etc. ,
  28. 28. Introduction to FLR FLR Core Cut the crap, what is FLR? TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next? A working environment for quantitative fisheries analysis in R!
  29. 29. Introduction to FLR FLR Core ... and where can I get it ? TeamIntroductionPhilosophyof FLRWhat isFLR?Design of Website (http://flr-project.org/)FLRWhat’s next Packages on repository? (install.packages(repos=”http://flr-project.org/R”)) Documentation on wiki (http://wiki.flr-project.org) and ”Teach Yourself FLR” (http://tyflr.flr-project.org)
  30. 30. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
  31. 31. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLRWhat’s next?
  32. 32. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next?
  33. 33. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next Everything is an object of a particular class?
  34. 34. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next Everything is an object of a particular class? Objects have:
  35. 35. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next Everything is an object of a particular class? Objects have: members (data) and
  36. 36. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next Everything is an object of a particular class? Objects have: members (data) and methods (functions associated with it that act on member data)
  37. 37. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next Everything is an object of a particular class? Objects have: members (data) and methods (functions associated with it that act on member data) Inheritence used to extend and create new classes (FLSR inherits from FLModel)
  38. 38. Introduction to FLR FLR Core Object oriented Team programming with S4IntroductionPhilosophyof FLR A programming language model organized around ”objects”What isFLR? rather than ”actions”Design ofFLR Uses R S4 classesWhat’s next Everything is an object of a particular class? Objects have: members (data) and methods (functions associated with it that act on member data) Inheritence used to extend and create new classes (FLSR inherits from FLModel) Classes can be members of other classes (most FLR classes include FLQuants as members)
  39. 39. Introduction to FLR FLR Core Design principles TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
  40. 40. Introduction to FLR FLR Core Design principles TeamIntroductionPhilosophyof FLRWhat is Classes to represent different elements of fisheries systemsFLR?Design ofFLRWhat’s next?
  41. 41. Introduction to FLR FLR Core Design principles TeamIntroductionPhilosophyof FLRWhat is Classes to represent different elements of fisheries systemsFLR? ’physical’ objects (e.g. FLStock class represents a fishDesign ofFLR stock)What’s next?
  42. 42. Introduction to FLR FLR Core Design principles TeamIntroductionPhilosophyof FLRWhat is Classes to represent different elements of fisheries systemsFLR? ’physical’ objects (e.g. FLStock class represents a fishDesign ofFLR stock)What’s next? ’methodological’ objects (e.g. FLBRP class containing methods to calculate BRP)
  43. 43. Introduction to FLR FLR Core Design principles TeamIntroductionPhilosophyof FLRWhat is Classes to represent different elements of fisheries systemsFLR? ’physical’ objects (e.g. FLStock class represents a fishDesign ofFLR stock)What’s next? ’methodological’ objects (e.g. FLBRP class containing methods to calculate BRP) Link objects to create simulations - Lego blocks (MSE example)
  44. 44. Introduction to FLR FLR Core Design principles TeamIntroductionPhilosophyof FLRWhat is Classes to represent different elements of fisheries systemsFLR? ’physical’ objects (e.g. FLStock class represents a fishDesign ofFLR stock)What’s next? ’methodological’ objects (e.g. FLBRP class containing methods to calculate BRP) Link objects to create simulations - Lego blocks (MSE example) Learning curve: trade off between flexibility and simplicity (no black boxes and no handle turning)
  45. 45. Introduction to FLR FLR Core FLR & S4 Team FLR hierarchical modelIntroductionPhilosophyof FLR FLCoreWhat isFLR? classesDesign of methodsFLRWhat’s next? inherits extends 2ndry pkg classes methods
  46. 46. Introduction to FLR FLR Core Packages Team FLR packages development modelIntroductionPhilosophyof FLR FLCoreWhat isFLR?Design ofFLRWhat’s next? FLEDA FLAssess FLash FLBRP FLXSA FL...
  47. 47. Introduction to FLR FLR Core MSE - The Lego block Team approachIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?
  48. 48. Introduction to FLR FLR Core What’s next ? TeamIntroductionPhilosophyof FLRWhat isFLR?Design ofFLRWhat’s next?

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