- Isis-fish-docs-commits - mailman.cloud.codelutin.com

r133 - trunk/src/site/rst/v4/user
by slehuta＠users.forge.codelutin.com Aug. 19, 2013

Aug. 19, 2013

Author: slehuta Date: 2013-08-19 09:54:26 +0200 (Mon, 19 Aug 2013) New Revision: 133 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/133 Log: >From scmwebeditor -- Modified: trunk/src/site/rst/v4/user/FAQ.rst Modified: trunk/src/site/rst/v4/user/FAQ.rst =================================================================== --- trunk/src/site/rst/v4/user/FAQ.rst 2013-04-24 11:50:11 UTC (rev 132) +++ trunk/src/site/rst/v4/user/FAQ.rst 2013-08-19 07:54:26 UTC (rev 133) @@ -429,6 +429,7 @@ * la migration a lieu * le changement de classe n'a pas lieu + * le recrutement a lieu FIXME ca sera modifié ???

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r132 - trunk/src/site/rst
by echatellier＠users.forge.codelutin.com April 24, 2013

April 24, 2013

Author: echatellier Date: 2013-04-24 13:50:11 +0200 (Wed, 24 Apr 2013) New Revision: 132 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/132 Log: >From scmwebeditor -- mise en forme de la page Modified: trunk/src/site/rst/download.rst Modified: trunk/src/site/rst/download.rst =================================================================== --- trunk/src/site/rst/download.rst 2013-04-24 11:39:14 UTC (rev 131) +++ trunk/src/site/rst/download.rst 2013-04-24 11:50:11 UTC (rev 132) @@ -5,7 +5,7 @@ .. * $Id$ .. * $HeadURL$ .. * %% -.. * Copyright (C) 1999 - 2012 Ifremer, Code Lutin, Chatellier Eric +.. * Copyright (C) 1999 - 2013 Ifremer, Code Lutin, Chatellier Eric .. * %% .. * This program is free software: you can redistribute it and/or modify .. * it under the terms of the GNU General Public License as @@ -33,43 +33,45 @@ La version Java d'ISIS-Fish est la seule supportée sur ce site. Vous pouvez télécharger la dernière version (ou les anciennes) à partir d'ici. -`Telechargement <http://forge.codelutin.com/projects/isis-fish/files>`_ +* `Téléchargement <http://forge.codelutin.com/projects/isis-fish/files>`_ +Régions +------- Base Golfe de Gascogne ----------------------- +~~~~~~~~~~~~~~~~~~~~~~ Voici une base de démonstration (plus évoluée que la base DemoRegion) utilisable à partir de la version 3.3 d'ISIS-Fish. -`Base Golfe de Gascogne`_ +* `Base Golfe de Gascogne`_ .. _Base Golfe de Gascogne: downloads/GolfeDeGascogneDemoV3.3.0.3.zip Base Bay of Biscay Anchovy --------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~~~ Une seconde base disponible: Bay of Biscay Anchovy ISIS-Fish V3.3.0.8 -`Base BoB Anchovy`_ +* `Base BoB Anchovy`_ .. _Base BoB Anchovy: downloads/DataBaseAnchovyBoBHindcast_commented.zip Base Bay of Biscay Pelagic Fishery ----------------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here is the multi-species multi-fleet database for the pelagic fishery in the Bay of Biscay. -`Base BoB Pelagic`_ +* `Base BoB Pelagic`_ .. _Base BoB Pelagic: downloads/RegionGolfeGascognePelagique300710.zip Base Channel Flatfish Fishery ----------------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here is the database for the flatfish fishery in the English Channel V4.2.1.1. -`Base Channel Flatfish`_ +* `Base Channel Flatfish`_ .. _Base Channel Flatfish: downloads/Base_Channel_Flatfish.zip @@ -80,10 +82,7 @@ La version R d'ISIS-Fish nommée FLISIS et faisant partie du projet FLR n'est pas supportée sur ce site. Vous pouvez néanmoins la télécharger à partir d'ici. -Telechargement__ (dernière version : Janvier 2009) +* `Telechargement <downloads/FLIsis_1.1.2.zip>`_ (dernière version : Janvier 2009) +* `Site du projet`_ -__ downloads/FLIsis_1.1.2.zip - -`Site du projet`_ - .. _Site du projet: http://flr-project.org/doku.php?id=applications:isisflr

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r131 - trunk/src/site/rst
by echatellier＠users.forge.codelutin.com April 24, 2013

April 24, 2013

Author: echatellier Date: 2013-04-24 13:39:14 +0200 (Wed, 24 Apr 2013) New Revision: 131 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/131 Log: >From scmwebeditor -- test to fix synthax Modified: trunk/src/site/rst/download.rst Modified: trunk/src/site/rst/download.rst =================================================================== --- trunk/src/site/rst/download.rst 2013-04-24 10:03:04 UTC (rev 130) +++ trunk/src/site/rst/download.rst 2013-04-24 11:39:14 UTC (rev 131) @@ -33,11 +33,9 @@ La version Java d'ISIS-Fish est la seule supportée sur ce site. Vous pouvez télécharger la dernière version (ou les anciennes) à partir d'ici. -Telechargement__ +`Telechargement <http://forge.codelutin.com/projects/isis-fish/files>`_ -__ http://forge.codelutin.com/projects/isis-fish/files - Base Golfe de Gascogne ----------------------

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r130 - trunk/src/site/rst
by loic＠users.forge.codelutin.com April 24, 2013

April 24, 2013

Author: loic Date: 2013-04-24 12:03:04 +0200 (Wed, 24 Apr 2013) New Revision: 130 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/130 Log: >From scmwebeditor -- Modified: trunk/src/site/rst/download.rst Modified: trunk/src/site/rst/download.rst =================================================================== --- trunk/src/site/rst/download.rst 2013-04-24 10:00:32 UTC (rev 129) +++ trunk/src/site/rst/download.rst 2013-04-24 10:03:04 UTC (rev 130) @@ -66,7 +66,16 @@ .. _Base BoB Pelagic: downloads/RegionGolfeGascognePelagique300710.zip +Base Channel Flatfish Fishery +---------------------------------- +Here is the database for the flatfish fishery in the English Channel V4.2.1.1. + +`Base Channel Flatfish`_ + +.. _Base Channel Flatfish: downloads/Base_Channel_Flatfish.zip + + ISIS-Fish (Version R) ---------------------

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r129 - trunk/src/site/resources/downloads
by loic＠users.forge.codelutin.com April 24, 2013

April 24, 2013

Author: loic Date: 2013-04-24 12:00:32 +0200 (Wed, 24 Apr 2013) New Revision: 129 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/129 Log: >From scmwebeditor -- add the file : Base_Channel_Flatfish.zip Added: trunk/src/site/resources/downloads/Base_Channel_Flatfish.zip Added: trunk/src/site/resources/downloads/Base_Channel_Flatfish.zip =================================================================== (Binary files differ) Property changes on: trunk/src/site/resources/downloads/Base_Channel_Flatfish.zip ___________________________________________________________________ Added: svn:mime-type + application/octet-stream

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r128 - in trunk/src/site/en/rst/v4: . user
by bpoussin＠users.forge.codelutin.com March 11, 2013

March 11, 2013

Author: bpoussin Date: 2013-03-11 17:14:48 +0100 (Mon, 11 Mar 2013) New Revision: 128 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/128 Log: fix rst syntaxe errors Modified: trunk/src/site/en/rst/v4/index.rst trunk/src/site/en/rst/v4/user/usermanual.rst Modified: trunk/src/site/en/rst/v4/index.rst =================================================================== --- trunk/src/site/en/rst/v4/index.rst 2013-01-25 09:46:44 UTC (rev 127) +++ trunk/src/site/en/rst/v4/index.rst 2013-03-11 16:14:48 UTC (rev 128) @@ -27,17 +27,17 @@ ======================= * `FAQ`_ : Frequently asked questions -.. * `Warning`_ -.. * `Installation`_ -.. * `User manual`_ -.. * `Changes in version 4.0`_ -.. * `Migration from 3.x to 4.0`_ -.. * `Tutorials`_ -.. * `Developer manual`_ -.. * `APIs documentation`_ -.. * `ISIS scripts examples`_ -.. * `R scripts examples`_ -.. * `Note to CAPARMOR users`_ +* `Warning`_ +* `Installation`_ +* `User manual`_ +* `Changes in version 4.0`_ +* `Migration from 3.x to 4.0`_ +* `Tutorials`_ +* `Developer manual`_ +* `APIs documentation`_ +* `ISIS scripts examples`_ +* `R scripts examples`_ +* `Note to CAPARMOR users`_ .. _Warning: user/warning.html .. _Installation: user/installation.html Modified: trunk/src/site/en/rst/v4/user/usermanual.rst =================================================================== --- trunk/src/site/en/rst/v4/user/usermanual.rst 2013-01-25 09:46:44 UTC (rev 127) +++ trunk/src/site/en/rst/v4/user/usermanual.rst 2013-03-11 16:14:48 UTC (rev 128) @@ -42,7 +42,7 @@ .. _User interface: usermanual/GUI.html .. _Fishery input: usermanual/inputs.html .. _Simulation launcher: usermanual/launcher.html -.. _Lanceur d'analyse de sensibilite: usermanual/sensitivity.html +.. _Sensitivity analysis launcher: usermanual/sensitivity.html .. _Results rendering: usermanual/results.html .. _Script editor: usermanual/scripts.html .. _Simulation queue: usermanual/queue.html

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r127 - trunk/src/site/en/rst/v4/user
by jcouteau＠users.forge.codelutin.com Jan. 25, 2013

Jan. 25, 2013

Author: jcouteau Date: 2013-01-25 10:46:44 +0100 (Fri, 25 Jan 2013) New Revision: 127 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/127 Log: Fix typo Modified: trunk/src/site/en/rst/v4/user/FAQ.rst Modified: trunk/src/site/en/rst/v4/user/FAQ.rst =================================================================== --- trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-25 09:46:27 UTC (rev 126) +++ trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-25 09:46:44 UTC (rev 127) @@ -343,7 +343,7 @@ N(Z1,t+1) ~= N(Z1,t)-F(met)* N(Z1,t), N(Z2,t+1)= N(Z2,t+1)-exp(-M/12) N(Z2,t) (if no migrations) * To describe a refuge phenomenon, it might be good to add a migration of - individuals in Z1 and Z2 in density dependecy... ? + individuals in Z1 and Z2 in density dependency... ? Impact of a MPA zone if the MPA is included in the pop zone

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r126 - trunk/src/site/en/rst/v4/user
by jcouteau＠users.forge.codelutin.com Jan. 25, 2013

Jan. 25, 2013

Author: jcouteau Date: 2013-01-25 10:46:27 +0100 (Fri, 25 Jan 2013) New Revision: 126 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/126 Log: Fix rst errors Modified: trunk/src/site/en/rst/v4/user/FAQ.rst Modified: trunk/src/site/en/rst/v4/user/FAQ.rst =================================================================== --- trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-24 16:43:55 UTC (rev 125) +++ trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-25 09:46:27 UTC (rev 126) @@ -343,7 +343,7 @@ N(Z1,t+1) ~= N(Z1,t)-F(met)* N(Z1,t), N(Z2,t+1)= N(Z2,t+1)-exp(-M/12) N(Z2,t) (if no migrations) * To describe a refuge phenomenon, it might be good to add a migration of -individuals in Z1 and Z2 in density dependecy... ? + individuals in Z1 and Z2 in density dependecy... ? Impact of a MPA zone if the MPA is included in the pop zone @@ -462,7 +462,7 @@ * `PATH` must contain : `%R_HOME%\bin` Tips and tricks --------------- +--------------- Fill in a table from a txt or csv file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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r125 - in trunk/src/site/en/rst/v4/user: . usermanual
by jcouteau＠users.forge.codelutin.com Jan. 24, 2013

Jan. 24, 2013

Author: jcouteau Date: 2013-01-24 17:43:55 +0100 (Thu, 24 Jan 2013) New Revision: 125 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/125 Log: Start translating usermanual Added: trunk/src/site/en/rst/v4/user/usermanual.rst trunk/src/site/en/rst/v4/user/usermanual/ trunk/src/site/en/rst/v4/user/usermanual/GUI.rst trunk/src/site/en/rst/v4/user/usermanual/introduction.rst Added: trunk/src/site/en/rst/v4/user/usermanual/GUI.rst =================================================================== --- trunk/src/site/en/rst/v4/user/usermanual/GUI.rst (rev 0) +++ trunk/src/site/en/rst/v4/user/usermanual/GUI.rst 2013-01-24 16:43:55 UTC (rev 125) @@ -0,0 +1,198 @@ +.. - +.. * #%L +.. * IsisFish +.. * +.. * $Id$ +.. * $HeadURL$ +.. * %% +.. * Copyright (C) 1999 - 2010 Ifremer, Code Lutin +.. * %% +.. * This program is free software: you can redistribute it and/or modify +.. * it under the terms of the GNU General Public License as +.. * published by the Free Software Foundation, either version 3 of the +.. * License, or (at your option) any later version. +.. * +.. * This program is distributed in the hope that it will be useful, +.. * but WITHOUT ANY WARRANTY; without even the implied warranty of +.. * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +.. * GNU General Public License for more details. +.. * +.. * You should have received a copy of the GNU General Public +.. * License along with this program. If not, see +.. * <http://www.gnu.org/licenses/gpl-3.0.html>. +.. * #L% +.. - + +============== +User interface +============== + +Main window +=========== + +User interface is constituted of a window with tabs. Each tab allows you to use +the simulator in a different way. + +.. image:: mainWindow.png + +This windows contains 6 tabs : + +- simulation launching +- results rendering +- fishery input +- script, management rule, export, analysis plan, ... writing +- sensitivity analysis launching +- simulation queue + +It is also possible to open thos tabs in a new window from the *window* menu. + +The file menu +------------- + +The first sub-menu *server synchronisation* allows you to synchronise scripts +files with the server. + +The second sub-menu *quit* closes and quits ISIS-Fish. + +The window menu +--------------- + +The six sub-menus are the equivalent of the six tabs. They open the +corresponding tab in a new window. + +The configuration menu +---------------------- + +The sub-menus allows you to configurate different parts of ISIS-Fish : +* General configuration +* VCS configuration +* Caparmor use configuration + +For some options, you have to quit and launch ISIS-Fish back so that the new +values are taken into account, such as the language. + +The help menu +------------- + +The sub-menus allows you to reach different helps on ISIS-Fish. +* This website +* The different APIs documentation +* The application logs window (useful in case of error or unusual behaviour) +* The simulator information window. + +The status bar +-------------- + +The status bar, located at the bottom of the window indicates, on the right, the +memory used and then the memory allocated to ISIS-Fish. + +The central zone allows ISIS-Fish to indicate messages and the left part +indicates the progression of task being executed. + +Simulation launch +================= + +The simulationlaunch tab allows you to parametrise the simulations and execute +them. + +.. image:: simulationTab.png + +This tab is constituted of other tabs allowing you to modify : + +- Basis **Parameters** for the simulation : identifier, description, fishery, + strategies, populations, rules, number of years +- **Pre-simulation script**, to activate it, you have to check the *use a + pre-simulation script* box in the Parameters tab. The pre-simulation script is + BSH executed before all the simulations and allows to modify the database. +- **Simulation plan**, to activate it, you have to check the "Use an analysis + plan" box on the Parameters tab. +- **Results export** that allows you to select export scripts to use and the + directory in which to store results. +- **Results choice** allows you to choose the results that will be stored to be + visualised in the rendering results tab. +- **Advanced parameters** that allows you to change the simulator to use, + activate or unactivate cache, activate or unactivate statistics, add free + parameters you can get back in the management rules, simulator,... + +If a management rule or an export needs a result that is not selected, then this +result will be automatically added to the list of wanted results. + +When launching the simulation, the current date and time will be added to the +simulation name. + +Results rendering +================= + +The rendering results tab allows you to visualise results in graph, map or +numbers. It also allows you to delete old simulations. + +.. image:: resultTab.png + +To open an old simulation, select the wanted simulation in the combo box and +click on *open a new window*. + +.. image:: resultWindowGraph.png + +.. image:: resultWindowMap.png + +Fishery input +============= + +The fishery input window allows you to visualise and modify fisheries. + +You can select your fishery in the combo box to see it appear. + +.. image:: inputTab.png + +.. image:: inputTabRegion.png + +Scripts writing +=============== + +The script tab allows you to modify all the scripts : + +- scripts +- simulators +- exports +- rules +- analysis plans +- equation models +- sensitivity analyses + +.. image:: scriptTab.png + +All those files are text files on the filesystem. So it is possible to use any +text editor to modify them. See +http://isis-fish.labs.libre-entreprise.org/othertools.html +for more explanations. + +Sensitivity analysis launch +=========================== + +The sensitivity analysis launch tab allows you to parametrise sensitivity +analyses, run them and analyse their results. + +.. image:: sensitivityTab.png + +This tab is made of different tabs that allow you to modify : + +- basis **Parameters** of the sensitivity analysis : identifier, description, + fishery, strategies, populations, rules, number of years +- **Sensitivity analysis** allows you to chose the type of analysis used and + parametrise it. +- **Results export** that allows you to select export scripts to use and the + directory in which to store results. +- **Results choice** allows you to choose the results that will be stored to be + visualised in the rendering results tab. +- **Advanced parameters** that allows you to change the simulator to use, + activate or unactivate cache, activate or unactivate statistics, add free + parameters you can get back in the management rules, simulator,... +- **Results analysis** that allows you to see the (simple) results of a finished + sensitivity analysis. + +If a management rule or an export needs a result that is not selected, then this +result will be automatically added to the list of wanted results. + +When launching the sensitivity analysis, the current date and time will be added +to the analysis identifier. The identifier of each simulation is ended by _ +followed by the number of the simulation in the sensitivity analysis. Added: trunk/src/site/en/rst/v4/user/usermanual/introduction.rst =================================================================== --- trunk/src/site/en/rst/v4/user/usermanual/introduction.rst (rev 0) +++ trunk/src/site/en/rst/v4/user/usermanual/introduction.rst 2013-01-24 16:43:55 UTC (rev 125) @@ -0,0 +1,123 @@ +.. - +.. * #%L +.. * IsisFish +.. * +.. * $Id$ +.. * $HeadURL$ +.. * %% +.. * Copyright (C) 1999 - 2010 Ifremer, Code Lutin +.. * %% +.. * This program is free software: you can redistribute it and/or modify +.. * it under the terms of the GNU General Public License as +.. * published by the Free Software Foundation, either version 3 of the +.. * License, or (at your option) any later version. +.. * +.. * This program is distributed in the hope that it will be useful, +.. * but WITHOUT ANY WARRANTY; without even the implied warranty of +.. * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +.. * GNU General Public License for more details. +.. * +.. * You should have received a copy of the GNU General Public +.. * License along with this program. If not, see +.. * <http://www.gnu.org/licenses/gpl-3.0.html>. +.. * #L% +.. - + +Introduction +============ + +Goals +----- + +Most of the fisheries are complex systems because of the diversity in exploited +resources (multi-specific) and fishing operations (multi-vessels). Those +fisheries are said mixed or composite. The complexity of those fisheries also +comes from spatial and seasonal heterogeneity of resources and fishing +distributions. In mixed fisheries, resources are exploited either simultaneously +or sequentially by fishing units (boat and fishermen) doing different +fishing activities. So it is difficult to evaluate the resources and +exploitation dynamics, and the resulting fishing mortality for the exploited +populations. The diversity in fishing activities adn associated catches is due +to the multiplicity in fishing locations, targeted species and gears used, but +also to other factors such as fishermen individual behaviour and environmental +and economic conditions. + +Besides, fishermen know spatio-temporal resource distribution, and they allocate +their fishing effort accordingly. At big scales, those spatial distribution +variations are mostly due to ontogenic moves and migrations, leading to +concentration of some demographic stages in some zones at some period of time in +the year, in relation with some life-cycle process (reproduction, feeding). + +In this context, it is essential to take into account the spatial and seasonal +allocation of the fishing effort between fishing locations to evaluate the +fishery dynamics. In mixed fisheries, those aspects are all the more important +that fishermen can not only change of location but also of gear and +target-species. Models spatially explicit are required to understand those +fisheries dynamics. + +ISIS-Fish is a spatial and seasonal simulation model that describes resources, +exploitation and management dynamics. It has been developed to explore the +consequences of different management measures on fisheries dynamics. It allows +to compare respective impacts of conventional measures such as Total Allowed +Catches (TAC), fishing effort controls, technical measures on gears and Marine +Protected Areas (MPA) in a broad way, i.e. spatialised management measures. + +ISIS-Fish is as generic as possible to be applied to a a lot of different +fisheries. The software has a database allowing to integrate the fishery +knowledge while being easily modified. That knowledge contains the parameters +describing each population and each fishing activity. + +ISIS-Fish allows a big flexibility for several hypothesis of the model, such as +relations between spawning stocks and reproduction, selectivity relations, +etc. ; and that in order to guarantee a use by lots of demersal and benthic +fisheries. Management measures and the answer from fishermen to those measures +and environmental and economical conditions can be coded interactively thanks to +a script language. + +ISIS-Fish applications to several european fisheries are in progress, in several +national and european research project. + +Good to know before starting up... +---------------------------------- + + * Despite all the attention given to conviviality and intuitivity in the + software supporting the model, ISIS-Fish stays before all a model. So reading + and understanding underlying equations and hypotheses is a mandatory stage + before parametrisation. Do not hesitate to ask clarifications using + mailing-lists if you need help. + * Several parameters input in ISIS-Fish, as well as management rules and + analysis plans creation need understanding Java language. We think basic + knowledge of this language is required to use the software. Tutorials on + experiment plans are available on this site as well as links to Java + tutorials. + * The methods linked to ISIS-Fish objects are documented in Java and ISIS-Fish + APIs. Mastering those pages is required in the software use. + * ISIS-Fiqh is a collaborative tool. We invite you to exchange using the wiki + and mailing-lists, your questions, thoughts and scripts at all the users + benefits. + * At last, we warn future users that regarding above points and ISIS-Fish model + complexity, parametrisation is a step requiring time that should not be + under-estimated. + +Model description +----------------- + +ISIS-Fish is intended to evaluate spatialised and seasonal management measures +on mixed fisheries. That goes through exploitation variables control such as +catches and fishing effort. + +The simulator relies on three sub-models ; a population dynamics model, a +fishing activity model and a management model. Each sub-model has a spatial and +a seasonal dimension. + +.. image:: modelesFr.jpg + +The fishery region is defined by its edges and is cut into meshes. The mesh +spatial resolution is chosen in function of the dynamics to describe and the +available data. Zones (ie a group of contiguous meshes) are then independently +defined for each population, fishing activity and management measure. + +The model has a monthly time step. Seasons (ie a month row) are also defined +independently for each population, fishing activity and management measure. In +each zone, and for each season, the fishing effort of a specific activity, or a +population abundance, are supposedly homogeneous and uniformly distributed. Copied: trunk/src/site/en/rst/v4/user/usermanual.rst (from rev 121, trunk/src/site/rst/v4/user/usermanual.rst) =================================================================== --- trunk/src/site/en/rst/v4/user/usermanual.rst (rev 0) +++ trunk/src/site/en/rst/v4/user/usermanual.rst 2013-01-24 16:43:55 UTC (rev 125) @@ -0,0 +1,50 @@ +.. - +.. * #%L +.. * IsisFish +.. * +.. * $Id$ +.. * $HeadURL$ +.. * %% +.. * Copyright (C) 1999 - 2011 Ifremer, Code Lutin, Chatellier Eric +.. * %% +.. * This program is free software: you can redistribute it and/or modify +.. * it under the terms of the GNU General Public License as +.. * published by the Free Software Foundation, either version 3 of the +.. * License, or (at your option) any later version. +.. * +.. * This program is distributed in the hope that it will be useful, +.. * but WITHOUT ANY WARRANTY; without even the implied warranty of +.. * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +.. * GNU General Public License for more details. +.. * +.. * You should have received a copy of the GNU General Public +.. * License along with this program. If not, see +.. * <http://www.gnu.org/licenses/gpl-3.0.html>. +.. * #L% +.. - + +User documentation +------------------ + +- Introduction_ +- `User interface`_ + + + `Fishery input`_ + + `Simulation launcher`_ + + `Sensitivity analysis launcher`_ + + `Results rendering`_ + + `Script editor`_ + + `Simulation queue`_ +- `Experiment plan - analysis plan`_ +- `Sensitivity analyses`_ + +.. _Introduction: usermanual/introduction.html +.. _User interface: usermanual/GUI.html +.. _Fishery input: usermanual/inputs.html +.. _Simulation launcher: usermanual/launcher.html +.. _Lanceur d'analyse de sensibilite: usermanual/sensitivity.html +.. _Results rendering: usermanual/results.html +.. _Script editor: usermanual/scripts.html +.. _Simulation queue: usermanual/queue.html +.. _Experiment plan - analysis plan: usermanual/analysisPlan.html +.. _Sensitivity analyses: ../downloads/manuel_sensitivity.pdf

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r124 - trunk/src/site/en/rst/v4/user
by jcouteau＠users.forge.codelutin.com Jan. 24, 2013

Jan. 24, 2013

Author: jcouteau Date: 2013-01-24 15:27:50 +0100 (Thu, 24 Jan 2013) New Revision: 124 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/124 Log: Finish FAQ translation Modified: trunk/src/site/en/rst/v4/user/FAQ.rst Modified: trunk/src/site/en/rst/v4/user/FAQ.rst =================================================================== --- trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-22 16:56:23 UTC (rev 123) +++ trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-24 14:27:50 UTC (rev 124) @@ -32,6 +32,7 @@ ------------------------------------------------ The numbers follow this pattern : + * the first number gives ISIS major version. If you got 3.1.3.1, you are in version 3. If you got 4.0.0.0 you are in version 4. * the second gives the database version in this major version. If you got @@ -115,6 +116,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In the rules or plan script (script editor), + * at the imports levels, add : import fr.ifremer.isisfish.util.Doc * on top of the parameter to document (for example public Zone param_zone = null;), add @Doc("the parameter Zone correspond to ???") @@ -243,6 +245,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The following message appear :: + You don't use correct repository script for your application version 3.2.0.8. Do you want to switch your repository ? @@ -279,3 +282,218 @@ The tip consists in entering a huge vessel speed (fo example 10^9). The trip length becomes really small ~0. +Model +----- + +Seasons definition for a population +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +In ISIS, the seasons correspond to a modification of the parameters linked to +events having an effect on the population (Reproduction, class change, +migration,...) + +To define seasons, you have to place different events on a time line. Seasons +will be the consecutive months between two events. + +Biological and migration events chronology at year scale +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Warning : class change and reproduction happens each month of the season whereas +the migration happens on the first month of the season. You do not have to +specify a season for recruitment as it can happen at any time in the season. + +FIXME Mail de Stéphanie du 11/07/07 : le changement de classe pour une +population structurée en age ne se fait qu'une fois dans la saison, le code +pourrait etre modifié pour éviter d'avoir à définir une saison d'un mois pour le +changement de classe. Il y a des avantages et inconvénients (cf réponse +d'Hilaire) On abandonne ? + +Take care to modelisation hypothesis +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +ISIS base hypothesis : all the state variables are supposed homogeneous at the +defined zone scale - For example If a class of a pop is distributed on Zpop at a +time step t, then this class number of individuals is homogeneously distributed +on Zpop. An effort on a part of Zpop impacts all the individuals of the zone by +diluting on all the zone pop:: + + (N(Zpop,t+1) ~= N(Zpop,t)-F(met)*(N(Zpop,t))). + +Would it be pertinent to make an impact on only the intersection between the +metier zone and the pop zone?:: + + (N(Zpop,t+1) ~= N(Zpop,t)-F(met)*(N(Zpop,t)*(inter(Zmet,Zpop)/Zpop)) + +If we want to evaluate the impact of an AMP included in Zpop, + +* Not distinguishing 2 population zones in Zpop [Z1=Zpop-Zg et Z2=Zg], will + have as consequence that the Z2 abundance will be impacted by the possible + catches in Z1 (because at each time step, the catches that could happen in Z1 + will impact the Zpop abundance:: + + N(Zpop,t+1) ~= N(Zpop,t)-F(met)*(N(Zpop,t)) + + and with the homogeneous hypothesis in Zpop, the individuals numbers in Z2 + will be equals to N(Zpop,t+1)*Z2/Zpop. + +* Distinguishing 2 population zones Z1=Zpop-Zg and Z2=Zg, leads to Z2 abundance + not being impacted by the Z1 catches (allows to model the fact that fishes in + Z2 are pledged to this zone):: + + N(Z1,t+1) ~= N(Z1,t)-F(met)* N(Z1,t), N(Z2,t+1)= N(Z2,t+1)-exp(-M/12) N(Z2,t) (if no migrations) + +* To describe a refuge phenomenon, it might be good to add a migration of +individuals in Z1 and Z2 in density dependecy... ? + +Impact of a MPA zone if the MPA is included in the pop zone + + * If only one pop zone Zpop + * If Zg included in Zpop + * If the metier impacting the pop is distributed on Zmet=Zpop + * If the metier reallocates its effort on the remaining zone : Zmet-Zg=Z1, + +N(Zpop,t+1) = N(Zpop,t)-F(met)/(F(met)+M/12)exp(-F(met)+M/12)*N(Zpop,t), N(Z1,t+1) = N(Zpop,t+1)*Z1/Zpop, N(Z2,t+1) = N(Zpop,t+1)*Z2/Zpop, + + * If Zg grows up (for example nZg=kZg), F(met) does not change, the individuals number + +N(Zpop,t+1) = N(Zpop,t)-{F(met)/(F(met)+M/12)*exp(-F(met)+M/12)}* N(Zpop,t) N(Z1,t+1) = N(Zpop,t+1)*[Zpop-kZg]/Zpop, N(Z2,t+1) = N(Zpop,t+1)*kZg/Zpop, + +**ie with a modelisation of the distribution zone of the pop in one zone (ie no +heterogeneity between the part of the pop zone in the MPA and the other), a zone +size change cannot have any impact** + +If we do the suggested hypothesis : N(Zpop,t+1) ~= N(Zpop,t)-F(met)*(N(Zpop,t)*(inter(Zmet,Zpop)/Zpop)). + +**In this case, the impact (difference between the individuals number for the +big MPA - individual numbers for the small MPA) = (k-1)* Zg)/Zpop F(met)/(F(met)+M/12)*exp(-F(met)+M/12)}* N(Zpop,t)** + +Additional remark : superposition of population zones +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +:?: ''To check again, but a priori : '' + +If necessary, it is possible to create population zones that overlap for the +same population. If the natural mortality is the same for both zones, the +catches in the intersection zone will be rightly computed. If the natural +mortality is the same in both zones, the effort E(str, met, grp) and then the +fishing mortality F(str, met, grp) and the catches rate CR(str, met, grp) +are computed independently for each pop zone but identical, so we got : + + * pop zone 1 : E -> F -> CR + * pop zone 2 : E -> F -> CR + +and the catches will be B1*CR + B2*CR = (B1+B2)*CR + +(and that works whether we are in the by cell model or by zone model) + +Catchability in ISIS-Fish +~~~~~~~~~~~~~~~~~~~~~~~~~ + +The catchability in ISIS-Fish is the biological part of the parameter +(disponibility) as stated by Mahévas et al. 2001 = accessibility*vulnerability. +The part due to boat and gear is taken into account explicitly in ISIS-Fish by +the selectivity/targeting/fishing efficiency/etc parameters. +The disponibility parameter usually represents the probability variations of the +catches due to to the change of spatial distribution. +Those variations are modeled explicitly in ISIS as the model is spatialised. +So the parameter compensate for the other causes of probability variations of +the catches by effort unit related to the fish behaviour (schooling aggregation, +burying, vertical distribution change,...). + +see +Mahevas, S., Trenkel, V.M., Doray, M. and Peyronnet, A. 2011. Hake catchability by the french trawler fleet in the bay of biscay: estimating technical and biological components. ICES JOURNAL OF MARINE SCIENCE 68: pp. 107-118 +Laurec, A., et J. C. Le Guen. Dynamique des populations marines exploitées Tome1 : Concepts et Modèles. Centre National pour l’Exploitation des Océans, 1981. 602. +Gascuel: http://halieutique.agrocampus-ouest.fr/pdf/136.pdf +citing: +Anonyme, 1979. Monitoring of fish stock abundance : the use of catch and effort data. +FAO Fish. Tech. Paper. 155 : 101 p. +Chadwick M., R.N. O'Boyle, 1990. L'analyse des données de captures et d'effort. In: +Méthodes d'évaluation des stocks halieutiques, Brêthes J.C., R.N. O'Boyle éd., Univ. +Québec à Rimouski, Vol. I et II, 77-101. + +Simulations +----------- + +What happens at t=0 ? +~~~~~~~~~~~~~~~~~~~~~ + +During a simulation, the first time step is particular, and all the events +usually happening in january do not necessary happen : +Lors d'une simulation, le premier pas de temps est particulier, et tous les +événements se déroulant habituellement en janvier n'arrivent pas forcement : + + * migration happens + * class change does not happen + +FIXME will it be modified ??? + +:-( Take care while entering initial fish numbers an results from january from +year 0. They are not comparable with those from other years of simulation. + +Simulation by cell +~~~~~~~~~~~~~~~~~~ + +To do a simulation by cell, in the simulation (or sensitivity analysis) +launching interface, in the "Advanced Parameters" tab, we can add an +"effortByCell" tag which value is true. + +Sensitivity analysis +-------------------- + +ISIS-Fish closes itself when I launch a sensitivity analysis +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +It comes from an incomplete R configuration. Report to the point "Sensitivity +analysis does not work" + +From 3.3.0.0 ISIS-Fish version, an error should show up in the logs (debug.txt) +and ISIS-Fish should not close itself. + +Sensitivity analysis does not work +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +THe most common mistake come from an incomplete R configuration for ISIS-Fish. + +You should have R 2.9.0 version. + +On Windows, you should configurate the two environment variables : + + * `R_HOME` to C:\Program Files\R\R-2.9.2 + * `PATH` must contain : `%R_HOME%\bin` + +Tips and tricks +-------------- +Fill in a table from a txt or csv file +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +In user interfaces, you have to right-click on the table to fill and choose +'import from a file'. + +Big integers are problematic +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +You have to write 39E3 instead of 39000 + +Why 41/1000 gives 0 ? +~~~~~~~~~~~~~~~~~~~~~ + +In my rule, I divide 41 by 1000 and the result is 0, why ? + +In Java, everything is typed. What is done in this operation is an euclidian +division, 41 and 1000 being integers. To have the result of a "classic" +division, you have to do 41.0/1000.0. Both numbers being decimals (float or +double), the number will be with decimal (double or float). + +More generally, in Java, on an operation between two types, Java keeps the +bigger precision. For exemple, betwwen two integers, you will have an integer +between two doubles, you will have a double, but between an intyeger and a +double, you will have a double. You can have more info here (in french) : +http://www.siteduzero.com/tutoriel-3-10276-les-variables-et-les-operateurs.html#ss_part_2 + +How do I do an exponential (or any other "evolved" mathematical function) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +For most of usual mathematical operation, you have to use static methods from +Math class. + +More info (in french) : http://jmdoudoux.developpez.com/cours/developpons/java/chap-math.php

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