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