January 2013 - Isis-fish-docs-commits - mailman.cloud.codelutin.com

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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r123 - in trunk/src/site/en/rst/v4/user: . tutorials
by jcouteau＠users.forge.codelutin.com Jan. 22, 2013

Jan. 22, 2013

Author: jcouteau Date: 2013-01-22 17:56:23 +0100 (Tue, 22 Jan 2013) New Revision: 123 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/123 Log: Continue translating FAQ into english. Add tuto that are linked from FAQ (not translated) Added: trunk/src/site/en/rst/v4/user/tutorials/ trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst 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 2013-01-21 15:43:25 UTC (rev 122) +++ trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-22 16:56:23 UTC (rev 123) @@ -117,10 +117,165 @@ 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 ???") + null;), add @Doc("the parameter Zone correspond to ???") Insert comments in a script ~~~~~~~~~~~~~~~~~~~~~~~~~~~ System.out.println (); +How to use APIs ? +~~~~~~~~~~~~~~~~~ + +cf tutorial_ . + +.. _tutorial: tutorials/useAPI.html + + +How to create simulation plan scripts +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +`cf tutorial`_ + +.. _cf tutorial: tutorials/simulationPlan.html + +What is the structure of an analysis plan or management rules script ? +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +cf simulation procedure at the bottom of `this page`_ and `this one`_ + +.. _this page: ../devel/architecture.html + +.. _this one: usermanual/analysisPlan.html + +A parameter of my rule behaves strangely, what is happening ? +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The rules parameters variables (thos which start by \param_) are initialized at +the beginning of each simulation and not each time step. So you have not to +modify them but use intermediate variables. + +User interfaces +--------------- + +Verifying fishery parameters +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +* For all the fishery. In the region interface : bottom button to check. + + - blue : ok + - orange : parameters with a problem +* For an equation. In the equation editor : check button - syntax verification +* For a script (rule, AnalysisPlan,...). In the script editor : check button - + syntax verification. You can check the differences between your version and + the server version using the server menu from the script editor interface. + +What "tag" is for in the launcing interface, in the advanced parameters +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Parameterize exports, the simulator or equations. + +Example : In the simulator, simulate economical variables:: + + if (!"false".equalsIgnoreCase(param.getTagValue().get("ecoResult"))) { + control.setText("Add economics results"); + saveGravityModel(date, resManager, gravityModel); + } + +Here the tag is called ecoResult + +Effort description +~~~~~~~~~~~~~~~~~~ + +The variables 'Fishing operation number' and 'gear number per operation' are +taken into account in the equations for the "effort standardisation by trip" +this way:: + + StdEffortPerHour = Fstd * FishingOperationNumber * GearNumberPerOperation. + +So they have to be fille din when Fstd is computed at FishingOperation*gear +scale. + +If Fstd is computed at trip scale, you HAVE TO put 1 in both variable (or +catches will be nil). The "fishingOperationLength" variable is not used in +equations. + +Units... +~~~~~~~~ + +Trip types : + + * Trip length in hours + * Minimum time between two trips : unused + +Vessel type + + * Trip max length : unused + * speed in km/h + * activity interval : unused + +Enter a management rule application month in the simulation launching interface +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +That is the number of the month that is queried, so a number between 0 and 11 +(0 : january, 11 : december). Otherwise you will have a bug ! + +Did the simulation run ? +~~~~~~~~~~~~~~~~~~~~~~~~ + +* Ensure the simulation is in "simulation finished" state in the simulation + queue + +* Select the simulation in the table (or in simulation result interface) and + click on "see the logs" + +* Select fatal, error and warning : If something appears, there is a bug. Below + ERROR is the exception. You have to look into the stacktrace and watch for a + line with ifremer.isisfish and see what it says. + +See Numbers and biomasses in the results window +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Small tweak : In the results window, the numbers, biomass of a population for a +month is the number/biomass at the end of the previous time step. + +You do not use the correct repository for your ISIS-Fish version +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +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 ? + +This message appear when you use a new major version of ISIS-Fish. It simply +asks you if you want to use the new script version that works with your new +version. + +Modeling tips +------------- + +Split males and females with different growth +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We create consecutive length classes for males and others for the females that +will follow. For examples, for males we got those classes:: + + 60-70 70-77 77-110 110-166 + +and for females :: + + 60-70 70-78 78-86 + +you click on 'recruit classes'. For the first length, enter '60'. +Then for the max lengths, enter : +'70;77;110;166;70;78;86' and validate. That will create a 4th class with +minimal length of 166 and maximal length of 70 ! + +In the population group interface, modify the minimal length of the 4th class +(the first female class) : from 166 to 60. You save and that's all !!! + +To do not take into account the trip time in the effort +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The tip consists in entering a huge vessel speed (fo example 10^9). The trip +length becomes really small ~0. + Copied: trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst (from rev 121, trunk/src/site/rst/v4/user/tutorials/simulationPlan.rst) =================================================================== --- trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst (rev 0) +++ trunk/src/site/en/rst/v4/user/tutorials/simulationPlan.rst 2013-01-22 16:56:23 UTC (rev 123) @@ -0,0 +1,208 @@ +.. - +.. * #%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% +.. - + +Tutorial to use simulation plans +================================ + +This tutorial have not been translated yet. Here is the French version + +Un plan d'analyse est un ensemble d'expériences (simulations) pour lesquelles on +va modifier la valeur de certains paramètres selon un protocole défini pour +répondre à une question. On distingue des plans de simulations pour lesquels + +* *les expériences sont indépendantes* . C'est à dire que l'ordre des + simulations n'a pas d'importance et que l'on pourrait par exemple les lancer + sur des ordinateurs différents. Les valeurs que les paramètres devront prendre + à chaque nouvelle simulation sont déterminées au préalable. + +* *les expériences sont séquentielles* . Les valeurs des paramètres de la + simulation n+1 dépendent des résultats de la simulation n. + +Expériences Indépendantes : exemple d'une analyse de sensibilité +---------------------------------------------------------------- + +Dans le cas d'expériences indépendantes, la première étape est de définir les +paramètres à modifier et les différentes valeurs qu'ils devront prendre +(appelées « modalités »). On les organise ensuite selon un plan d'expérience +adéquat (plan complet, factoriel, optimisé...) qu'on écrit sous forme de matrice. +Des méthodes sont déjà disponibles pour réaliser ce type de plans sous +ISIS-Fish. Ils sont décrits ici mais libre à l'utilisateur d'écrire ses propres +scripts si la méthode actuellement utilisée ne répond pas à ses besoins. Voici +la description et le fonctionnement des scripts existants : ils nécessitent +l'écriture de 3 types de fichiers : un script de plan d'analyse, une matrice +d'expérience et des fichiers paramètre : + +La matrice d'expérience +~~~~~~~~~~~~~~~~~~~~~~~ + +*La matrice d'expérience* est une matrice [expériences x paramètres] : chaque +colonne correspond à l'un des paramètres à modifier et chaque ligne contient +les modalités des paramètres pour une expérience donnée. Les modalités sont +codées par des entiers (-1 ;0 ;1 etc). Cette matrice est copiée dans un +fichier .txt sans en-tête de colonnes ni de lignes. + +Les fichiers paramètres +~~~~~~~~~~~~~~~~~~~~~~~ + +*Les fichiers paramètres* : un fichier .txt par paramètre donnant la +correspondance entre la valeur de la modalité (-1 ;0 ;1) dans la matrice et la +valeur du paramètre. Ce paramètre peut être un réel, une liste de réels, une +équation… Si l'on nomme les modalités –1 et 1, le fichier est de la forme + +Pour un paramètre qui est une liste +___________________________________ + +:: + + -1=0.5;0.8;0.9;0.11 + 1=0.5;0.11;0.15;0.41 + +Pour un paramètre qui est une équation +______________________________________ + +:: + + -1=if(condition = true) return 5 ; else return 3 ; + 1=if(condition = true) return 7 ; else return 3 ; + +Pour un paramètre qui est un réel +_________________________________ + +:: + + -1=0.8 + 1=1.2 + +Autres +______ + +On peut aussi modifier les paramètres des règles de gestion...(voir +exemple). Il faut alors indiquer dans le .txt tous les paramètres public de +la règle. Attention pour certaines règles de gestion il faut définir la +population, l'engin, la zone... ciblée par la règle dans les paramètres. +Pour ce faire il n'est pas possible d'écrire le nom de la population, de la +zone... il faut déterminer le code correspondant qui est du genre + +:: + + fr.ifremer.isisfish.entities.Zone#1169028645767#0.37798185123822536 + +Pour cela on peut faire tourner une simulation avec la règle en question +correctement paramétrée et aller voir dans les logs (fichier debug.txt dans +le même dossier que le .bat de lancement), ces codes sont inscrits à coté du +nom du paramètre au moment de l'initialisation des règle de gestion. + +*Attention !!!!* dans ces fichiers la syntaxe est importante: + +* Pas d'espace +* Pas de « ; » à la fin des lignes +* Pas de « + » devant un chiffre quand il désigne une modalité (+1=NON ; 1=OUI) + +Les fichier matrix.txt et les fichiers paramètres.txt doivent être placés *dans +un même dossier* de préférence localisé dans le dossier contenant le .bat de +lancement d'ISIS-Fish (qui est la racine pour le logiciel). + +Exemple +~~~~~~~ + +On propose ici la matrice et les fichiers paramètres d'une analyse +de sensibilité sur les paramètres de croissance, capturabilité, selectivité et +la période de fermeture d'un cantonnement. + +`Fichiers parametres et matrice`_ + +.. _Fichiers parametres et matrice: ../../downloads/Exemple_directory.zip + +*Le script de plan de simulation* (écrit à partir de l'éditeur de scripts) +permet de récupérer et modifier les valeurs des paramètres en fonction de la +matrice d'expérience pour chaque simulation. (Voir le manuel pour l'explication +de la structure des scripts de plans de simulation.) + +On joint ici le script commenté correspondant à l'analyse de sensibilité +précédante. Le script contient les méthodes nécessaires à lire les fichiers +matrice.txt et les fichiers contenant les modalités des paramètres. Il contient +aussi le code servant à modifier les valeurs de ces paramètres dans la base de +donnée (pour connaitre les méthodes permettant d'accéder aux différents +paramètres de la base de donnée, se référer aux APIs). + +`Script d'analyse de sensibilite`_ + +.. _Script d'analyse de sensibilite: ../../downloads/Exemple_PlanSimulation.java + +Plans sequentiels : exemple de calibration par la méthode du simplexe +--------------------------------------------------------------------- + +Dans ce cas, les modalités prises par les paramètres à la simulation suivante +dépendent des résultats des simulations précédentes. Il faut donc écrire +l'algorithme de calcul de ces nouvelles valeurs en fonction des résultats de +simulation dans le script du plan d'analyse. Il faut également écrire le code +permettant de modifier la valeur des paramètres pour la remplacer par la +nouvelle valeur calculée. + +Exemple +~~~~~~~ + +L'exemple reprend un script qui permet de calibrer deux paramètres (ici la +capturabilité) par la méthode du simplexe à pas variable à partir des +débarquements trimestriels. + +`Script de calibration`_ + +.. _Script de calibration: ../../downloads/calibration.java + +Lancement d'un Plan d'analyse +----------------------------- + +Quand les scripts sont écrits, c'est tout simple ! + +Dans l'interface de lancement de simulation on prépare sa simulation comme +d'habitude à l'exception des règles de gestion : il ne faut pas charger une +règle si elle doit être modifiée par le plan car elle sera ajoutée par le plan +d'analyse à la suite des règles entrées dans l'interface. On coche la case +« Utiliser le plan d'analyse ». On sélectionne le plan Exemple_PlanAnalyse ou +CalibrationExpeceq1q2 dans la liste déroulante. On remplit les paramètres du +plan et on lance la simulation. + +PS : Attention à bien vérifier les différentes étapes listées dans le Pense-Bête +sinon gare aux 500 simulations sans effectifs initiaux... ;-) + +Biblio intéressante +------------------- + +* Drouineau, H., Mahévas, S., Pelletier, D. and Beliaeff, B. 2006. Assessing the + impact of different management options using ISIS-Fish: the French + Hake-Nephrops mixed fishery of the Bay of Biscay. Aquatic living resource, + 19 : 15-29. +* Saltelli, A., Tarantola, S., Campolongo, F. and Ratto, M. 2004. Sensitivity + Analysis in Practise. A guide to Assessing Scientific Models. J.W.&. Sons. pp. +* Kleijnen, J.P.C. 1998. Experimental Design for Sensitivity Analysis, + Optimization, and Validation of Simulations Models. In Handbook of simulation. + Principles, Methodology, Advances, Applications and Practise, pp. 173-224. Ed. + by Banks, J. Wiley, New York. Engeneering and Management Press. 864 pp. +* Walters, F.H., Parker, L.R., Morgan, S.L. and Deming, S.N. 1991. Sequential + Simplex optimization: a technique for improving quality and productivity in + research, development, and manufacturing (Chemometrics series). B.R. CRC Press + LLC. 402 pp. +* Nocedal, J., and Wright, S.J. 2006. Numerical Optimization. Mikosch, T. V., Resnick, S. I. , andRobinson, S. M. (Eds.). 2nd Ed., Springer Series in Operations Research, New York. \ No newline at end of file Copied: trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst (from rev 121, trunk/src/site/rst/v4/user/tutorials/useAPI.rst) =================================================================== --- trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst (rev 0) +++ trunk/src/site/en/rst/v4/user/tutorials/useAPI.rst 2013-01-22 16:56:23 UTC (rev 123) @@ -0,0 +1,137 @@ +.. - +.. * #%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% +.. - + +Tutorial on APIs use +==================== + +This tutorial have not been translated to english yet. + +Avant tout il faut savoir, que toutes les valeurs saisies dans l'interface de +saisie par l'utilisateur sont stoquées dans les objets d'ISIS correspondants. +Pour modifier ces valeurs avant ou en cours de simulation, il faut connaitre +leur nature et leur structure, savoir comment y accéder et les modifier. +Pour savoir comment y accéder il faut connaitre les dépendances entre objets +(objets qui sont des attributs d'autres objets). Pour cela on consulte +l'architecture de la base de donnée ( `Modele ISIS-Fish`_ ) qui se reflète dans +l'architecture de l'interface de saisie. + +Pour savoir comment passer d'un objet a un autre il faut connaitre les méthodes +appliquables aux objets : tout est dans l'API. + +Remarque : Il vaut mieux commencer par se familiariser avec les differents types +d'objets JAVA (double, boolean, string, integer, equation, matrix,...), les +attributs et les methodes (cf tutoriaux JAVA). + +Voici un exemple "pas à pas" pour le cas ou l'on voudrait modifier l'equation de +mortalité naturelle dans un plan d'analyse par exemple. On veut remplacer +provisoirement la valeur de la base par une autre. On crée un objet String +rempli avec l'autre valeur par exemple:: + + String mortalitenaturelle = "if (groupe.getId() == 0) return 1.5; else return 0.2;" + +Se poser la question : "Dans la base de donnée où se trouve la mortalité naturelle ?" +------------------------------------------------------------------------------------- + +Réponse : dans l'interface de saisie, elle est dans la branche "population" et +l'onglet "equations". +(au passage le titre de l'onglet nous renseigne sur le type d'objet auquel on a +affaire : ya de grandes chances pour que parmi la batterie d'objets possibles +(int, double, matrice...) la mortalité naturelle soit une equation ;-) ) + +En francais on dirait "dans population, va chercher l'objet equation de +mortalité naturelle, et attribut lui la valeur du string mortalitenaturelle", ya +pu qu'a le dire en java. + +Ouvrir la page des APIs +----------------------- + +Dans la colonne de gauche de l'API (sous "all classes") on cherche l'entite +"population" et on clique dessus. + +Les méthodes disponibles +------------------------ + +Toutes méthodes que l'on peut appliquer à un objet population (colonne de +droite) s'affichent , et le type d'objet qu'elles renvoient (colonne de gauche). + +c'est a dire que les lignes de commandes qu'on ecrira seront de la forme:: + + objet_renvoyé_indiqué_à_gauche nomObjet = population.methode_ecrite_à_droite(argument de la methode); + +Il y a surtout deux grands types de méthodes : + +* les méthodes "get" : qui vont chercher un objet +* les méthodes "set" : qui assignent une valeur a un objet. + +Dans notre exemple on veut changer l'equation de mortalité naturelle, c est donc +un set ! + +On cherche une méthode qui parle de mortalité naturelle... +---------------------------------------------------------- + +On trouve getNaturalDeathRate() qui renvoit un objet equation (c'est l'objet +equation qui contient la valeur de l'equation de mortalite naturelle remplie par +l'utilisateur) et setNaturalDeathRate(Equation naturalDeathRate) pour laquelle +on doit passer un objet equation (une equation de naturalDeathRate) en argument. + +(en cliquant sur le nom de la méthode on a une description sommaire de ce +qu'elle fait) + +setNaturalDeathRate() parait être ce qu'on veut faire... +mais la méthode setNaturalDeathRate prend en argument une equation, on ne peut +donc pas faire:: + + pop.setNaturalDeathRate(mortalitenaturelle); + +puisque mortalitenaturelle n'est pas une equation mais un string. + + +Créer une équation +------------------ + +Du coup il faut trouver autre chose qui fasse le lien entre un string et une +equation. En cliquant sur "equation" dans la page d'API on tombe sur la page des +méthodes qui s'appliquent aux objets qui sont des equations. On trouve une +méthode .setContent(String ) qui prend en argument un string. Ca veut dire que +si on a une equation, on peut lui changer sa valeur en utilisant cette methode +avec un string en argument. +L'equation dont on veut changer la valeur on sait la récupérer:: + + Equation eqMortalite = pop.getNaturalDeathRate(); + +L'objet eqMortalite est un objet equation:: + + eqMortalite.setContent(mortalitenaturelle); + +et là on a le droit vu que mortalitenaturelle est un string et que la méthode +prend un string en argument. + +et voilà c'est fait ! + +remarque : on pourrait le faire en 1 ligne:: + + pop.getNaturalDeathRate().setContent(mortalitenaturelle); + +.. _Modele ISIS-Fish: ../isisFishModel.html

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r122 - in trunk/src/site: . en/rst en/rst/v4 en/rst/v4/user
by jcouteau＠users.forge.codelutin.com Jan. 21, 2013

Jan. 21, 2013

Author: jcouteau Date: 2013-01-21 16:43:25 +0100 (Mon, 21 Jan 2013) New Revision: 122 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/122 Log: Begin translating FAQ to english Added: trunk/src/site/en/rst/v4/ trunk/src/site/en/rst/v4/index.rst trunk/src/site/en/rst/v4/user/ trunk/src/site/en/rst/v4/user/FAQ.rst Modified: trunk/src/site/site_en.xml Copied: trunk/src/site/en/rst/v4/index.rst (from rev 121, trunk/src/site/rst/v4/index.rst) =================================================================== --- trunk/src/site/en/rst/v4/index.rst (rev 0) +++ trunk/src/site/en/rst/v4/index.rst 2013-01-21 15:43:25 UTC (rev 122) @@ -0,0 +1,53 @@ +.. - +.. * #%L +.. * IsisFish +.. * +.. * $Id$ +.. * $HeadURL$ +.. * %% +.. * Copyright (C) 2011 Ifremer, CodeLutin, 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% +.. - + +Documentation version 4 +======================= + +* `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: user/warning.html +.. _Installation: user/installation.html +.. _User manual: user/usermanual.html +.. _Tutorials: user/tutorials.html +.. _FAQ: user/FAQ.html +.. _Developer manual: devel/index.html +.. _APIs documentation: user/API.html +.. _ISIS scripts examples: user/scripts.html +.. _R scripts examples: user/scriptsR.html +.. _Changes in version 4.0: user/changements40.html +.. _Migration from 3.x to 4.0: user/migrationv3v4.html +.. _Note to CAPARMOR users: user/tutorials/utilCaparmor.rst Copied: trunk/src/site/en/rst/v4/user/FAQ.rst (from rev 121, trunk/src/site/rst/v4/user/FAQ.rst) =================================================================== --- trunk/src/site/en/rst/v4/user/FAQ.rst (rev 0) +++ trunk/src/site/en/rst/v4/user/FAQ.rst 2013-01-21 15:43:25 UTC (rev 122) @@ -0,0 +1,126 @@ +.. - +.. * #%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% +.. - + +Frequently Asked Questions (FAQ) +================================ + +.. contents:: + +What does the numbers 3.1.3.1 or 4.0.0.0 means ? +------------------------------------------------ + +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 + 3.1.3.1, you are in version 1 of the database. If you got 4.0.0.0 you are in + version 0. + * the third number gives you the scripts version to use + (isis-fish-4/isis-database) + * the last number represents the minor version. In 3.1.3.1, the minor version + is 1. + +When you already got ISIS-Fish, you can use any other version with the same +major, base and scripts numbers. It means that only the minor number changes. + +If you want to use an ISIS-Fish version with an upper base number, ISIS-Fish +will automagically convert your database into this version. You will not be able +to use an ISIS-Fish version with a lower base number. + +It is possible to use ISIS-Fish in two different major versions because they do +not share the same configuration files. So they are two completely different +installations. + +You can launch version 3 and version 4 at the same time. + +What are my limits when I write scripts ? +----------------------------------------- + +You have to never modify an object returned by a script method because a caching +system is used. If you do so, you modify the cache object, and on the next call, +you will get the modified object and not the one you want. For example, if you +return a ``List``, you have to, in the method that gets the list, do a copy of +that ``List`` before modifying it. If you just read the ``List`` content, you +have nothing to do. + +Scripts : objects and syntax +---------------------------- + +Know ISIS objects and methods +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + * List of objects, methods and links between objects (UML model) : + ../../v3/devel/images/IsisFishModel.png . + This figure gives you the name of objects and the name of the attached methods + * ISIS-Fish API : http://www.isis-fish.org/apidocs/index.html + * Scripts access : in the software, using the scripts edition interface. Most + of the equations are in ``scripts/SiMatrix.java``. All the other scripts are + available online : http://www.isis-fish.org/xref/ . The source are also + viewable from the svn repo : + http://svn.forge.codelutin.com/svn/isis-fish/trunk/ + +Update scripts +~~~~~~~~~~~~~~ + +This can be done via synchronisation with the server : File/Server +synchronization. This action compares the scripts on the PC with those on the +server and indicates the differences. You have then to check the scripts you +want to update and validate. + +Warning : If an error is indicated in a script, the synchronisation will modify +the said script. If modifications happen betwen the local version and the server +versions, the lines in error will be marked with '<<<<'. You will have the local +version and the server version. You have to choose the version to keep and +delete or comment the other one so that the script can work. + +All the scripts are available here : +http://svn.forge.codelutin.com/svn/isis-fish-data/trunk/ + +Local scripts +~~~~~~~~~~~~~ + +If you have local scripts, they are not synchronized. + +Inherited scripts +~~~~~~~~~~~~~~~~~ + +If a local script have been written from a script on the server, it is necessary +to keep track of the script of origin. So in cas the script of origin is +modified on the server, the user can find the local inherited scripts and modify +them back. + +Add a contextual help on rules and analysis plans +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +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 ???") + +Insert comments in a script +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +System.out.println (); + Modified: trunk/src/site/site_en.xml =================================================================== --- trunk/src/site/site_en.xml 2012-12-20 15:15:22 UTC (rev 121) +++ trunk/src/site/site_en.xml 2013-01-21 15:43:25 UTC (rev 122) @@ -65,6 +65,9 @@ <item name="Roadmap" href="http://forge.codelutin.com/projects/isis-fish/roadmap" /> <item name="Download" href="download.html" /> + <item name="Documentation" href="v4/index.html"> + <item name="FAQ" href="v4/user/FAQ.html"/> + </item> <item name="Publications" href="publications.html" /> <item name="Research projects" href="research.html" /> <item name="License" href="license.html" />

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