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

r293 - trunk
by echatellier＠users.forge.codelutin.com March 2, 2016

March 2, 2016

Author: echatellier Date: 2016-03-02 16:31:46 +0100 (Wed, 02 Mar 2016) New Revision: 293 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/293 Log: Fix swe url Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2016-03-02 15:23:42 UTC (rev 292) +++ trunk/pom.xml 2016-03-02 15:31:46 UTC (rev 293) @@ -140,6 +140,7 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <jrstPluginVersion>2.2-SNAPSHOT</jrstPluginVersion> <siteDeployClassifier/> + <scmwebeditorUrl>https://scmwebeditor.nuiton.org/scmwebeditor/edit.action</scmwebeditorUrl> </properties> <distributionManagement>

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r292 - trunk/src/site/rst/v4/user
by echatellier＠users.forge.codelutin.com March 2, 2016

March 2, 2016

Author: echatellier Date: 2016-03-02 16:23:42 +0100 (Wed, 02 Mar 2016) New Revision: 292 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/292 Log: Fix links Modified: trunk/src/site/rst/v4/user/API.rst Modified: trunk/src/site/rst/v4/user/API.rst =================================================================== --- trunk/src/site/rst/v4/user/API.rst 2016-03-01 17:02:30 UTC (rev 291) +++ trunk/src/site/rst/v4/user/API.rst 2016-03-02 15:23:42 UTC (rev 292) @@ -44,11 +44,11 @@ .. _Javadoc ISIS-Fish: ../../apidocs/index.html .. _src: ../../xref/index.html .. _Javadoc JAVA: http://docs.oracle.com/javase/8/docs/api/ -.. _Javadoc ToPIA: http://maven-site.nuiton.org/topia/topia-persistence/apidocs/index.html -.. _Javadoc Nuiton-Matrix: http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/index.html -.. _MatrixND: http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/org/nuiton… -.. _Javadoc Nuiton-Utils: http://maven-site.nuiton.org/nuiton-utils/apidocs/index.html +.. _Javadoc ToPIA: http://topia.nuiton.org/v/2.11/topia-persistence/apidocs/ +.. _Javadoc Nuiton-Matrix: http://nuiton-matrix.nuiton.org/v/latest/apidocs/ +.. _MatrixND: http://nuiton-matrix.nuiton.org/v/latest/apidocs/org/nuiton/math/matrix/Mat… +.. _Javadoc Nuiton-Utils: http://nuiton-utils.nuiton.org/v/latest/apidocs/ .. _Javadoc SSJ: http://umontreal-simul.github.io/ssj/docs/master/namespaces.html -.. _Javadoc Nuiton-j2r: http://maven-site.nuiton.org/nuiton-j2r/apidocs/index.html +.. _Javadoc Nuiton-j2r: http://nuiton-j2r.nuiton.org/v/latest/apidocs/ .. _Javadoc JDistLib: http://jdistlib.sourceforge.net/javadoc/ .. _jdistlib: http://jdistlib.sourceforge.net/

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r291 - trunk/src/site/rst/v4/user/changes
by echatellier＠users.forge.codelutin.com March 1, 2016

March 1, 2016

Author: echatellier Date: 2016-03-01 18:02:30 +0100 (Tue, 01 Mar 2016) New Revision: 291 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/291 Log: >From scmwebeditor -- Ajout d'une doc sur les scripts d'export Modified: trunk/src/site/rst/v4/user/changes/changements44.rst Modified: trunk/src/site/rst/v4/user/changes/changements44.rst =================================================================== --- trunk/src/site/rst/v4/user/changes/changements44.rst 2016-03-01 16:19:57 UTC (rev 290) +++ trunk/src/site/rst/v4/user/changes/changements44.rst 2016-03-01 17:02:30 UTC (rev 291) @@ -223,7 +223,17 @@ * ``export``: appelée à la fin de chaque pas de temps * ``exportEnd``: appelée à la fin de la simulation +Script d'export +--------------- +Les scripts d'export du dépôt "officiel" ont été migrés et utilise maintenant le fonctionnement par pas de temps pour être exportés durant la simulation. +Ce changement a aussi été l'occasion d'effectuer d'autre changements aux scripts d'export: + +* déplacement de la colonne ``step`` en première position +* ajout d'entêtes au fichier csv + +Les scripts du dépôt "communauté" n'ont pas encore été migré mais continueront de fonctionner. + Mortalité par pêche "autres" ---------------------------- Une equation de mortalité par pêche "autres" a été ajoutée dans l'onglet "Stocks". Elle permet de spécifier une mortalité due à des flottilles non explicitement modélisées. La structure est identique à celle de l'equation de mortalité naturelle (par groupe et potentiellement par zone).

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r290 - trunk/src/site/rst/v4/user
by echatellier＠users.forge.codelutin.com March 1, 2016

March 1, 2016

Author: echatellier Date: 2016-03-01 17:19:57 +0100 (Tue, 01 Mar 2016) New Revision: 290 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/290 Log: >From scmwebeditor -- Java 8 API Modified: trunk/src/site/rst/v4/user/API.rst Modified: trunk/src/site/rst/v4/user/API.rst =================================================================== --- trunk/src/site/rst/v4/user/API.rst 2016-03-01 16:09:41 UTC (rev 289) +++ trunk/src/site/rst/v4/user/API.rst 2016-03-01 16:19:57 UTC (rev 290) @@ -5,7 +5,7 @@ .. * $Id$ .. * $HeadURL$ .. * %% -.. * Copyright (C) 1999 - 2014 Ifremer, Code Lutin, Chatellier Eric +.. * Copyright (C) 1999 - 2016 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 @@ -43,7 +43,7 @@ .. _Le modele de donnees: isisFishModel.html .. _Javadoc ISIS-Fish: ../../apidocs/index.html .. _src: ../../xref/index.html -.. _Javadoc JAVA: http://docs.oracle.com/javase/7/docs/api/ +.. _Javadoc JAVA: http://docs.oracle.com/javase/8/docs/api/ .. _Javadoc ToPIA: http://maven-site.nuiton.org/topia/topia-persistence/apidocs/index.html .. _Javadoc Nuiton-Matrix: http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/index.html .. _MatrixND: http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/org/nuiton…

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r289 - trunk
by echatellier＠users.forge.codelutin.com March 1, 2016

March 1, 2016

Author: echatellier Date: 2016-03-01 17:09:41 +0100 (Tue, 01 Mar 2016) New Revision: 289 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/289 Log: Fix scmwebeditor url Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2016-03-01 16:07:52 UTC (rev 288) +++ trunk/pom.xml 2016-03-01 16:09:41 UTC (rev 289) @@ -140,7 +140,6 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <jrstPluginVersion>2.2-SNAPSHOT</jrstPluginVersion> <siteDeployClassifier/> - <scmwebeditorUrl>https://scmwebeditor2.nuiton.org/scmwebeditor2/edit.action</scmwebeditorUrl> </properties> <distributionManagement>

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r288 - trunk/src/site/rst/v4/user
by echatellier＠users.forge.codelutin.com March 1, 2016

March 1, 2016

Author: echatellier Date: 2016-03-01 17:07:52 +0100 (Tue, 01 Mar 2016) New Revision: 288 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/288 Log: >From scmwebeditor -- Fix ssj Modified: trunk/src/site/rst/v4/user/API.rst Modified: trunk/src/site/rst/v4/user/API.rst =================================================================== --- trunk/src/site/rst/v4/user/API.rst 2016-02-12 09:04:56 UTC (rev 287) +++ trunk/src/site/rst/v4/user/API.rst 2016-03-01 16:07:52 UTC (rev 288) @@ -48,7 +48,7 @@ .. _Javadoc Nuiton-Matrix: http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/index.html .. _MatrixND: http://maven-site.nuiton.org/nuiton-matrix/nuiton-matrix/apidocs/org/nuiton… .. _Javadoc Nuiton-Utils: http://maven-site.nuiton.org/nuiton-utils/apidocs/index.html -.. _Javadoc SSJ: http://simul.iro.umontreal.ca/ssj/doc/html/index.html +.. _Javadoc SSJ: http://umontreal-simul.github.io/ssj/docs/master/namespaces.html .. _Javadoc Nuiton-j2r: http://maven-site.nuiton.org/nuiton-j2r/apidocs/index.html .. _Javadoc JDistLib: http://jdistlib.sourceforge.net/javadoc/ .. _jdistlib: http://jdistlib.sourceforge.net/

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r287 - trunk/src/site/resources/js
by echatellier＠users.forge.codelutin.com Feb. 12, 2016

Feb. 12, 2016

Author: echatellier Date: 2016-02-12 10:04:56 +0100 (Fri, 12 Feb 2016) New Revision: 287 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/287 Log: Fix url Modified: trunk/src/site/resources/js/maven-isisfish.js Modified: trunk/src/site/resources/js/maven-isisfish.js =================================================================== --- trunk/src/site/resources/js/maven-isisfish.js 2016-02-12 09:01:41 UTC (rev 286) +++ trunk/src/site/resources/js/maven-isisfish.js 2016-02-12 09:04:56 UTC (rev 287) @@ -77,7 +77,7 @@ // current page var url = scmurl + "?address=" + scm + "/src/site/" + siteSourcesType + "/" + path; - scmurl += "&scmType=SVN"; + url += "&scmType=SVN"; console.log("Add scmwebeditor with url = " + url); var html = "| <a class='externalLink' href='" + url + "'>Éditer la page</a>";

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r286 - in trunk: . src/site src/site/resources/images src/site/resources/js
by echatellier＠users.forge.codelutin.com Feb. 12, 2016

Feb. 12, 2016

Author: echatellier Date: 2016-02-12 10:01:41 +0100 (Fri, 12 Feb 2016) New Revision: 286 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/286 Log: Use scmwebeditor 0.7 Modified: trunk/pom.xml trunk/src/site/resources/images/IsisFishModel.png trunk/src/site/resources/js/maven-isisfish.js trunk/src/site/site_en.xml trunk/src/site/site_fr.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2016-02-12 08:55:51 UTC (rev 285) +++ trunk/pom.xml 2016-02-12 09:01:41 UTC (rev 286) @@ -140,6 +140,7 @@ <license.organizationName>Ifremer, Codelutin</license.organizationName> <jrstPluginVersion>2.2-SNAPSHOT</jrstPluginVersion> <siteDeployClassifier/> + <scmwebeditorUrl>https://scmwebeditor2.nuiton.org/scmwebeditor2/edit.action</scmwebeditorUrl> </properties> <distributionManagement> Modified: trunk/src/site/resources/images/IsisFishModel.png =================================================================== (Binary files differ) Modified: trunk/src/site/resources/js/maven-isisfish.js =================================================================== --- trunk/src/site/resources/js/maven-isisfish.js 2016-02-12 08:55:51 UTC (rev 285) +++ trunk/src/site/resources/js/maven-isisfish.js 2016-02-12 09:01:41 UTC (rev 286) @@ -5,7 +5,7 @@ * $Id:$ * $HeadURL:$ * %% - * Copyright (C) 2011 - 2015 Ifremer, Codelutin, Eric Chatellier + * Copyright (C) 2011 - 2016 Ifremer, Codelutin, Eric Chatellier * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -77,6 +77,7 @@ // current page var url = scmurl + "?address=" + scm + "/src/site/" + siteSourcesType + "/" + path; + scmurl += "&scmType=SVN"; console.log("Add scmwebeditor with url = " + url); var html = "| <a class='externalLink' href='" + url + "'>Éditer la page</a>"; Modified: trunk/src/site/site_en.xml =================================================================== --- trunk/src/site/site_en.xml 2016-02-12 08:55:51 UTC (rev 285) +++ trunk/src/site/site_en.xml 2016-02-12 09:01:41 UTC (rev 286) @@ -6,7 +6,7 @@ $Id: site_fr.xml 3124 2010-11-29 18:14:09Z chatellier $ $HeadURL$ %% - Copyright (C) 1999 - 2015 Ifremer, Code Lutin, Chatellier Eric + Copyright (C) 1999 - 2016 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 Modified: trunk/src/site/site_fr.xml =================================================================== --- trunk/src/site/site_fr.xml 2016-02-12 08:55:51 UTC (rev 285) +++ trunk/src/site/site_fr.xml 2016-02-12 09:01:41 UTC (rev 286) @@ -6,7 +6,7 @@ $Id: site_fr.xml 3124 2010-11-29 18:14:09Z chatellier $ $HeadURL$ %% - Copyright (C) 1999 - 2015 Ifremer, Code Lutin, Chatellier Eric + Copyright (C) 1999 - 2016 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

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r285 - trunk/src/site/rst/v4/user/changes
by echatellier＠users.forge.codelutin.com Feb. 12, 2016

Feb. 12, 2016

Author: echatellier Date: 2016-02-12 09:55:51 +0100 (Fri, 12 Feb 2016) New Revision: 285 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/285 Log: >From scmwebeditor -- Fix Modified: trunk/src/site/rst/v4/user/changes/changements44.rst Modified: trunk/src/site/rst/v4/user/changes/changements44.rst =================================================================== --- trunk/src/site/rst/v4/user/changes/changements44.rst 2016-02-12 08:44:35 UTC (rev 284) +++ trunk/src/site/rst/v4/user/changes/changements44.rst 2016-02-12 08:55:51 UTC (rev 285) @@ -43,7 +43,7 @@ - l'équation de reproduction sert à décrire la ponte. Le résultat est une matrice 1D (result [ZoneRepro]) contenant le nombre d'oeufs pondus dans chaque zone de reproduction à chaque mois de repro. -Si aucune equation de recrutement n'est implémentée (défaut:"return 0;"), le processus de recrutement par défaut suppose : +Si aucune équation de recrutement n'est implémentée (défaut:"return 0;"), le processus de recrutement par défaut suppose : * l'application à ces oeufs de la mortalité du group "null" durant toute la période précédant le recrutement, * le recrutement se fait dans les zones de recrutement telles que définies par la matrice de correspondance des zones de repro-recrutement (onglet zones)

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r284 - trunk/src/site/en/rst
by echatellier＠users.forge.codelutin.com Feb. 12, 2016

Feb. 12, 2016

Author: echatellier Date: 2016-02-12 09:44:35 +0100 (Fri, 12 Feb 2016) New Revision: 284 Url: http://forge.codelutin.com/projects/isis-fish-docs/repository/revisions/284 Log: Update publication Modified: trunk/src/site/en/rst/publications.rst Modified: trunk/src/site/en/rst/publications.rst =================================================================== --- trunk/src/site/en/rst/publications.rst 2016-01-20 15:56:47 UTC (rev 283) +++ trunk/src/site/en/rst/publications.rst 2016-02-12 08:44:35 UTC (rev 284) @@ -5,7 +5,7 @@ .. * $Id$ .. * $HeadURL$ .. * %% -.. * Copyright (C) 1999 - 2012 Ifremer, Code Lutin, Chatellier +.. * Copyright (C) 1999 - 2016 Ifremer, Code Lutin, Chatellier .. * %% .. * This program is free software: you can redistribute it and/or modify .. * it under the terms of the GNU General Public License as @@ -32,6 +32,18 @@ ===== ======================================================================================================================================================================================================================================================================================================================================================================================================================================================== ============================================================================================== =========================================================== Year Publication Download Original publication ===== ======================================================================================================================================================================================================================================================================================================================================================================================================================================================== ============================================================================================== =========================================================== +2015 **Lehuta, S.**, Vermard, Y., Marchal, P. 2015. A spatial model of the mixed demersal fisheries in the Eastern Channel. In Marine Productivity: Perturbations and Resilience of Socio-ecosystems. Ceccaldi, H.J. et al. (Eds.). p.187-195. +2015 **Reecht, Y.**, Gasche L., Lehuta S., Vaz S., Smith R.J., Mahévas S., Marchal P. 2015. Toward a Dynamical Approach for Systematic Conservation Planning of Eastern English Channel Fisheries. In Marine Productivity: Perturbations and Resilience of Socio-ecosystems. Ceccaldi, H.J. et al. (Eds.). pp.175-185. http://archimer.ifremer.fr/doc/00293/40421/ +2013 **Gasche, L.**, Mahévas, S., et Marchal, P. 2013. Supporting fisheries management by means of complex models: can we point out isles of robustness in a sea of uncertainty ? Plos One, 8(10). http://archimer.ifremer.fr/doc/00166/27746/ +2013 **Lehuta, S.**, Mahévas, S., Le Floc’h, P. 2013. Simulation-based bio-economic indicators of management impact: assessing relevance and robustness for the pelagic fishery of the Bay of Biscay. Canadian Journal of Fisheries and Aquatic Sciences, 70: 1741–1756. `Canadian Journal of Fisheries and Aquation Science <http://www.nrcresearchpress.com/journal/cjfas/>`_ +2013 **Lehuta, S.**, Petitgas, P., Mahévas, S., Vermard, Y., Huret, M, Uriarte, A and Record, N.R. 2013. Selection and validation of a complex fishery model using an uncertainty hierarchy. Fisheries Research, 143, 57-66. `Here <http://archimer.ifremer.fr/doc/00148/25965/24150.pdf>`__ `Fisheries research <http://www.journals.elsevier.com/fisheries-research/>`_ +2013 **Thébaud,O.**, Doyen,L., Innes, J. , Macher, C., Planque, B., Lample, M., Mahévas, S., Quaas, M., Mullon, C. , Smith, T., et Vermard, Y.. (2013). Building ecological-economic models and scenarios of marine resource systems: workshop report. Marine Policy +2013 **Mahévas, S.**, Lehuta, S. Illustration d’une analyse de sensibilité pour l’utilisation d’un modèle complexe en gestion des pêches ». In Analyse de sensibilité et exploration de modèles - Applications aux modèles environnementaux. Quae. Ed.Robert Faivre, Bertrand Iooss,David Makowski, Stéphanie Mahévas, Hervé Monod. +2013 **Mahévas, S.**, Iooss, B. 2013. Grilles de sélection d’une méthode d’analyse de sensibilité globale ». In Analyse de sensibilité et exploration de modèles - Applications aux modèles environnementaux. Quae. Ed. Robert Faivre, Bertrand Iooss,David Makowski, Stéphanie Mahévas, Hervé Monod. +2013 **Iooss, B.**, Mahévas, S. 2013. Revue et objectifs des méthodes d’analyse de sensibilité globale. Dans Analyse de sensibilité et exploration de modèles - Applications aux modèles environnementaux. Quae. Ed. Robert Faivre, Bertrand Iooss, David Makowski, Stéphanie Mahévas, Hervé Monod. +2013 **R. Faivre, B. Iooss, S. Mahévas, D. Makowski, H. Monod,** editors. Analyse de sensibilité et exploration de modèles. Applications aux modèles environnementaux. Editions Quae, 2013.(http://www.quae.com/fr/r2142-analyse-de-sensibilite-et-exploration-de… +2012 **Deporte N.**, C.Ulrich, S. Mahévas, S.Demanèche, F. Bastardie. 2012. Regional me´tier definition: a comparative investigation of statistical methods using a workflow applied to internationalotter trawl fisheries in the North Sea.ICES Journal of Marine Science 69(2): 331-342 +2011 **Mahévas, S** et al., (2011) « An investigation of human vs. technology-induced variation in catchability for a selection of European fishing fleets », Ices Journal Of Marine Science 68, no. 10 : 2252-2263. 2011 **Hussein, C.**, M.Verdoit-Jarraya, J.Pastor, A.Ibrahim, G.Saragoni, D.Pelletier, S. Mahévas, P.Lenfant, 2011. 'Assessing the impact of artisanal and recreational fishing and protection on a white seabream (Diplodus sargussargus) population in the north-western Mediterranean Sea using a simulation model. Part2: Sensitivity analysis and management measures.' **Fisheries Research** 108, Issue 1, Pages 174-183 `Here <https://w3.ifremer.fr/archimer/doc/00030/14115/11337.pdf>`__ `Fisheries research <http://www.journals.elsevier.com/fisheries-research/>`_ 2011 **Hussein, C.**, M.Verdoit-Jarraya, J.Pastor, A.Ibrahim, G.Saragoni, D.Pelletier, S. Mahévas, P.Lenfant (2011) 'Assessing the impact of artisanal and recreational fishing and protection on a white seabream (Diplodus sargussargus) population in the north-western Mediterranean Sea using a simulation model. Part1: Parameterization and simulations.' **Fisheries Research** 108, Issue 1, Pages 163-173 `Here <https://w3.ifremer.fr/archimer/doc/00030/14114/11351.pdf>`__ `Fisheries research <http://www.journals.elsevier.com/fisheries-research/>`_ 2011 **Marchal, P.**, Little, L.R., and Thébaud, O., 2011. 'Quota allocation in mixed-fisheries: a bioeconomic modelling approach applied to the Channel flatfish fisheries.' **ICES Journal of Marine Science**, 68, 1580–1591. `Here <https://w3.ifremer.fr/archimer/doc/00044/15492/12971.pdf>`__ `sciencedirect <http://www.sciencedirect.com/>`_

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