July 2017 - Isis-fish-users - mailman.cloud.codelutin.com

Equation de recrutement ISIS 4.4.1.0-rc-1
by Audric Vigier 14 Dec '17

14 Dec '17

Bonjour, Je souhaite utiliser une équation de recrutement seule pour décrire la distribution spatio-temporelle du recrutement pour plusieurs années. Le problème est multiple : -bien que l'équation de recrutement compile, ISIS-Fish ne l'utilise pas. Dans le debug, je retrouve une erreur fatale : 2017-05-26 16:22:05,124 INFO [Thread-12] (SubProcessSimulationLauncher.java:302) run - dans un sous processus>2017-05-26 16:22:05,121 FATAL [SimThread sim_simuGdGCalib2010NoAlgo_2017-05-26-16-19] (PopulationImpl.java:863) getRecruitmentMatrix - Error in matrix recruitment creation 2017-05-26 16:22:05,124 INFO [Thread-12] (SubProcessSimulationLauncher.java:302) run - dans un sous processus>fr.ifremer.isisfish.IsisFishRuntimeException: Impossible d'évaluer l'équation: [recopie toute l'équation] -Malgré l'erreur fatale, ma simu ISIS tourne jusqu'à la fin. Le recrutement a donc dû être modélisé d'une certaine manière (très différente du contenu de l'équation), mais je ne vois pas comment. J'aurais préféré que la simu s'arrête dès que l'erreur est renvoyée. La région, la simu, le debug et l'équation de recrutement sont disponibles à ce lien pendant 3 semaines : https://filesender.renater.fr/?s=download&token=e3846c36-45ae-898f-2045-684… . Pour ce debuggage, pas besoin des règles de gestion auxquelles je ferai appel plus tard. Bon week-end, Audric -- Audric Vigier Doctorant à Ifremer, unités EMH (Nantes) et STH/LBH (Brest) E-mail : audric.vigier(a)ifremer.fr Tel : +33 (0)2 40 37 41 64 (8164)

4 7

Fwd: debug.text
by smahevas 28 Jul '17

28 Jul '17

et un deuxieme merci de ton aide stephanie -------- Courriel original -------- OBJET: debug.text DATE: 2017-07-20 16:29 DE: serghini mansour <serghini2002(a)yahoo.com> À: "smahevas(a)ifremer.fr" <smahevas(a)ifremer.fr> Bonne reception

2 3

Library to do radar plots
by Sigrid Lehuta 27 Jul '17

27 Jul '17

I used the R library ggradar library(ggplot2) devtools::install_github("ricardo-bion/ggradar", dependencies=TRUE) library(ggradar) Example of use : ### Radar : catch@year /species, arrows are species, lines are years meanErrYear <- aggregate(percErr~year+sp, data=caaY, FUN=mean) MEY <- reshape(meanErrYear,direction = "wide",idvar="year",timevar="sp") MEY <- rbind(MEY, c(99,colMeans(MEY[,-1]))) MEY <- replace(MEY,MEY>100,100) # avoid to big values ggradar(MEY,grid.min = 0,grid.mid = 50, grid.max = 100,legend.title = "Year")

1 0

Fwd: *******SPAM*******
by smahevas 20 Jul '17

20 Jul '17

Eric, un premier bug de lancement de simulation avec la base atelier golfe de gascogne sans regle par un utilisateur du groupe marocain une idee? merci Stephanie -------- Courriel original -------- OBJET: *******SPAM******* DATE: 2017-07-20 16:35 DE: Jilali Bensbai <j.bensbai(a)gmail.com> À: smahevas(a)ifremer.fr merci -- BENSBAI Jilali Chef URD Exploitation et Gestion Des Pêches INRH-Casa Tel : +212661598386 Other émail : bensbai(a)inrh.ma j_bensbai(a)yahoo.fr

1 0

Re: [Isis-fish-users] ISIS-Fish info
by Stephanie MAHEVAS 20 Jul '17

20 Jul '17

Dear all first, I recommend you to install the version 4.4.0.2 of ISIS-fish and not the last one, which is still under testing. Second, do you understand French because the manual is still in French .... :-\ ? Le 14/07/2017 10:13, Silvia Angelini a écrit : > Dear Dr. Mahévas, > > here we are Silvia Angelini and Lorenzo D'Andrea, we are two researchers > working with Dr. Tommaso Russo of the University of Tor Vergata in Rome. > Tommaso probably contacted you before to inform that we are using > ISIS-Fish in the framework of the MANTIS project. MANTIS aims at > investigating how a network of marine managed areas (MMAs) can contribute > to improve sustainable fisheries in the Mediterranean. In particular, we > would like to explore the effect of spatial closures and other management > measures for the most important species of the trawl fishery in the our > two case studies, that are one in the Adriatic Sea and the other one in > the Strait of Sicily (SoS). > > We start setting the ISIS-Fish model for the stock of Mullus barbatus > living in the SoS, but to proceed with the work we need to ask some > clarifications, summarised in the list that you can find hereunder. Can we > gently ask some help for clarifing our doubts? I try to answer your questions but I recommend you to read carefully the two papers of reference of the model (attached to this email). It should help you to understand the processes described and the way they can be set in the interfaces. More information are available and updated on the website of ISIS-Fish but unfortunately most tutorials are in French... You can also explore (as a source of ideas) some databases of fisheries modeled with ISIS-fish and available on the website http://www.isis-fish.org/download.html (Base de donnees Golfe de Gascogne Prospective ou Base Channel Faltfish Fishery). > > 1) About the population structure, we tried to include the growth both > manually or using the growth equation but in both cases the resulting ages > and lengths do not match our expectations; Is it age or length structured? I recommend to start with an age-structured model. if you specify a length-structured model and you want the age of the length group, you need to specify the inverse growth curve. Can you send us your database (exported from the interface Region, http://www.isis-fish.org/v4/user/usermanual/inputs.html#menu-region) and a table with what you expect ? > 2) In the Species-Zones section, why all the areas are present in both > boxes, spawning and recruitment areas? You first define the population zones (the definition of zones is given in Mahevas et al 2004). Then you precise the recruitment zone (where recruitment takes place) and the spawning zone (where reproduction (concentration of spawners) takes place). And finaly the matrix below allows you to specify the connectivity between spawning zones and recruitment zones. > 3) About the life history traits, can you explain how to include the > maturity ogive and the reproduction rate? you need to set an equation in the user-interface example of maturity ogive : double lg=group.getLength(); double Maturite=(1/(1+Math.exp(-0.2*(lg-42.85)))); return Maturite; example of reproduction rate if (group == null) return 0.0; else return 0.4; more examples in http://www.isis-fish.org/v4/user/usermanual/inputs.html#onglet-saisie-des-e… > 4) About the recruitment section: Do we have to include the reproduction > equation? no a stock-recruitment equation is enough Fisrt define the spawning season and the number of months between spawning and recruitement. If recruitment spreads over several month you can also define the distribution of recruitment Then, Reproduction equation should be : return 0; Recruitment equation should be implemented in the interface below the reproduction equation, box - "recruitment equation". Two examples are available here : http://www.isis-fish.org/v4/user/scripts.html > 5) About the accessibility: How can we get these values? What do they > represent? The accessibility of each age group in each area? this parameter is defined in Mahevas et al 2014. It is more availability than accessibility. It represent the proportion of abundance available to fishing (whatever the metier). It is used to compute fishing mortality, multiplying catchability and the standardized fishing effort. You can set it to 1 if you do not have any knowledge about it. Otherwhise it can be estimated during the calibration step of the model. > > 6) About the price, is this one interpreted as €/kg? It depends on the unity of your weight/age or weight/length relationship. If this one is in kg then price should be in kg. If it is in g than it should be in g. > 7) About the stocks section: do we have to fill the Fbar min and max group > as in the stock assessment? What is the 'abundance reference month'? And > which is the difference of selecting or not selecting 'F computed on > landings'? yes abundance reference month is the month at which the assessment working group is supposed to estimate the annual abundance and the annual fishing mortality (generally january) > > 8) Gears section: what is the standardisation effort? in Mahevas et al 2004 and Pelletier et al 2009 > > 9) About the 'Set of vessels' section: what does 'Fixed costs' mean? There > is a list of costs in the 'metier parameters’ section again in Pelletier et al 2009 > We are sorry for the long list of questions, but there are different > points in which we are stuck. Thank you so much for your help. > > Best regards > > Silvia and Lorenzo > > I hope these few elements will help you.... The "good" way of doing when you have some troubles with ISIS-Fish is to ask your question on the ISIS-Fish mailing list. To subscribe the users mailing list, you should fill a template (http://list.isis-fish.org/cgi-bin/mailman/listinfo/isis-fish-users) Finaly, if you have some funds for traveling, you can also plan a stay in Nantes to interact face-to-face with Isis-fish users and developpers.... Best Stephanie -- ...................................................................... Stephanie MAHEVAS (Stephanie.Mahevas(a)ifremer.fr) IFREMER/EMH (Ecologie et Modèles pour l'Halieutique) Tel: (33) 2 40 37 41 81 Fax: (33) 2 40 37 40 75 o \ o / _ o __| \ / |__ o _ \ o / o /|\ | /\ ___\o \o | o/ o/__ /\ | /|\ / \ / \ | \ /) | ( \ /o\ / ) | (\ / | / \ / \ ......................................................................

2 1

Modele en longueur : Modif bornes des classes au cours d'une simu
by Sigrid Lehuta 19 Jul '17

19 Jul '17

Hello, On aurait besoin de modifier les bornes des classes de longueur (ou au moins la taille moyenne), dans un modèle structuré en longueur, au cours d'une simu. Est ce possible dans une règle de gestion ? Les classes sont initialement entrées via l'option : entrer toutes les valeurs. Est ce possible par exemple de recréer les classes ds une règle de gestion par cette même methode ? et dans ce cas est ce que c'est modifié pour toute la simu ou juste ce pas de temps ? Sinon je me demandais si on peut utiliser setMaxLength <http://www.isis-fish.org/apidocs/fr/ifremer/isisfish/entities/PopulationGro…>(double maxLength) (resp. min length) et idem est ce que c'est modifié pour toute la simu ou juste ce pas de temps ? Merci !

2 1

Configuration ISIS
by Sigrid Lehuta 18 Jul '17

18 Jul '17

Steph et moi sommes un peu perdues dans les config de nos ISIS respectifs (V4.4.0.2) Voir aussi les mails de Steph. nous ne comprenons pas les differences qui existent entre nos .bat et nos isis-config-4, en particulier en ce qui concerne la memoire, alors que nous ne pensions pas avoir modifiés les paramètres par défaut (du moins pas consciemment)... Voici les fichiers en pj (les bat sont transformés entxt sinon google ne veut pas les envoyer). Pouvez vous éclairer notre lanterne ? Merci

2 1