Hi,
If I may, here are a few additional details to complete Stephanie's answer (see below).

Thanks for your feedback on the model and its documentation. We will do our best to improve it so the answers to your questions can be found more easily on the website and in the software. Feel free to use the mailing list for anything that can't be found in the website or the articles.

Regards,
Sigrid


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.

ISIS will automatically use all zones of presence of the population as potential spawning and recruitment zones. You then need to clic on the zones that are actually spawning zones and recruitment zones in each list (they are going to become highlighted in blue and added to the connectivity matrix below) to really select them as spawning 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


the values can then be used in the  recruitment equation using the call :
group.getMaturityOgive() and group.getReproductionRate() 
 
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)

Fbar min and max are used to compute fishing mortality values comparable to the ones used in assessments. The model will run even if you don't inform these parameters. Indeed there are actually 2 types of fishing mortality computed in ISIS and available as results :
- MatrixFishingMortality [strategy x metier x group x zone x month] which is not comparable to assessment F, because at a much more disaggregated scale and computed based on standardized effort and accessibility. This is the one used to compute the catches.

- MatrixFishingMortalityPerGroup [grp x year] which is comparable to assessment F per group because computed based on catches and abundances at a yearly scale. It is used to compute the global F MatrixTotalFishingMortality as the mean of MatrixFishingMortalityPerGroup for the groups between group min et group max defined in the interface.



--
......................................................................
Stephanie MAHEVAS (Stephanie.Mahevas@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\  / )    |  (\  / |   / \   / \
......................................................................


_______________________________________________
Isis-fish-users mailing list
Isis-fish-users@list.isis-fish.org
http://list.isis-fish.org/cgi-bin/mailman/listinfo/isis-fish-users