-
Notifications
You must be signed in to change notification settings - Fork 2
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
expand on and clean up predator fleet text #109
Comments
where is that examples? Related to predator fleets I mean. |
@MauroMardones The manual does not currently have example input for a predator fleet but does try clearly describe how it can be incorporated (fleet type = 4) in the data file and then the needed parameter line in the control file. Can you provide more information on what exactly you are looking for? |
I am trying to generate a time series vector of an index of predation on the fishery, perhaps even with sd. But when I want add it, it's not clear to me if I should assign it as an index (which is what I think) or define it as discard fleet anyway. As I told you, I'm thinking of an index more than anything else. According to the manual it is possible but I am not clear where to assign it and if I add lines to the If you can help me with that. ill appreciate @chantelwetzel-noaa |
Hi @MauroMardones, I just tried adding a predator fleet for the first time in the attached files (based on the "simple_small" model used for testing r4ss https://github.com/r4ss/r4ss/tree/main/inst/extdata/simple_small). The changes I made were as follows: Data file:
Control file:
The input files after these changes are in the this zip file: simple_small_predator.zip. It runs in SS3 version 3.30.21 and estimates the M2_pred1 parameter at 0.044, resulting in a total natural mortality M1 + M2 = 0.05 + 0.044 = 0.094, which is close to the 0.1 value used in generating the data for this model. What I didn't do was add catch data or discard data for the predator fleet and I note that the fit to the predator effort index is poor (my made-up index slowly declines whereas the expected values are constant). @Rick-Methot-NOAA, what additional steps would a user need to take to fit a predator effort index? I presume that if I had made the index very precise, the model could have used recdevs to better fit it, but in general I assume folks are trying to represent changes in predator abundance via an index, not changes in the prey. |
Thank you very much for these ideas and examples. I'm going to configure the model with my data this week and I'll see how it goes. I didn't quite understand that about the I will see my results and tell you. Thank you so much |
@MauroMardones, as you say we have a plan to discuss further by email with others and then circle back to improve the SS3 documentation. Just to clarify the point about mortality:, the |
Hi @iantaylor-NOAA . Im adding krill data this week. Please just check it this. In #_Q_setup for fleets with cpue or survey data SURVEY 2 its predator fleet right? ('cause its mentioned as fleet 4) Takk firir in advance! |
Predator vignette on ss3-website now exists and expands on predator fleets. Closing this issue but feel free to reopen if further expansion or clean up of predator info needs to be done. |
Thanks Ely. I see new features (1+) about Predator fleets. I will check this. Thanks for to inform this. |
https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#predator-fleet-mortality
https://nmfs-stock-synthesis.github.io/doc/SS330_User_Manual.html#predator-fleets
Text on predator fleets can use editing for clarity. Also, including example inputs would be helpful. This text will also need expanding based on recent developments (e.g., by area) once these are merged into main.
The text was updated successfully, but these errors were encountered: