repair density-dependent parameter functionality - #780
Conversation
iantaylor-NOAA
left a comment
iantaylor-NOAA
left a comment
There was a problem hiding this comment.
Looks good for getting things working again.
I haven't used the density dependence much, so set up the attached model simple_small_DD.zip to include both a density dependent L_at_Amin and an environmental variable link to L_at_Amax which ended up with parameter labels and L_at_Amin_Fem_GP_1_ENV_add_DD and L_at_Amax_Fem_GP_1_ENV_addX.
This made me wonder about a few more trivial changes:
- Change from "X" to an empty string "" for the standard environmental link parameter.
- It looks like the ENVIRONMENTAL_DATA output is not included in Report.sso unless there is environmental data in the data file. However, perhaps that table should be reported in cases where a DD link is used but no environmental data is provided in order for users to have access to the columns of processed time series data.
- It looks like this text in the user manual (here: https://github.com/nmfs-ost/ss3-doc/blob/main/13output.tex#L129) needs to be revised to note that there is both summary numbers and summary biomass:
Density-dependence can be used by linking to population quantities that have already been calculated at the start of the year. These include summary biomass, spawning biomass, and recruitment deviations. These three quantities are mapped into the -1, -2, and -3 columns of the environmental data matrix where they can be used as if there were environmental data input.
|
good suggestions. The "X" was just leftover from debugging and will get removed. |
- SS3 change is in nmfs-ost/ss3-source-code#780
* Update environmental data description in 13output.tex Include summary numbers as noted in ss3-source-code PR [#780](nmfs-ost/ss3-source-code#780 (review)) * Reorder environmental data description and columns
2 participants
Concisely describe what has been changed/addressed in the pull request.
What tests have been done?
Where are the relevant files?
What tests/review still need to be done?
Is there an input change for users to Stock Synthesis?
Additional information (optional).