function calc_stage2age

[ghost]

This function is meant to turn the Atlantis 'age classes' which are essentially stage classes for some species and turn them into true age classes.

New models will have the output 'ANNAGEBIO.nc' or some netcdf file similarly named which gives the age-specific information, but old models do not have this output. We have currently hit a roadblock for how to determine age specific biomass and from that numbers at age. Previously we were planning on creating the function calc_Z to determine mortality, but now realize that may not be possible, and a new approach is needed.

• determine conceptual approach to changing stage biomass into age biomass
• write the code which turns the conceptual model into a function calc_stage2age
• upload to Github
• document
• test that it plays nice with the other functions

[ghost]

Hi folks,

I am working on this function calc_stage2age still -- the basic outline of the code has been uploaded. But one thing I am struggling with is: I think we want models to give quarterly outputs so that we can use those outputs for surveys. However, when I talked to Beth about estimating Z, she said that if we use numbers at stage outputs from the same time every year (365 day output I assume) then the species should be in the same stage of their recruitment and it should work. (For a very rough approximation)

But if we have quarterly outputs then we have a 91 day output giving 364 days... not a full year. So I am struggling with how to write the code -- do we try to estimate annual mortality using the outputs from every 364 days? I want it to be flexible so that it reads in the toutinc to determine output increments, and then only takes out the time steps that are approximately the same time every year, and not quarterly changes in numbers... does that make sense?

I can explain more if that is confusing.

[kellijohnson-NOAA]

[x] - fix load_yoy, which is called by calc_state2age
[ ] - calc_Z needs to take a dataset and not just the name of the text file
[ ] - in calc_state2age check which ones are on, and all groups will not be in the young of the year file

[ghost]

• - also for the calc_Z function: need to add to the output, a column that just says what name of species it is --- which is the second element of the species_info input