function calc_stage2length

[ghost]

calc_stage2length is currently written, but needs to be edited to:

• [x] needs to read the load_biol_prm file and not call the biol.prm directly, same with load_groups_csv function needs to be called instead of directly reading in the csv file
• [x] document
• [x] test that it plays nice with the other functions

[gavinfay]

I have revised calc_age2length to play better with others. I do not believe this needs to be specialized to deal with stage data as that is being done by another function and should happen before the call to calc_age2length.

Function outputs numbers at length by age, box, time, etc. Figured this was easier and that aggregation can be done by functions later in the process. The data frame containing the numbers at length (lenout$natlength) has two additional columns to our 'normal' data frames to capture the length bin structure. This is needed I think. Function is still assuming one CV for length at age among species, which is an argument to the function. Function works with test SETAS data. Loop to calculate mean length at age is slow and should be improved on (current code is only doing a few lines of the data frames) - the issue is that nums only contains elements where numbers are >0 whereas structn and reserven contain all combinations of box, age, etc.

[gavinfay]

Above loop now vectorized.

[kellijohnson-NOAA]

excellent work, i am closing this issue