function calc_pred_diet

[ghost]

This function needs to be created (edited?)

• [ ] take in outputs from load_diet_comp and also biomass to spit out stomach content of predator per box in biomass rather than proportions
• [x] upload to Github
• [ ] document
• [ ] test that it plays nice with the other functions

[kellijohnson-NOAA]

@gavinfay and @hodgsone any idea why the values taken from the .nc file using load_nc for a given predator are multiplied by the volume information for a polygon? The function takes the atoutput column from a predator of a given age class, timestep, and polygon and multiplies it by the volume, the percentage of the diet that is made up of the given prey, where all percentages sum to one for a predator, age class, timestep, and polygon. Again why are we multiplying by volume? I guess I am confused on what the atoutput column is? @alketh had noted that the output returned from calc_pred_diet returned unrealistic values.

[alketh]

Hey guys,

the function used to load in all the values for the "eat" and "grazing" variables from the productivity netcdf file (output[...]PROD.nc). Based on the netcdf documentation the units are given in nitrogen per volume (per individual ?). Therefore we need to multiply by the volume of the box to get eaten biomass for the whole area.

However, up to this point I am not sure if the diet proportions extracted from "DietCheck.txt" actually make sens from a biological point of view. Unfortunately, there is no documentation about the units used in "DietCheck.txt". In addition the units used in the productivity netcdf file might simply be wrong. I tried to get an idea of the units looking at the ATLANTIS sourcecode but couldn't make any sense of it (even after days of searching..). Last but not least, the units might differ between age-based and invertebrate groups due to the fact that invertebrates are modeled as biomass pools and not as individuals. It might be a good idea to add Beth and Bec to the discussion!

Cheers, Alex

Am 23/06/2016 um 01:19 schrieb Kelli Johnson:

@gavinfay https://github.com/gavinfay and @hodgsone https://github.com/hodgsone any idea why the values taken from the .nc file using |load_nc| for a given predator are multiplied by the volume information for a polygon? The function takes the atoutput column from a predator of a given age class, timestep, and polygon and multiplies it by the volume, the percentage of the diet that is made up of the given prey, where all percentages sum to one for a predator, age class, timestep, and polygon. Again why are we multiplying by volume? I guess I am confused on what the atoutput column is? @alketh https://github.com/alketh had noted that the output returned from |calc_pred_diet| returned unrealistic values.

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Alexander Keth Institute for Hydrobiology and Fisheries Science University of Hamburg Olbersweg 24 22767 Hamburg Germany Tel.: +49 (0)40 428 38 6708 Fax: +49 (0)40 428 38 6618

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[kellijohnson-NOAA]

@alketh thanks for the reminder about units. I backed up a step and used calc_biomass_age to see if the output of catches in tons matched the output in the "catch.txt" file that reports catches for all fisheries in tons. It does not. So I think we have an issue somewhere. Why do we not multiply by the volume in the calc_biomass_age function. Also according to the wiki the dietcheck.txt file uses the following units: If the prey is an inverebrate value units are mgN/m^3 per second If the prey is a vertebrate value units are nums per second

[alketh]

@kellijohnson personally, I wouldn't put to much confidence into the wiki regarding statements about units. To my knowledge the numbers ("Nums" variable) is reported in absolute numbers per timestep, ageclass, group, box, and layer (NOT as density). Therefore, there is no need to multiply the numbers by volume to calculate biomass of the age-structured groups.

Am 24/06/2016 um 01:37 schrieb Kelli Johnson:

@alketh https://github.com/alketh thanks for the reminder about units. I backed up a step and used |calc_biomass_age| to see if the output of catches in tons matched the output in the "catch.txt" file that reports catches for all fisheries in tons. It does not. So I think we have an issue somewhere. Why do we not multiply by the volume in the |calc_biomass_age| function. Also according to the wiki the dietcheck.txt file uses the following units: If the prey is an inverebrate value units are mgN/m^3 per second If the prey is a vertebrate value units are nums per second

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Alexander Keth Institute for Hydrobiology and Fisheries Science University of Hamburg Olbersweg 24 22767 Hamburg Germany Tel.: +49 (0)40 428 38 6708 Fax: +49 (0)40 428 38 6618

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[alketh]

Hey,

my email account at the University of Hamburg is going to expire soon. Please use my following new email address In case you want to stay in touch with me:

alexander.keth@posteo.net

Best regards Alexander Keth