Catch - Whole Region Data

[RGamble1]

• Create global biomass removal catch time series file from Sean L’s data
  • Write R script to take Sean L's data file and convert to correct units for species and groups in atneus

[RGamble1]

• Create Catch data apportioned to Atlantis group codes from:
  https://github.com/NOAA-EDAB/Atlantis-Catch-Files/blob/master/Atlantis_1_5_groups_svspp_nespp3.csv

[sgaichas]

See if this is a start, this is by species rather than Atlantis group code but should be able to change that in the group_by statement (modified from DiagnosticsDoc.Rmd)

# NOTE: THIS FILE NOT TO BE POSTED ON GITHUB DUE TO POTENTIAL CONFIDENTIALITY CONCERNS
# ask Sean for it

load(here("diagnostics", "comland_meatwt_deflated_stat_areas.RData"))

# from https://github.com/NOAA-EDAB/Atlantis-Catch-Files/blob/master/Atlantis_1_5_groups_svspp_nespp3.csv

spcodes <- readr::read_csv("Atlantis_1_5_groups_svspp_nespp3.csv")

# time series in case we want to plot them

comlandts <- merge(comland, spcodes) %>%
  group_by(YEAR, Name) %>%
  summarise(SPPLIVMT, sum) 

[RGamble1]

Catch data has been created. Next step is to truncate it to the appropriate time period for hindcast and create the time series file to be used in Atlantis.

• Create time series file

(Removed truncation of time series checkbox per discussion below)

[sgaichas]

Clarification: My understanding of the 1981-2010 time period is that it was just for comparing Atlantis outputs to other sources. This doesn't necessarily mean Atlantis needs to hindcast only for these years. I don't recall what decision we made for input time series into Atlantis. Do we want to truncate the catch data that drives the Atlantis model as an input or do we want all catch prior to 1981 back to when we want the model to start? Similarly, do we want to force the model with catch past 2010, or stop there so we have a few years of data set aside to compare model forecasts with?

Catch data has been created. Next step is to truncate it to the appropriate time period for hindcast and create the time series file to be used in Atlantis.

* [x]  Truncate catch data to 1981 - 2010

* [ ]  Create time series file

[RGamble1]

TS file for entire region removal of each group using the comland file + R script put here:

TS file: https://github.com/NOAA-EDAB/Atlantis-Catch-Files/blob/master/catch_10_31_19_RG.ts
R script: https://github.com/NOAA-EDAB/Atlantis-Catch-Files/blob/master/catch_file_creator.R

• Test catch time series in master branch Atlantis

• Clean up the Atlantis-Catch-Files github and merge into main Atlantis github repository