NEUS 2.2.1

Summary

Consists of pull request #249 to #264

• General calibration of several species biomass
• Added spatial comparisons functionality for biomass and catch
• Updated reference data from survdat and commercial landings
• Added environmental thresholds functionality
• Updated initial and forced spatial distributions
• New calibration tools for effort-based fleets and density dependent movement

Important model changes

• at_biology.prm -
• at_run.prm - initial scalars
• neus_init.nc - spatial distribution updates based on bottom trawl survey data for Groundfish species

NEUS 2.2.0

Uses Atlantis codebase v6681

Summary

• Contains all pull requests from #228 to #243
• Updated age structure of functional groups with associated age-based parameter changes in neus_groups.csv, at_biology.prm, at_harvest.prm, and neus_init.nc
• Updated code-base to v6681, with additional new parameters and a new neus_migrations.csv
• General calibration of v6681 biology.prm to match previous release calibration criteria
• Bug fixes and development of cloud calibration workflow

NEUS 2.1.0

Uses Atlantis codebase v6536

Summary

Contains baseline calibration of NEUSv2 such that it meets persistence and reasonability criteria as well as adequate sensitivity to fishing pressure. Include pull requests #115 to #223

Specific changes include:

• New initial size-at-age & numbers & numbers-at-age
• flagtempsensitive turned on with q10=2
• full review of diet parameters and comparisons to stomach contents database
• Fixed incorrect catch forcing by incorporating NAFO data and new comlandr updates
• Updated physics to 2021 with GLORYS12V1 updates
• All species either use Beverton-Holt or pupping recruitment (no constant catch)
• General calibration of species mum, C, mL, mQ, BHalpha, BHbeta, and/or pPREY

Code changes

• Improved the organization of R, data, and data-raw directories
• Improved the performance of post-processing routines
• Creation of batch processing routines
• Scripts for creating and analyzing fishing sensitivity scenarios

NEUS 2.0.1

Uses Atlantis codebase v6536

Summary

• Change spawn=recruits parameterization to beverton-holt and fixed-per-individual
• Changed growth-at-age curve to peak at intermediate age class
• Changed catch spin-up to be fixed level for first 15 years
• Changed catch-at-age proportions
• Various R scripts and data file changes

Parameter Files

• currentVersion/at_biology.prm
  -- Changed to Beverton-Holt recruitment: MAK, HER, WHK, BLF, SUF, WIF, MPF, BUT, GOO, COD, SHK, POL, RHK, BSB, SCU, RED, DRM, STB, HAD, YTF
  -- Changed to fixed recruits per individual: WSK, LSK, SK, PIN, DOG
  -- Diet changes: FDF, DOG
  -- Biomass tuning: SCA, BMS, ZG, WIF, TYL, TAU, SDF, FDF, SMO, SK, INV
  -- Reshape growth-at-age: MAK, HER, WHK, BLF, SUF, MPF, BUT, GOO, COD, SHK, POL, RHK, BSB, SCU, RED, DRM, STB, HAD, YTF, DOG, WSK, LSK, PIN
  -- Various recruitment change
  -- Various mortality changes
• currentVersion/at_harvest.prm - Changed default catch-at-age proportions for fished species only: 0.005 0.005 0.01 0.01 0.08 0.11 0.16 0.18 0.2 0.25
• currentversion/neus_init.nc - Decreased sinking rate for PL and DF, set PS sinking to 0

Forcing Files

• currentversion/CatchFiles/total_catch.ts - Added spinup period for all fished groups

Data Files

• Geometry/NEUSlookup.csv : Added Column headers
• data-raw/Emax_Catchability.RData - Updated
• data-raw/Emax_Catchability.rds - Updated
• data/MEN_biomass_2017_assessment.txt - Assessment data for Menhaden

New R Scripts

• R/GLORYS/make_GLORYS_files_extract.R - Extracts cell-level data on fluxes and state variables without aggregating them to boxes/faces
• R/GLORYS/call_make_GLORYS_files_extraction.R - Wrapper script for make_GLORYS_files_extract.R
• R/GLORYS/make_GLORYS_NEUS_statevar_summary.R - Combines Atlantis-formatted GLORYS data inot a single data file "GLORYS_Atlantis_Level_Statevars_all.csv"
• R/Testing_mumC_shape.R - Function to change the mum-age or C-age relationship for functional groups
• R/call_edit_diet.R - Wrapper script to run edit_param_pprey() for ease of use
• R/edit_param_BH.R - Functions to retreive (get_param_BH) and change (edit_param_BH) the beverton-holt alpha/beta recruitment parameters
• R/edit_param_KDENR.R - Functions to retreive (get_param_KDENR) and change (edit_param_KDENR) the fixed-recruitment parameters
• R/get_recruit_params.R - Extracts recruitment-related parameters for all groups (KSPA, FSP, FSPB, KWSR, KWRR)
• R/get_recruit_type.R - Extracts recruitment type for all groups
• R/make_biomass_functional_group.R - Produces table with biomass aggregated functional group, by EPU, with the option to standardize biomass by box area/volume
• R/make_catch_file_spinup.R - Adds a constant catch spinup period for all groups with significant fisheries
• R/make_recruit_diagnostics.R - Creates diagnostic table for key recruitment ouputs (requires print statements in log file)
• R/make_recruit_figs.R - Plots recruitment-related metrics for a give run (requires recruitment print outs in log file)
• R/make_recruit_init_test.R - Creates theoretical values for Beverton-Holt alpha/beta based on initinal conditions and target behavior
• R/make_recruit_output.R - Returns initial conditions and recruitment data to a table
• R/model_BH.R - Testbed for manipulating possible recruitment parameter combinations using Atlantis formulations
• R/parse_recruit_log.R - Converts log.txt recruitment prints into a table
• R/plot_biomass_comparison.R - Plots NEUS output compared to survdat and StockSMART data
• R/plot_functional_group_system.R - Plot ecosystem-wide biomass in terms of guilds
• R/plot_neus_stock_recruit.R - Plots Recruitment vs adult biomass
• R/plot_prey_prevalence.R - Makes plot of top predators/prey for realized diets
• R/reshape_mumC.R - Function to change mum/C by age
• R/call_edit_param_init_scalar.R - wrapper script for edit_param_init_scalar()

Changed R Scripts

• R/call_run_comparisons.R - Edited file directories
• R/check_spawn_calculation.R - Added plots for recruitment and spawn calculations
• R/edit_init_param.R - Commented out examples
• R/force_diagnostics.R - updated paths to repository directory
• R/get_init_agedist.R - Improved generalizations
• R/make_atlantis_diagnostic_tables.R - Separate StockSMART and survdat data for reasonabilty; combines all diagnostics into single table
• R/make_catch_file.R - Removes spinup code to put into separate script
• R/parse_spawn_log.R - Converts log.txt spawning prints into a table
• R/plot_realized_foodweb.R - Creates trophic-level based foodweb plot option
• data-raw/create_emax_qs.R - Cleans up Emax data and joins to NEUS groups
• data-raw/create_fishbase_stats.R - Tidy output data
• data-raw/create_stockSMART_data.r - pulls recent StockSMART data
• data-raw/create_survdat_biomass.r - tidy data and calculate variability

neus-atlantis 2.0.0

Uses Atlantis codebase v6536

• Reorganization of functional groups
• Forcing of state variables: advection, temperature, salinity
• Forcing of tracer variables: diatoms, pico-phytoplankton, dinoflagellates, surface labile detritus
• Forcing times series: solar radiation, fisheries catch
• Recalibrated so all species persist

See forthcoming publication for model details