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NEFSC / READ-EDAB-neusAtlantis

https://github.com/NEFSC/READ-EDAB-neusAtlantis/wiki

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Ne groundfish spatial #257

Closed jcaracappa1 closed 1 week ago

jcaracappa1 commented 3 weeks ago

Summary

Utilities for manipulating spatial distribution parameters in the biology.prm and init.nc input files. Reference points for spatial biomass. Corrections to the seasonal movement parameters and initial abundance distributions.

New R Scripts/Functions

call_spatial_comaprisons.R : Script to create spatial comparisons for sets of runs using the atlantisprocessing package
ddepend_batch_run.R : Script to generate a run set on a VM for testing distribution parameters
edit_param_ddepend.R : Function to edit ddepend parameters
edit_param_env_move.R : Function to edit min/max temperature and salinity bounds
edit_param_init_dist.R : Function to edit initial conditions spatial distribution
edit_param_seasonal_movement.R : Function to edit Fxxx_Sy parameters for prescribed movement
get_init_spatial_dist.R : Script to extract spatial distribution data from initial conditions
get_param_seasonal_migration.R : Deleted and replaced by edit_param_seasonal_movement.R
rescale_groundfish_scallop_spatial.R : Script to edit the seasonal movement and intitial distributions based on a survey reference dataset
scale_forcing_ts.r : Andy's function to scale ts files

R Script/Function changes

call_neus_post_prcocess/call_run_comparison cleanup old arguments
make_spatial_reference.R : Update input file for survey to add season

Parameter Files

at_biology.prm : Updated seasonal movement parameters
neus_init.nc : Updated intial spatial distributions

Other

landings_by_box_species.rds : Reference file for spatial landings
seasonal_movements.csv : Reference for seasonal movement parameters
spatial_reference_initial_conditions.R : based on earliest survdat entries by species
spatial_reference_survdat_2011_2021.rds : spatial biiomass for 2011 to 2021

jcaracappa1 commented 3 weeks ago

@RGamble1 @andybeet part of the ongoing branch cleanup.

andybeet commented 3 weeks ago

Can you point me to the plots from run based on the NE_groundfish_spatial?

jcaracappa1 commented 3 weeks ago

Joe_Proj/Atlantis_Runs/NE_groundfish_new_movement_2

jcaracappa1 commented 3 weeks ago

NE_groundfish_new_movement_2Model_Comparison_Biomass.pdf

jcaracappa1 commented 1 week ago

Updated WOL spatial distribution and calibrated affected species.

andybeet commented 1 week ago

new plots: rescale_spatial_1bModel_Comparison_Biomass.pdf

@RGamble1 looks good to me

RGamble1 commented 1 week ago

Looks good to me @jcaracappa1 @andybeet.

Merging