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WORK_LOG
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Dec 2020
Fixed all issues. Completed testing of input files. Ran all cross-factorial sensitivity analyses with HYCOM, Mercator, and SABGOM models.
Final release files are "scaledGOMATLrelYYYYYYYY.txt"
****************************************************************************************************************************************
9 Sep 2020
- fixed issue with spawning dates identified in Beaufort meeting. There was error with date specification; resolved in RSmap_SA codes.
- RESOLVED issue to line up start dates -- based on 95% cutoff the Atl start date is May 22 and GoM start date is May 16 (every 6 days) until Sep 25 for both regions
- FINALIZED RS_CMS_releasefile_ATL.r and RS_CMS_releasefile_GOM.r files
- FINALIZED scaling code (scale_releases_1to1.r)
- scaledGOMATLrel2013.txt" is single year release file ready for testing!
****************************************************************************************************************************************
3 Mar 2020
- going back to check codes but found issue. RS_CMS_releasefile_ATL.r has different set of dates.
ATLreleaseForScaling_SABGOM.RData should start with releases on Mar 1 and current version of RS_CMS_releasefile_ATL.r code results in Feb 29 start
UNRESOLVED - leave extant version of ATLreleaseForScaling_SABGOM.RData for now.
- Added additional vertical matrices based on lane snapper and gray snapper LH for sensitivities.
- scaledGOMATLrel20040617.txt is a test run file for one date
- edited post_proc file to account for increased resolution in .xyz settlement file
NOTE WORK FLOW:
- first build files for separate regions using RS_CMS_releasefile_GoM.r and RS_CMS_releasefile_ATL.r
- parse out 95% spawning activity
- assign depth of releases based on .nc nest files
- then combine using scale_releases_1to1.r
****************************************************************************************************************************************
28 Feb 2020
- Changed scaling routine after deciding it will be easier to subsampl for changes in age structure post-simulation for now, scale abundances Gulf vs Atl so that they are 1:1 by area
- Differences in abundance and age structure will be accounted for by sub-sampling simulation data
scaledGoMAtl.RData - this is new scaled GOM/ATL map, scaled such that densities (abundance per area) are 1:1 between WFS and all of Atlantic.
****************************************************************************************************************************************
17 Dec 2019
Fixed error in FINAL_MAPPING_RESULTS_ext.RData - error merging AL artificial reef interpolation data
GoM map now includes interpolation to Keys
Edited scale_releases.r to reflect 2-area scaling (Gulf vs. Atl only)
TO DO: scale Gulf/Atl 1:1 and create release file, run simulation - check areal domain for Kyle's HB calculation
From Kyle Jul 31: In the headboat data analysis, the mean ratio of CPUE from the West coast of FL to the Atlantic is 4.4 with 95%CI of (4.1, 4.7) - check that this is in number?
****************************************************************************************************************************************
6 Dec 2019
Fix error in FINAL_MAPPING_RESULTS_ext.RData - error merging AL artificial reef interpolation data
****************************************************************************************************************************************
25 Sept 2019
Modified original code to extend distribution map down to Tortugas
C:\Users\mandy.karnauskas\Desktop\completed_manuscripts\RS_mapping_with_platforms_FINAL_wALK
new map is: FINAL_MAPPING_RESULTS_ext.RData
****************************************************************************************************************************************
23 Sept 2019
FIXED PENDING ISSUES FROM 12 Sept
Continue cleaning of release files for 3 different regions
- extract all dates and subset by threshold spawning activity -- set to encompass 95% of spawning activity
- dates aligned -- starting Mar 1 every 6 days
GROUP QUESTIONS:
- how to set minimum spawning depth? - current at 13m, is this a good cutoff?
New files:
scale_releases.r (for combining three regions and scaling)
****************************************************************************************************************************************
12 Sept 2019
Cleaned up release files for 3 different regions
PENDING ISSUES THAT NEED TO BE FIXED:
Selected dates are off peak spawning seasons --> need to extract all dates and subset by threshold spawning activity
Need to align dates across GoM-Atl to facilitate post-processing --> every 6 days, but on same days
Forgot to incorporate total area in the ratio calculation. CPUE should be scaled on a per-area basis, not total across region.
Started work to modify date extraction on Tortugas release file code; adopt for other regions when complete and tested.
****************************************************************************************************************************************
9Sept2019
Dug up old settlement polygon file, refined polygons in Atl to match resolution in Gulf
****************************************************************************************************************************************
12June2019
ran ATL simulations and put in new folder: runGulf_HYCOM150
* note - error with 2009 in GoM runs 0 - throwing -5 exit code for some dates (missing oc data -why??)
* only 2008 run with Atlantic
added some additional checks to post_proc_GoM_Atl code - screening traj_files for random errors
****************************************************************************************************************************************
11June2019
- cleaned up file names, organized in MASTER_codes folder and cleaned up codes
** changed code for assigning depth of spawning -- now specific to hydrodynamic nest to avoid (-1) exit code error
** release files now have nest descriptor in filename (e.g., RS_ATL_releaseHatteras_HYCOM150.txt)
New files:
nest_1_20080501000000_HYCOM150.nc HYCOM 1/50 degree nest for depth extract
RS_ATL_release_HYCOM150.txt updated release file for entire Atlantic based on egg production map, using HYCOM 1/50 nest
RS_ATL_releaseHatteras_HYCOM150.txt updated release file for Hatteras hotspot based on egg production map, using HYCOM 1/50 nest
RS_ATL_releaseMain_HYCOM150.txt updated release file for Atlantic S of 34N based on egg production map, using HYCOM 1/50 nest
RS_CMS_releasefile_ATL.r release file building off Atlantic statistical egg production map
RS_CMS_releasefile_GoM.r release file building of MCF paper SSB distribution
RS_CMS_releasefile_Tortugas.r release file building off SEAMAP reef fish video survey sent by Matt Campbell on Mon, Mar 11, 12:57 PM
new folder: runGulf_HYCOM150
this is the first Gulf-wide run with HYCOM 1/50 deg model (years 2008 and 2009)
model attributes:
nnests: 1
timeMax: 2592000
timeStep: 2700
releaseFilename: fullGoM_release_HYCOM150.txt
turb: .true.
horDiff: 20
vertDiff: 0.00100000004749745
turbTimestep: 2700
avoidcoast: .true.
polygon: .true.
polyFilename: redSnapperSett_GOM_ATL.xyz
settlementStart: 26
ibio: .true.
ibioFilename: vert_matrix_red_sd0
ibioTimestep: 2700
massSpawning: .true.
larvaStart: 1