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pfmc-assessments_to_SIS_2023.R
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pfmc-assessments_to_SIS_2023.R
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# processing 2023 assessment model output to SIS
# not yet using relative paths because so far this is only run by Ian on his computer
# Pacific Hake (already processed)
# "\\\\nwcfile.nmfs.local/fram/Assessments/Archives/Pacific Hake_Whiting/PWhiting2023"
# Canary
canary <- r4ss::SS_output("\\\\nwcfile.nmfs.local/fram/assessments/Archive_temp/CanaryRF_2023/2_base_model/7_3_5_reweight")
save(canary, file = "output/canary2023.Rdata")
# Copper SCA and NCA
# read output from model Copper Rockfish in (Southern CA)
copper_sca <- r4ss::SS_output("\\\\nwcfile/FRAM/Assessments/Archive_temp/CopperRF_2023/2_base_model/sca/15.0_south_post_star_base")
save(copper_sca, file = "c:/github/PFMC-SIS/output/copper_sca_2023.Rdata")
copper_nca <- r4ss::SS_output("\\\\nwcfile/FRAM/Assessments/Archive_temp/CopperRF_2023/2_base_model/nca/10.0_north_post_star_base")
save(copper_nca, file = "c:/github/PFMC-SIS/output/copper_nca_2023.Rdata")
# Petrale
petrale <- r4ss::SS_output("\\\\nwcfile.nmfs.local/fram/Assessments/Archive_temp/Petrale_sole_2023/2_base_model")
save(petrale, file = "c:/github/PFMC-SIS/output/petrale_2023.Rdata")
# Black WA, OR, CA
black_wa <- r4ss::SS_output("\\\\nwcfile.nmfs.local/fram/Assessments/Archive_temp/BlackRF_2023/2_base_model/Washington")
save(black_wa, file = "c:/github/PFMC-SIS/output/black_wa_2023.Rdata")
black_or <- r4ss::SS_output("\\\\nwcfile.nmfs.local/fram/Assessments/Archive_temp/BlackRF_2023/2_base_model/Oregon")
save(black_or, file = "c:/github/PFMC-SIS/output/black_or_2023.Rdata")
black_nca <- r4ss::SS_output("\\\\nwcfile.nmfs.local/fram/Assessments/Archive_temp/BlackRF_2023/2_base_model/California/North")
save(black_nca, file = "c:/github/PFMC-SIS/output/black_nca_2023.Rdata")
black_cca <- r4ss::SS_output("\\\\nwcfile.nmfs.local/fram/Assessments/Archive_temp/BlackRF_2023/2_base_model/California/Central")
save(black_cca, file = "c:/github/PFMC-SIS/output/black_cca_2023.Rdata")
# Rex Sole
rex <- r4ss::SS_output("\\\\nwcfile/FRAM/Assessments/Archive_temp/Rex_sole_2023/2_base_model/run")
save(rex, file = "c:/github/PFMC-SIS/output/rex_2023.Rdata")
# Shortspine Thornyhead
sst <- r4ss::SS_output("\\\\nwcfile/FRAM/Assessments/Archive_temp/Shortspine_thornyhead_2023/2_base_model")
save(sst, file = "c:/github/PFMC-SIS/output/rex_2023.Rdata")
sablefish <- r4ss::SS_output("\\\\nwcfile/FRAM/Assessments/Archive_temp/Sablefish_2023/2_base_model")
save(sablefish, file = "c:/github/PFMC-SIS/output/sablefish_2023.Rdata")
# # optionally load files created above instead of re-running SS_output()
# load("c:/github/PFMC-SIS/output/canary2023.Rdata")
# load(file = "c:/github/PFMC-SIS/output/petrale_2023.Rdata")
# load(file = "c:/github/PFMC-SIS/output/canary_2023.Rdata")
SIS_dir <- "c:/github/PFMC-SIS/SIS_info_2023" # not sure where this should go yet
dir.create(SIS_dir)
year <- 2023
# Copper SCA
r4ss::get_SIS_info(model = copper_sca,
dir = SIS_dir,
stock = "Copper_SCA",
month = 5,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Billions of eggs",
contact = "Chantel.Wetzel@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "4.Minor gaps in some sector(s)",
abundance_input_data = "3.Limited fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "1.Informative or used to process input data"
)
# Copper NCA
r4ss::get_SIS_info(model = copper_nca,
dir = SIS_dir,
stock = "Copper_NCA",
month = 5,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Billions of eggs",
contact = "Melissa.Monk@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "4.Minor gaps in some sector(s)",
abundance_input_data = "3.Limited fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "1.Informative or used to process input data"
)
# Canary
r4ss::get_SIS_info(model = canary,
dir = SIS_dir,
stock = "Canary Rockfish",
month = 7,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Millions of eggs",
contact = "Brian.Langseth@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "5.Near complete knowledge",
abundance_input_data = "4.Comprehensive fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "4.Supports fishery composition",
ecosystem_linkage = "2.Random variation not mechanistic"
)
# Petrale
r4ss::get_SIS_info(model = petrale,
dir = SIS_dir,
stock = "Petrale Sole",
month = 7,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Trillions of eggs",
contact = "Ian.Taylor@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "5.Near complete knowledge",
abundance_input_data = "4.Comprehensive fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "5.Very complete",
ecosystem_linkage = "2.Random variation not mechanistic"
)
# Black Rockfish WA
r4ss::get_SIS_info(model = black_wa,
dir = SIS_dir,
stock = "Black Rockfish WA",
month = 7,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Billions of eggs",
contact = "Jason.Cope@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "3.Minor gaps across sectors",
abundance_input_data = "3.Limited fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "1.Informative or used to process input data"
)
# Black Rockfish OR
r4ss::get_SIS_info(model = black_or,
dir = SIS_dir,
stock = "Black Rockfish OR",
month = 7,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Billions of eggs",
contact = "Jason.Cope@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "3.Minor gaps across sectors",
abundance_input_data = "3.Limited fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "1.Informative or used to process input data"
)
# Black Rockfish Central CA
r4ss::get_SIS_info(model = black_nca,
dir = SIS_dir,
stock = "Black Rockfish Northern CA",
month = 7,
sciencecenter = "SWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Billions of eggs",
contact = "Edward.Dick@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "3.Minor gaps across sectors",
abundance_input_data = "3.Limited fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "1.Informative or used to process input data"
)
# Black Rockfish Central CA
r4ss::get_SIS_info(model = black_cca,
dir = SIS_dir,
stock = "Black Rockfish Central CA",
month = 7,
sciencecenter = "SWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Billions of eggs",
contact = "Edward.Dick@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "3.Minor gaps across sectors",
abundance_input_data = "3.Limited fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "1.Informative or used to process input data"
)
# Shortspine Thornyhead
r4ss::get_SIS_info(model = sst,
dir = SIS_dir,
stock = "Shortspine Thornyhead",
assessment_type = "Stock Monitoring Updates",
month = 5,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Millions of eggs",
contact = "Joshua Zahner <jzahner@uw.edu>",
review_result = "Full Acceptance",
catch_input_data = "5.Near complete knowledge",
abundance_input_data = "4.Comprehensive fishery independent",
bio_input_data = "2.Empirical and proxy-based",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "2.Random variation not mechanistic"
)
# Rex Sole
r4ss::get_SIS_info(model = rex,
dir = SIS_dir,
stock = "Rex Sole",
assessment_type = "Stock Monitoring Updates",
month = 5,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "Millions of eggs",
contact = "Markus Min <mmin@uw.edu>",
review_result = "Full Acceptance",
catch_input_data = "5.Near complete knowledge",
abundance_input_data = "4.Comprehensive fishery independent",
bio_input_data = "3.Mostly empirical estimates",
comp_input_data = "3.Gaps but supports age-structured assessment",
ecosystem_linkage = "2.Random variation not mechanistic"
)
# Sablefish
r4ss::get_SIS_info(model = sablefish,
dir = SIS_dir,
stock = "Sablefish",
assessment_type = "Stock Monitoring Updates",
month = 8,
sciencecenter = "NWFSC",
Mgt_Council = "PFMC",
SpawnOutputLabel = "mt",
contact = "Kelli.Johnson@noaa.gov",
review_result = "Full Acceptance",
catch_input_data = "5.Near complete knowledge",
abundance_input_data = "4.Comprehensive fishery independent",
bio_input_data = "4.Track changes over time",
comp_input_data = "4.Support fishery composition",
ecosystem_linkage = "3.Direct Linkage(s)"
)