From dc3558026f7cdce1b9a3cba553d6a56d8add7b3b Mon Sep 17 00:00:00 2001 From: Chantel Wetzel - NOAA Federal Date: Mon, 16 Dec 2024 06:42:05 -0800 Subject: [PATCH] add initial configurations for 2025 species Add all the initial error structures and surveys to run for each benchmark assessment. Additional work will need to be done to refine the set-up as need, particularly for data-limited species (e.g., rougheye). --- data-raw/configuration.csv | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/data-raw/configuration.csv b/data-raw/configuration.csv index 14f317f..5fa40aa 100644 --- a/data-raw/configuration.csv +++ b/data-raw/configuration.csv @@ -11,12 +11,19 @@ species,fxn,source,family,formula,min_depth,max_depth,min_latitude,max_latitude, "sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Slope",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Slope",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "arrowtooth flounder","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-Inf,34,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "aurora rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-183,-Inf,-Inf,Inf,-Inf,Inf,TRUE,250,"off","iid",FALSE "big skate","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-500,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "blackgill rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-183,-850,35,Inf,-Inf,Inf,TRUE,200,"off","off",FALSE "bocaccio","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-500,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "chilipepper","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-500,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"chilipepper","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-500,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"chilipepper","nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,46.25,-Inf,Inf,TRUE,500,"iid","iid",FALSE +"chilipepper","nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,46.25,-Inf,Inf,TRUE,500,"iid","iid",FALSE "curlfin sole","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::tweedie(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-450,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "darkblotched rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-675,33.5,Inf,-Inf,Inf,TRUE,250,"off","iid",FALSE "Dover sole","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE @@ -33,9 +40,18 @@ species,fxn,source,family,formula,min_depth,max_depth,min_latitude,max_latitude, "Pacific spiny dogfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-700,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","iid",FALSE "redbanded rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-675,33.5,Inf,-Inf,Inf,TRUE,200,"off","iid",FALSE "rosethorn rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-675,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",FALSE +"rougheye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-875,33.5,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +"rougheye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-875,33.5,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +"rougheye and blackspotted rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +"rougheye and blackpotted rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +"rougheye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Slope",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +"rougheye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Slope",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +c("rougheye rockfish","rougheye and blackpotted rockfish"),"nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +c("rougheye rockfish","rougheye and blackpotted rockfish"),"nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear",-55,-Inf,-Inf,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE "sharpchin rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_lognormal(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-475,33,Inf,-Inf,Inf,TRUE,200,"iid","off",FALSE "splitnose rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-700,-Inf,Inf,-Inf,Inf,TRUE,500,"iid","off",FALSE "stripetail rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-500,-Inf,Inf,-Inf,Inf,TRUE,500,"off","iid",FALSE -"widow rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-675,33.5,Inf,-Inf,Inf,TRUE,200,"off","off",FALSE -"yelloweye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-325,34.5,Inf,-Inf,Inf,TRUE,200,"off","off",FALSE +"widow rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-675,33.5,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE +"yelloweye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-325,34.5,Inf,-Inf,Inf,TRUE,200,"iid","off",TRUE "yellowtail rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear + pass_scaled",-55,-425,33.5,Inf,-Inf,Inf,TRUE,400,"iid",off,TRUE +"yellowtail rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial",sdmTMB::delta_gamma(),"catch_weight ~ 0 + fyear",-55,-425,33.5,Inf,-Inf,Inf,TRUE,400,"iid",off,TRUE