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add initial configurations for 2025 species
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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).
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@chantelwetzel-noaa
chantelwetzel-noaa committed Dec 16, 2024
1 parent 8f380fe commit dc35580
Showing 1 changed file with 18 additions and 2 deletions.
20 changes: 18 additions & 2 deletions data-raw/configuration.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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

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