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