diff --git a/.gitignore b/.gitignore index b4e7d0e..5d41394 100644 --- a/.gitignore +++ b/.gitignore @@ -4,7 +4,6 @@ .Rhistory *.RData *.rds -*.rda **/wcgbts/* **/afsc* **/nwfsc* diff --git a/data-raw/configuration.R b/data-raw/configuration.R index f3777a7..c6e9f0a 100644 --- a/data-raw/configuration.R +++ b/data-raw/configuration.R @@ -2,7 +2,6 @@ configuration <- tibble::as_tibble(read.csv( file.path("data-raw", "configuration.csv") )) - utils::write.csv( configuration, file = here::here("data-raw", "configuration.csv"), diff --git a/data-raw/configuration.csv b/data-raw/configuration.csv index 57fd241..1285fc9 100644 --- a/data-raw/configuration.csv +++ b/data-raw/configuration.csv @@ -49,7 +49,7 @@ "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,"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,"off","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)","NWFSC.Combo","sdmTMB::delta_gamma()","catch_weight ~ 0 + fyear*split_mendocino + 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*split_mendocino",-55,-425,33.5,Inf,1980,Inf,TRUE,400,"iid","off",TRUE "sablefish","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope","sdmTMB::tweedie()","catch_weight ~ 0 + fyear",-183,-Inf,34.5,Inf,1997,Inf,TRUE,300,"iid","iid",FALSE "rougheye and blackspotted rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","Triennial","sdmTMB::delta_lognormal()","catch_weight ~ 0 + fyear",-55,-500,42,Inf,1980,-Inf,FALSE,100,"iid","off",TRUE @@ -61,3 +61,6 @@ "rougheye rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Slope","sdmTMB::delta_gamma()","catch_weight ~ 0 + fyear",-183,-Inf,34.5,Inf,1999,Inf,TRUE,100,"off","off",TRUE "chilipepper","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope","sdmTMB::delta_gamma()","catch_weight ~ 0 + fyear",-183,-Inf,34.5,Inf,1997,Inf,FALSE,100,"off","off",TRUE "chilipepper","nwfscSurvey::pull_catch(common_name = species,survey=source)","AFSC.Slope","sdmTMB::delta_lognormal()","catch_weight ~ 0 + fyear",-183,-Inf,34.5,Inf,1997,Inf,FALSE,100,"off","off",TRUE +"yellowtail rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo","sdmTMB::delta_lognormal()","catch_weight ~ 0 + fyear*split_mendocino + pass_scaled",-55,-425,33.5,Inf,-Inf,Inf,TRUE,400,"iid","off",TRUE +"yellowtail rockfish","nwfscSurvey::pull_catch(common_name = species,survey=source)","NWFSC.Combo","sdmTMB::delta_lognormal()","catch_weight ~ 0 + fyear + pass_scaled",-55,-425,40.1667,Inf,-Inf,Inf,TRUE,400,"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,-425,40.1667,Inf,-Inf,Inf,TRUE,400,"iid","off",TRUE diff --git a/data/configuration.rda b/data/configuration.rda new file mode 100644 index 0000000..cc3e2b4 Binary files /dev/null and b/data/configuration.rda differ