add default configuration for yellowtail as well

pfmc-assessments · Jan 15, 2025 · 1d05a26 · 1d05a26
1 parent dbfb9ac
commit 1d05a26
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Showing 4 changed files with 4 additions and 3 deletions.
diff --git 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
@@ -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
@@ -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