add WCGBTS length comps (ages and triennials still to come)

Rscripts/bins.R

@@ -0,0 +1,4 @@
+# variable names copied from lingcod
+# note that the variables in the lists created by r4ss::SS_read() are $lbin_vector and $agebin_vector
+len_bin <- seq(20, 56, 2)
+age_bin <- 1:25

Rscripts/process_rec_comps.R

@@ -214,10 +214,8 @@ rec_ages_smry_table |>
 # | 2023|        1247|        1251|           0|
 # | 2024|         613|           0|           0|
 
-# note variables in list created by r4ss::SS_read() are $lbin_vector and $agebin_vector
-len_bin <- seq(20, 56, 2)
-age_bin <- 1:25
-
+# get age and length bins
+source("Rdata/bins.R")
 # clean length comps
 #   exclude
 #   1. missing lengths (1 out of 59808)

Rscripts/process_survey_comps.R

@@ -0,0 +1,96 @@
+# process survey comps
+# see also explorations of changes in growth over space and time in the
+# "Survey data" section of /docs/data_summary_doc.qmd
+
+require(dplyr)
+require(ggplot2)
+
+dir_wcgbts <- here::here("Data/Raw_not_confidential/wcgbts")
+dir_tri <- here::here("Data/Raw_not_confidential/triennial")
+
+# pull survey data from data warehouse (skip unless it's been updated)
+new_pull <- FALSE
+if (new_pull) {
+  yt_survey_bio <- nwfscSurvey::pull_bio(
+    common_name = "yellowtail rockfish",
+    survey = "NWFSC.Combo",
+    dir = dir_wcgbts
+  )
+  yt_tri_bio <- nwfscSurvey::pull_bio(
+    common_name = "yellowtail rockfish",
+    survey = "Triennial",
+    dir = dir_tri
+  )
+  yt_survey_catch <- nwfscSurvey::pull_catch(
+    common_name = "yellowtail rockfish",
+    survey = "NWFSC.Combo",
+    dir = dir_wcgbts
+  )
+  yt_tri_catch <- nwfscSurvey::pull_catch(
+    common_name = "yellowtail rockfish",
+    survey = "Triennial",
+    dir = dir_tri
+  )
+} else {
+  # read saved data files TODO: update after 2024 survey data is available
+  load(file.path(dir_wcgbts, "bio_yellowtail rockfish_NWFSC.Combo_2025-01-14.rdata"))
+  yt_survey_bio <- x
+  load(file.path(dir_tri, "bio_yellowtail rockfish_Triennial_2025-01-14.rdata"))
+  yt_tri_bio <- x
+  load(file.path(dir_wcgbts, "catch_yellowtail rockfish_NWFSC.Combo_2025-01-15.rdata"))
+  yt_survey_catch <- x
+  load(file.path(dir_tri, "catch_yellowtail rockfish_Triennial_2025-01-15.rdata"))
+  yt_tri_catch <- x
+}
+
+# filter by latitude
+yt_n_survey_bio <- filter(yt_survey_bio, Latitude_dd > 40 + 1 / 6)
+yt_n_tri_bio <- purrr::map(yt_tri_bio, \(dat) filter(dat, Latitude_dd > 40 + 1 / 6))
+yt_n_survey_catch <- filter(yt_survey_catch, Latitude_dd > 40 + 1 / 6)
+yt_n_tri_catch <- filter(yt_tri_catch, Latitude_dd > 40 + 1 / 6)
+
+strata <- nwfscSurvey::CreateStrataDF.fn(
+  names = c("shallow", "deep"),
+  depths.shallow = c(55, 183),
+  depths.deep = c(183, 400), # note 99.9% of fish are less than 253m
+  lats.south = c(40.166667, 40.166667),
+  lats.north = c(49, 49)
+)
+
+# get age and length bins
+source(here::here("Rscripts/bins.R"))
+
+wcgbts_length_comps <- nwfscSurvey::get_expanded_comps(
+    bio_data = yt_n_survey_bio,
+    catch_data = yt_n_survey_catch,
+    comp_bins = len_bin,
+    strata = strata,
+    comp_column_name = "length_cm",
+    output = "full_expansion_ss3_format",
+    two_sex_comps = TRUE,
+    input_n_method = "stewart_hamel",
+    month = 7,
+    fleet = 999,
+    dir = dir_wcgbts
+  )
+
+wcgbts_raw_length_comps <- nwfscSurvey::get_raw_comps(
+    data = yt_n_survey_bio,
+    comp_bins = len_bin,
+    comp_column_name = "length_cm",
+    two_sex_comps = TRUE,
+    dir = dir_wcgbts)
+
+nwfscSurvey::plot_comps(
+  data = wcgbts_raw_length_comps,
+  dir = dir_wcgbts)
+file.copy(file.path(dir_wcgbts, "plots/length_frequency_sex_3.png"), 
+          file.path(dir_wcgbts, "plots/length_frequency_raw_sex_3.png"))
+file.copy(file.path(dir_wcgbts, "plots/length_r4ss_frequency_sex_3.png"), 
+          file.path(dir_wcgbts, "plots/length_r4ss_frequency_raw_sex_3.png"))
+nwfscSurvey::plot_comps(
+  data = wcgbts_length_comps,
+  dir = dir_wcgbts)
+
+# save processed data as RDS file
+saveRDS(wcgbts_length_comps$sexed, file = here::here("Data/Processed/ss3_wcgbts_length_comps.rds"))