From d102a697b4e21a7b7b8ea43fa879131989f09632 Mon Sep 17 00:00:00 2001 From: Brian Langseth Date: Tue, 10 Dec 2024 11:36:28 -0800 Subject: [PATCH] Add historical length data #30 Miller and Geibel Miller and Gotschall --- code/recfin_processing.R | 127 ++++++++++++++++++++++++++-- data/CAquillback_historical_bio.csv | 91 ++++++++++++++++++++ 2 files changed, 209 insertions(+), 9 deletions(-) create mode 100644 data/CAquillback_historical_bio.csv diff --git a/code/recfin_processing.R b/code/recfin_processing.R index ea98e19..133fd7c 100644 --- a/code/recfin_processing.R +++ b/code/recfin_processing.R @@ -226,7 +226,7 @@ ggsave(here('data_explore_figs',"recfin_mortality_district_fleet_percent.png"), #Load catch data ## -# MRFSS Recreational - 1980-2004 Landings mtons +# MRFSS Recreational - 1980-1989, 1993-2004 Landings mtons ca_mrfss = read.csv(here("data-raw","MRFSS-CTE510-California-quillback-1980---2004_17.Oct.2024.csv"), header = T) #Pull 2021 assessment values for comparison. These are recFIN landings + discards @@ -377,7 +377,7 @@ ggplot(aggAreaYr_mrfss, aes(y = tot_mt, x = YEAR)) + #-----------------------------------------------------------------------------# -# Load RecFIN bio sampling data ---- +# Process RecFIN bio sampling data ---- #-----------------------------------------------------------------------------# @@ -617,14 +617,15 @@ ggsave(here('data_explore_figs',"recfin_weight_area_density.png"), #-----------------------------------------------------------------------------# -# Load MRFSS bio sampling data ---- +# Process MRFSS bio sampling data ---- #-----------------------------------------------------------------------------# ## #Load the data ## -# MRFSS Recreational - 1980-2003 + +# MRFSS Recreational - 1980-1989, 1993-2003 ca_mrfss_bio <- read.csv(here("data-raw","MRFSS-SD509-CALIFORNIA-quillback-1980---2003_22.Nov.2024.csv"), header = T) @@ -876,13 +877,20 @@ ggsave(here('data_explore_figs',"mrfss_weight_area_density.png"), width = 6, height = 4) + +#-----------------------------------------------------------------------------# + +# Process historical bio sampling data ---- + +#-----------------------------------------------------------------------------# + ########################- -# Check the Deb Wilson-Vandenberg dataset ---- +## Deb Wilson-Vandenberg dataset 1987-1998 ---- ########################- -#To see if duplicates exist in 1997 and 1998 -#Copper rockfish 2023 assessment replaced 1997 and 1998 MRFSS PC data with Deb's estimates -#However, deb's estimates are total length so need to do conversions to FL +#To see if duplicates exist in 1997 and 1998 and process data +#Copper rockfish 2023 assessment replaced 1997 and 1998 MRFSS PC data with Deb's samples +#However, deb's samples are total length so need to do conversions to FL #Pull 2021 assessment file for deb length data. dir = "//nwcfile.nmfs.local/FRAM/Assessments/Archives/QuillbackRF/QuillbackRF_2021/6_non_confidential_data/postSSC_request_data" @@ -893,7 +901,7 @@ table(deb_bio$PORTNAME, useNA = "always") table(deb_bio$COUNTY, useNA = "always") #Assign County to codes in Deb's data to district from the lookup table. -#Have to load two workssheets from the lookup table: +#Have to load two worksheets from the lookup table: #First to get the county number, second to assign county number to district. #Although county 23 (Humboldt) has one INTSITE that is assigned to Wine, Deb's data doesn't have that #level of detail, so assign all Humboldt samples to Redwood. @@ -978,3 +986,104 @@ out_deb$length_cm <- 9.075 + out_deb$length_cm * 0.965 #convert to FL based on #write.csv(out_deb, here("data","CAquillback_deb_bio.csv"), row.names = FALSE) +########################- +## Miller and Gotschall 1957-1972 (Quillback lengths only for 1959-1960) ---- +########################- + +#Load the data - Table 3 is of lengths +milgot_bio <- data.frame(read_excel(here("data-raw", "Miller_Gotshall_catch_length_data.xlsx"), sheet = "Table 3", + col_types = c(rep("guess",7),"text"))) + +#Check variables +table(milgot_bio$Year) +table(milgot_bio$Month) +table(milgot_bio$Fishery) +table(milgot_bio$Species) +table(milgot_bio$Port) +table(milgot_bio$other.notes..comments) + +#Process data + +#Retain only quillback lengths +milgot_bio <- milgot_bio %>% dplyr::filter(Species == "QLBK") +#Expand dataset so each row equals one length (will remove the count column) +milgot_bio <- milgot_bio %>% tidyr::uncount(Count) + +#Simplify variables + +milgot_bio$length_cm <- milgot_bio$Length..cm. +milgot_bio$weight_kg <- NA +#Replace port with district +milgot_bio$area <- dplyr::case_when(milgot_bio$Port == "Bodega Bay" ~ "Bay", + milgot_bio$Port == "Ft. Bragg" ~ "Wine", + milgot_bio$Port == "Princeton" ~ "Bay", + milgot_bio$Port == "Shelter Cove" ~ "Wine", + TRUE ~ NA) +milgot_bio$mode <- dplyr::case_when(milgot_bio$Fishery %in% c("skiff", "Skiff") ~ "PR", + milgot_bio$Fishery == "CPFV" ~ "PC", + TRUE ~ NA) +milgot_bio$sex <- "U" +milgot_bio$disp <- "RETAINED" +milgot_bio$source <- "MilGot" + +out_milgot <- milgot_bio %>% dplyr::select(Year, + length_cm, + weight_kg, + sex, + area, + mode, + disp, + source) + + +########################- +## Miller and Gleibel 1959-1960 ---- +########################- + +#Load the data +milgle_bio <- data.frame(read_excel(here("data-raw", "bio_quillback_rockfish_Miller_NorCal_Lengths_59_72.xlsx"), sheet = "Sheet1")) + +#Check variables +table(milgle_bio$YEAR) +table(milgle_bio$NUMBER_OF_FISH) +table(milgle_bio$COAST_DIST) +table(milgle_bio$MODE) +table(milgle_bio$mode_description) +table(milgle_bio$Counties) + +#Process data + +#Expand dataset so each row equals one length (will remove the count column) +milgle_bio <- milgle_bio %>% tidyr::uncount(NUMBER_OF_FISH) + + +#Simplify variables + +milgle_bio$length_cm <- milgle_bio$LENGTH/10 +milgle_bio$weight_kg <- NA +#Replace port with district +milgle_bio$area <- dplyr::case_when(milgle_bio$Counties == "DelNorte_Humboldt" ~ "Redwood", + milgle_bio$Counties == "Mendocino_Sonoma" ~ "Wine", + milgle_bio$Counties == "SanFranciscoBay" ~ "Bay", + milgle_bio$Counties == "SantaCruz_Monterey" ~ "Central", + TRUE ~ NA) +milgle_bio$mode <- dplyr::case_when(milgle_bio$mode_description == "private_rental" ~ "PR", + milgle_bio$mode_description == "party_boat" ~ "PC", + TRUE ~ NA) +milgle_bio$sex <- "U" +milgle_bio$disp <- "RETAINED" +milgle_bio$source <- "MilGle" + +out_milgle <- milgle_bio %>% dplyr::select("Year" = YEAR, + length_cm, + weight_kg, + sex, + area, + mode, + disp, + source) + +#write.csv(cbind(out_milgot, out_milgle), here("data","CAquillback_historical_bio.csv"), row.names = FALSE) + + + \ No newline at end of file diff --git a/data/CAquillback_historical_bio.csv b/data/CAquillback_historical_bio.csv new file mode 100644 index 0000000..dad3cd2 --- /dev/null +++ b/data/CAquillback_historical_bio.csv @@ -0,0 +1,91 @@ +"Year","length_cm","weight_kg","sex","area","mode","disp","source" +1960,37,NA,"U","Bay","PC","RETAINED","MilGot" +1960,44,NA,"U","Bay","PC","RETAINED","MilGot" +1960,39,NA,"U","Bay","PC","RETAINED","MilGot" +1960,43,NA,"U","Bay","PC","RETAINED","MilGot" +1960,44,NA,"U","Bay","PC","RETAINED","MilGot" +1960,45,NA,"U","Bay","PC","RETAINED","MilGot" +1960,49,NA,"U","Bay","PC","RETAINED","MilGot" +1960,29,NA,"U","Bay","PC","RETAINED","MilGot" +1960,30,NA,"U","Bay","PC","RETAINED","MilGot" +1960,36,NA,"U","Bay","PC","RETAINED","MilGot" +1960,38,NA,"U","Bay","PC","RETAINED","MilGot" +1960,38,NA,"U","Bay","PC","RETAINED","MilGot" +1960,42,NA,"U","Bay","PC","RETAINED","MilGot" +1960,46,NA,"U","Bay","PC","RETAINED","MilGot" +1960,46,NA,"U","Bay","PC","RETAINED","MilGot" +1960,35,NA,"U","Bay","PC","RETAINED","MilGot" +1960,34,NA,"U","Bay","PC","RETAINED","MilGot" +1960,39,NA,"U","Bay","PC","RETAINED","MilGot" +1960,41,NA,"U","Bay","PC","RETAINED","MilGot" +1960,34,NA,"U","Bay","PC","RETAINED","MilGot" +1960,28,NA,"U","Bay","PR","RETAINED","MilGot" +1960,30,NA,"U","Bay","PR","RETAINED","MilGot" +1959,52,NA,"U","Wine","PR","RETAINED","MilGot" +1959,46,NA,"U","Wine","PR","RETAINED","MilGot" +1959,48,NA,"U","Wine","PR","RETAINED","MilGot" +1959,41,NA,"U","Wine","PR","RETAINED","MilGot" +1959,42,NA,"U","Wine","PR","RETAINED","MilGot" +1959,40,NA,"U","Wine","PR","RETAINED","MilGot" +1959,41,NA,"U","Wine","PR","RETAINED","MilGot" +1959,43,NA,"U","Wine","PR","RETAINED","MilGot" +1959,45,NA,"U","Wine","PR","RETAINED","MilGot" +1959,47,NA,"U","Wine","PR","RETAINED","MilGot" +1959,48,NA,"U","Wine","PR","RETAINED","MilGot" +1959,42.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,43.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,44.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,45.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,45.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,45.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,46.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,47.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,48.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,48.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,49.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,49.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,40.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,41.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,41.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,41.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,42.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,43.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,45.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,47.3,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,48.8,NA,"U","Redwood","PR","RETAINED","MilGle" +1959,27.8,NA,"U","Wine","PR","RETAINED","MilGle" +1959,34.3,NA,"U","Wine","PR","RETAINED","MilGle" +1959,34.8,NA,"U","Wine","PR","RETAINED","MilGle" +1959,36.3,NA,"U","Wine","PR","RETAINED","MilGle" +1959,37.3,NA,"U","Wine","PR","RETAINED","MilGle" +1959,39.3,NA,"U","Wine","PR","RETAINED","MilGle" +1959,41.8,NA,"U","Wine","PR","RETAINED","MilGle" +1959,42.8,NA,"U","Wine","PR","RETAINED","MilGle" +1959,43.3,NA,"U","Wine","PR","RETAINED","MilGle" +1959,43.3,NA,"U","Wine","PR","RETAINED","MilGle" +1959,43.8,NA,"U","Wine","PR","RETAINED","MilGle" +1959,45.8,NA,"U","Wine","PR","RETAINED","MilGle" +1959,47.8,NA,"U","Wine","PR","RETAINED","MilGle" +1960,34.3,NA,"U","Bay","PC","RETAINED","MilGle" +1960,34.8,NA,"U","Bay","PC","RETAINED","MilGle" +1960,35.8,NA,"U","Bay","PC","RETAINED","MilGle" +1960,39.3,NA,"U","Bay","PC","RETAINED","MilGle" +1960,40.8,NA,"U","Bay","PC","RETAINED","MilGle" +1960,29.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,30.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,36.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,37.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,38.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,38.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,39.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,41.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,42.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,43.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,43.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,44.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,44.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,45.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,46.3,NA,"U","Wine","PC","RETAINED","MilGle" +1960,46.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,49.8,NA,"U","Wine","PC","RETAINED","MilGle" +1960,23,NA,"U","Central","PC","RETAINED","MilGle"