load update

.Rproj.user/shared/notebooks/paths

@@ -1,7 +1,9 @@
 C:/Users/tmjackson/Documents/BSAIcrabR/R/add_calc_wt.R="C7E093D6"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/add_crab_year.R="557BAC7E"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/add_legal.R="912948E2"
+C:/Users/tmjackson/Documents/BSAIcrabR/R/clean_lat_lon.R="3259A04C"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/get_avg_wt.R="1761609E"
+C:/Users/tmjackson/Documents/BSAIcrabR/R/get_discards.R="72FE693C"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/get_dockside_comp.R="10AEE7AD"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/get_observer_comp.R="CD7A873D"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/get_retained_catch.R="DAC15420"
@@ -10,7 +12,11 @@ C:/Users/tmjackson/Documents/BSAIcrabR/R/load_crab_dump.R="497ED5C0"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/load_dockside.R="BD7E1529"
 C:/Users/tmjackson/Documents/BSAIcrabR/R/load_pot_dump.R="EE044C52"
 C:/Users/tmjackson/Documents/BSAIcrabR/_pkgdown.yml="D934123F"
+C:/Users/tmjackson/Documents/adfg_crab_observer/aigkc/code/aigkc_data_request.R="EB16A046"
 C:/Users/tmjackson/Documents/adfg_crab_observer/bbrkc/bbrkc_data_summary_example.Rmd="8AE866D6"
 C:/Users/tmjackson/Documents/adfg_crab_observer/bbrkc/code/bbrkc_BSAIcrabR_workflow.R="5E859338"
 C:/Users/tmjackson/Documents/adfg_crab_observer/misc/code/custom_functions.R="8CFCC967"
 C:/Users/tmjackson/Documents/adfg_crab_observer/misc/data/weight_parameters.csv="560DF23B"
+C:/Users/tmjackson/Documents/adfg_crab_observer/pigkc/code/pigkc_data_request.R="DEEE6C75"
+C:/Users/tmjackson/Documents/adfg_crab_observer/smbkc/code/smbkc_data_request.R="7A9A0835"
+C:/Users/tmjackson/Documents/adfg_crab_observer/tanner_crab/code/tanner_crab_data_request.R="BCD9F781"

NAMESPACE

@@ -3,7 +3,9 @@
 export(add_calc_wt)
 export(add_crab_year)
 export(add_legal)
+export(clean_lat_lon)
 export(get_avg_wt)
+export(get_discards)
 export(get_dockside_comp)
 export(get_observer_comp)
 export(get_retained_catch)

R/clean_lat_lon.R

@@ -0,0 +1,18 @@
+#' Clean Lat and Lon
+#'
+#' Clean latitude and longitude data across the dateline
+#' @param x Pot or observer data with columns longitude, latitude, and eastwest
+#' @return x with location information correctect across the date line to be negative
+#' @examples
+#' clean_lat_lon(pots)
+#' @export
+clean_lat_lon <- function(x) {
+
+  x %>%
+    mutate(longitude = ifelse(longitude > 0, longitude * -1, longitude),
+           longitude = ifelse(longitude == -9, NA, longitude),
+           longitude = ifelse(eastwest == "E", (-180 - longitude) + -180, longitude)) -> out
+
+  return(out)
+
+}

R/get_discards.R

@@ -0,0 +1,54 @@
+#' Get Directed Discards
+#'
+#' Estimate directed fishery discards by sex using subtraction method
+
+#' @param retained_catch NULL. Output of `get_retaied_catch()`.
+#' @param total_catch NULL. Output of `get_total_catch()`. 'by' argument could be anything as long as group or sex is included.
+#' @param stock NULL. Character string stock abbreviation: BSSC, WBT, EBT, BBRKC, EAG, WAG, PIGKC, SMBKC, PIBKC, PIRKC, WAIRKC.
+#' @return Data frame including crab year, fishery, sex, discards, and discard mortality.
+#' @examples get_discards(retained_catch, total_catch, stock = "BBRKC", handling_mortality = 0.3)
+#'
+#' @export
+#'
+get_discards <- function(retained_catch, total_catch, stock, handling_mortality = 0.3) {
+
+  # directed fishery codes
+  tibble(stock_abbrev = c("BSSC", "WBT", "EBT", "BBRKC", "EAG", "WAG", "PIGKC", "SMBKC", "PIBKC", "PIRKC", "WAIRKC"),
+         fish_code = c("QO", "QT", "TT", "TR", "OB", "RB", "QB", "QP", "QP", "QR", "RR")) %>%
+    filter(stock_abbrev == stock) %>%
+    pull(fish_code) -> fish_code
+
+  # summarise total catch
+  if("group" %in% names(total_catch)){
+    total_catch %>%
+      # add sex
+      mutate(sex = case_when(group == "female" ~ 2,
+                             group == "sublegal_male"~ 1,
+                             group == "legal_male"~ 1)) -> total_catch
+  }
+
+  if(sum(grepl("group|sex", names(total_catch))) == 0){
+    stop("Total catch must be by 'group', 'sex', or both  !!")
+  }
+
+  total_catch %>%
+    # filter for the directd fishery
+    filter(substring(fishery, 1, 2) == fish_code) %>%
+    group_by(crab_year, fishery, sex) %>%
+    summarise(total_catch_n = sum(total_catch_n, na.rm = T),
+             total_catch_wt = sum(total_catch_wt, na.rm = T)) %>% ungroup %>%
+    # join to retained catch
+    full_join(retained_catch %>%
+                mutate(sex = 1), by = c("crab_year", "fishery", "sex")) %>%
+    mutate(retained_n = ifelse(sex == 2, 0, retained_n),
+           retained_wt = ifelse(sex == 2, 0, retained_wt)) %>%
+    # add discards
+    mutate(discard_n = total_catch_n - retained_n,
+           discard_wt = total_catch_wt - retained_wt,
+           discard_mortality_n = discard_n * handling_mortality + retained_n,
+           discard_mortality_wt = discard_wt * handling_mortality + retained_wt) -> out
+
+  return(out)
+
+}
+

R/load_crab_dump.R

@@ -20,10 +20,14 @@ load_crab_dump <- function(path, stock, database_pull = F, clean = T) {
 
   obs %>%
     rename(sample_date = sampdate) %>%
+    {if(!("subdistrict" %in% names(.))){mutate(subdistrict = NA) %>% .} else{.}} %>%
+    {if(!("eastwest" %in% names(.))){mutate(eastwest = NA) %>% .} else{.}} %>%
+    {if(!("maturity" %in% names(.))){mutate(maturity = NA) %>% .} else{.}} %>%
+    {if(!("gearcode" %in% names(.))){mutate(gearcode = NA) %>% .} else{.}} %>%
     # reorder
-    transmute(fishery, trip, adfg, sample_date, spn, statarea, latitude, longitude,
-              eastwest, depth, soaktime, gearcode = ifelse("gearcode" %in% names(.), gearcode, NA), ring, mesh, biotwine_ok, spcode, sex, size, legal, shell, clutch, eggdev,
-              clutchcon, maturity = ifelse("maturity" %in% names(.), maturity, NA), parasite) -> out
+    transmute(fishery, trip, adfg, sample_date, spn, statarea, subdistrict, latitude, longitude,
+              eastwest, depth, soaktime, gearcode, ring, mesh, biotwine_ok, spcode, sex, size, legal, shell, clutch, eggdev,
+              clutchcon, maturity, parasite) -> out
   if(clean == T){
     # stock specific
     if(stock == "BBRKC"){
@@ -35,40 +39,66 @@ load_crab_dump <- function(path, stock, database_pull = F, clean = T) {
         # filter EI and QT fisheries in early 90s by stat areas e166
         filter(!(fishery %in% early_90s_tt & (statarea > 660000 | statarea < 0))) %>%
         # combine all tanner e166 fishery codes
-        mutate(fishery = ifelse(fishery %in% early_90s_tt, gsub("EI|QT", "TT", fishery), fishery)) %>%
+        mutate(fishery = ifelse(fishery %in% early_90s_tt, gsub("EI|QT", "TT", fishery), fishery),
+               fishery = paste0(substring(fishery, 1, 2), substring(crab_year, 3, 4))) %>%
         # fill in legal
         add_legal(., stock = stock) %>%
         # add regulatory group
         mutate(group = case_when(sex == 2 ~ "female",
                                  sex == 1 & legal == 0 ~ "sublegal_male",
-                                 sex == 1 & legal == 1 ~ "legal_male")) -> out
+                                 sex == 1 & legal == 1 ~ "legal_male"))  %>%
+        dyply::select(-subdistrict) -> out
     }
-    if(stock == "BSSC") {
+    if(stock %in% c("BSSC", "BSTC", "WBT", "EBT")) {
       ## fishery codes for early 90s tanner e166 fisheries
       early_90s_tt <- c("EI91", "EI92", paste0("QT", 93:96))
       ## data mgmt specific to bssc
       out %>%
         # fix transition to rationalization yr
         mutate(fishery = gsub("QO05r", "QO05", fishery),
                fishery = gsub("QO05o", "QO04", fishery),
-               # bbrkc test fish and cdq fisheries to TR
                fishery = gsub("CO|EO", "QO", fishery),
                # cdq rkc and bkc fisheries to PIBKC
                fishery = gsub("CK", "QP", fishery),
                # bbrkc test fish and cdq fisheries to TR
                fishery = gsub("XR|CR", "TR", fishery),
                fishery = ifelse((fishery %in% early_90s_tt) & (statarea > 660000 | statarea < 0), paste0("QT", substring(fishery, 3, 4)), fishery),
-               fishery = ifelse((fishery %in% early_90s_tt) & (statarea <= 660000 | statarea >= 0), paste0("TT", substring(fishery, 3, 4)), fishery)) %>%
+               fishery = ifelse((fishery %in% early_90s_tt) & (statarea <= 660000 | statarea >= 0), paste0("TT", substring(fishery, 3, 4)), fishery),
+               fishery = paste0(substring(fishery, 1, 2), substring(crab_year, 3, 4))) %>%
+        # fill in legal
+        add_legal(., stock = stock) %>%
+        # add regulatory group
+        mutate(group = case_when(sex == 2 ~ "female",
+                                 sex == 1 & legal == 0 ~ "sublegal_male",
+                                 sex == 1 & legal == 1 ~ "legal_male")) %>%
+        dyply::select(-subdistrict) -> out
+    }
+    if(stock %in% c("AIGKC", "EAG", "WAG")) {
+      ## data mgmt specific to gkc
+      out %>%
         # fill in legal
         add_legal(., stock = stock) %>%
         # add regulatory group
         mutate(group = case_when(sex == 2 ~ "female",
                                  sex == 1 & legal == 0 ~ "sublegal_male",
                                  sex == 1 & legal == 1 ~ "legal_male")) -> out
     }
+    if(stock == "EAG") {
+      out %>%
+        filter(subdistrict == "EAG") -> out
+    }
+    if(stock == "WAG") {
+      out %>%
+        filter(subdistrict == "WAG") -> out
+    }
+    if(stock == "PIGKC") {
+      out %>%
+        mutate(fishery = gsub("CO|EO", "QO", fishery)) %>%
+        dyply::select(-subdistrict) -> out
+    }
 
 
-    if(stock %in% c("BSTC", "WBT", "EBT", "AIGKC", "EAG", "WAG", "PIGKC", "SMBKC", "PIBKC", "PIRKC", "WAIRKC")){
+    if(stock %in% c("SMBKC", "PIBKC", "PIRKC", "WAIRKC")){
       stop(paste0("No method for ", stock, " yet !!"))
     }
 

R/load_dockside.R

@@ -21,18 +21,21 @@ load_dockside <- function(path, stock, database_pull = F, clean = T) {
   dock %>%
     # add crab year
     add_crab_year() %>%
+    {if(!("subdistrict" %in% names(.))){mutate(subdistrict = NA) %>% .} else{.}} %>%
     # reorder
-    transmute(crab_year, fishery, adfg, sample_date, spcode, size, legal, shell, numcrab) -> out
+    transmute(crab_year, fishery, adfg, sample_date, subdistrict, spcode, size, legal, shell, numcrab) -> out
 
   if(clean == T){
     # stock specific
     if(stock == "BBRKC"){
       out %>%
-        mutate(fishery = gsub("XR|CR", "TR", fishery)) %>%
-        filter(substring(fishery, 1, 2) == "TR") -> out
+        mutate(fishery = gsub("XR|CR", "TR", fishery),
+               fishery = paste0(substring(fishery, 1, 2), substring(crab_year, 3, 4))) %>%
+        filter(substring(fishery, 1, 2) == "TR") %>%
+        dyply::select(-subdistrict) -> out
     }
-    if(stock == "BSSC"){
-      early_90s_tt <- c("EI91", "EI92", paste0("QT", 93:96))
+    if(stock %in% c("BSSC", "BSTC", "EBT", "WBT")){
+      early_90s_tt <- c("EI89", "EI90", "EI91", "EI92", paste0("QT", 93:96))
       out %>%
         # fix transition to rationalization yr
         # cdq and eo fisheries to QO
@@ -44,11 +47,34 @@ load_dockside <- function(path, stock, database_pull = F, clean = T) {
                fishery = gsub("CO|EO", "QO", fishery),
                fishery = gsub("XR|CR", "TR", fishery),
                fishery = ifelse(fishery %in% early_90s_tt, paste0("QT", substring(fishery, 3, 4)), fishery),
-               fishery = ifelse(fishery %in% c("EO91", "EO92"), paste0(substring(fishery, 1, 2), as.numeric(substring(fishery, 3, 4))-1), fishery)) -> out
+               fishery = paste0(substring(fishery, 1, 2), substring(crab_year, 3, 4))) %>%
+        dyply::select(-subdistrict) -> out
+    }
+    if(stock %in% c("AIGKC", "EAG", "WAG")){
+      out %>%
+        # make XE fisheries EAG
+        mutate(subdistrict = ifelse(substring(fishery, 1, 2) == "XE", "EAG", subdistrict)) %>%
+        # fix subdistrict for OB08
+        mutate(subdistrict = case_when(crab_year != 2008 ~ subdistrict,
+                                       (crab_year == 2008 & adfg %in% c(35767, 37887)) ~ "WAG",
+                                       (crab_year == 2008 & adfg %in% c(103, 5992, 20556)) ~ "EAG",
+                                       (crab_year == 2008 & adfg == 5992 & sample_date > as_date("2008-12-1")) ~ "WAG")) -> out
+    }
+    if(stock == "EAG"){
+      out %>%
+        filter(subdistrict == "EAG") -> out
+    }
+    if(stock == "WAG"){
+      out %>%
+        filter(subdistrict == "WAG") -> out
+    }
+    if(stock %in% c("PIGKC")){
+      out %>%
+        dyply::select(-subdistrict) -> out
     }
 
 
-    if(stock %in% c("BSTC", "WBT", "EBT", "AIGKC", "EAG", "WAG", "PIGKC", "SMBKC", "PIBKC", "PIRKC", "WAIRKC")){
+    if(stock %in% c("SMBKC", "PIBKC", "PIRKC", "WAIRKC")){
       stop(paste0("No method for ", stock, " yet !!"))
     }
   }

R/load_pot_dump.R

@@ -23,10 +23,11 @@ load_pot_dump <- function(path, stock, database_pull = F, clean = T) {
     mutate(biotwine_ok = case_when(biotwine_ok == "-" ~ NA,
                                    biotwine_ok %in% c("n", "N") ~ "N",
                                    biotwine_ok %in% c("y", "Y") ~ "Y")) %>%
+    {if(!("subdistrict" %in% names(.))){mutate(subdistrict = NA) %>% .} else{.}} %>%
+    {if(!("eastwest" %in% names(.))){mutate(eastwest = NA) %>% .} else{.}} %>%
     rename(sample_date = sampdate) %>%
     # reorder
-    transmute(fishery, trip, adfg, sample_date, spn, statarea, latitude, longitude,
-              eastwest = ifelse("eastwest" %in% names(.), eastwest, NA), depth, soaktime, gearcode, ring, mesh, biotwine_ok, female, sublegal, tot_legal, msr_pot) -> out
+    transmute(fishery, trip, adfg, sample_date, spn, statarea, subdistrict, latitude, longitude, eastwest, depth, soaktime, gearcode, ring, mesh, biotwine_ok, female, sublegal, tot_legal, msr_pot) -> out
   if(clean == T){
     # stock specific
     if(stock == "BBRKC"){
@@ -38,9 +39,11 @@ load_pot_dump <- function(path, stock, database_pull = F, clean = T) {
         # filter EI and QT fisheries in early 90s by stat areas e166
         filter(!(fishery %in% early_90s_tt & (statarea > 660000 | statarea < 0))) %>%
         # combine all tanner e166 fishery codes
-        mutate(fishery = ifelse(fishery %in% early_90s_tt, gsub("EI|QT", "TT", fishery), fishery)) -> out
+        mutate(fishery = ifelse(fishery %in% early_90s_tt, gsub("EI|QT", "TT", fishery), fishery),
+               fishery = paste0(substring(fishery, 1, 2), substring(crab_year, 3, 4))) %>%
+        dyply::select(-subdistrict) -> out
     }
-    if(stock == "BSSC") {
+    if(stock %in% c("BSSC", "BSTC", "WBT", "EBT")) {
       ## fishery codes for early 90s tanner e166 fisheries
       early_90s_tt <- c("EI91", "EI92", paste0("QT", 93:96))
       ## data mgmt specific to bssc
@@ -55,11 +58,34 @@ load_pot_dump <- function(path, stock, database_pull = F, clean = T) {
                # bbrkc test fish and cdq fisheries to TR
                fishery = gsub("XR|CR", "TR", fishery),
                fishery = ifelse((fishery %in% early_90s_tt) & (statarea > 660000 | statarea < 0), paste0("QT", substring(fishery, 3, 4)), fishery),
-               fishery = ifelse((fishery %in% early_90s_tt) & (statarea <= 660000 | statarea >= 0), paste0("TT", substring(fishery, 3, 4)), fishery)) -> out
+               fishery = ifelse((fishery %in% early_90s_tt) & (statarea <= 660000 | statarea >= 0), paste0("TT", substring(fishery, 3, 4)), fishery),
+               fishery = paste0(substring(fishery, 1, 2), substring(crab_year, 3, 4))) %>%
+        dyply::select(-subdistrict) -> out
+    }
+    if(stock %in% c("AIGKC", "EAG", "WAG")) {
+      ## data mgmt specific to gkc
+      out %>%
+        clean_lat_lon() %>%
+        mutate(subdistrict = ifelse(fishery == "OB08" & longitude < -174, "WAG", subdistrict)) %>%
+        # remove pots without district info
+        filter(subdistrict != "-") -> out
+    }
+    if(stock == "EAG") {
+      out %>%
+        filter(subdistrict == "EAG") -> out
+    }
+    if(stock == "WAG") {
+      out %>%
+        filter(subdistrict == "WAG") -> out
+    }
+    if(stock == "PIGKC") {
+      out %>%
+        mutate(fishery = gsub("CO|EO", "QO", fishery)) %>%
+        dyply::select(-subdistrict) -> out
     }
 
 
-    if(stock %in% c("BSTC", "WBT", "EBT", "AIGKC", "EAG", "WAG", "PIGKC", "SMBKC", "PIBKC", "PIRKC", "WAIRKC")){
+    if(stock %in% c("SMBKC", "PIBKC", "PIRKC", "WAIRKC")){
       stop(paste0("No method for ", stock, " yet !!"))
     }