Merge remote-tracking branch 'origin/main'

DESCRIPTION

@@ -3,19 +3,13 @@ Package: nwfscDiscard
 Title: Northwest Fisheries Science Center
 Version: 2.0
 Date: 2018-04-13
-Authors@R: c(
-    person(
-      given = c("Chantel", "R."), 
-      family = "Wetzel", , 
-      email = "[email protected]", 
-      role = c("aut", "cre"),
-      comment = c(ORCID = "0000-0002-7573-8240")
-    )
-    )
-Description: Northwest Fisheries Science Center WCGOP data processing for use in
-  West Coast groundfish assessments. All scripts to process the available data are 
-  publicly available but the data are stored in a private location to maintain 
-  confidentiality. 
+Authors@R: 
+    person(c("Chantel", "R."), "Wetzel", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-7573-8240"))
+Description: Northwest Fisheries Science Center WCGOP data processing for
+    use in West Coast groundfish assessments. All scripts to process the
+    available data are publicly available but the data are stored in a
+    private location to maintain confidentiality.
 License: GPL (>=3)
 Depends:
     R (>= 4.2)

R/bootstrap_discard.R

@@ -110,7 +110,8 @@ boostrap_discard <- function(
   all_boot_data <- dplyr::left_join(
     y = boot_out,
     x = cf_data,
-    by = c("fleet", "year")) |>
+    by = c("fleet", "year")
+  ) |>
     dplyr::filter(n_vessels >= 3) |>
     data.frame()
 

R/calc_comps.R

@@ -49,7 +49,7 @@ calc_comps <- function(
     dplyr::ungroup() |>
     dplyr::filter(n_by_year != 0) |>
     dplyr::mutate(
-      prop_numbers = 100 * n/n_by_year,
+      prop_numbers = 100 * n / n_by_year,
       prop_weighted = 100 * weighted / w_by_year
     )
 
@@ -62,7 +62,7 @@ calc_comps <- function(
 
   comps_out_sexed <- comps_out_unsexed <- all_comps <- NULL
   out <- list()
-  if (any(comps[,"sex"] == "U")) {
+  if (any(comps[, "sex"] == "U")) {
     sub <- comps[comps$sex == "U", ]
     keep <- which(apply(sub[, 6:ncol(sub)], 1, sum) != 0)
     filter_comps <- sub[keep, ]
@@ -77,7 +77,8 @@ calc_comps <- function(
         vessels = length(unique(drvid)),
         ratio = fish / trips,
         nsamp = round(dplyr::case_when(
-          ratio < 44 ~ trips + 0.138 * fish, .default = 7.06 * hauls
+          ratio < 44 ~ trips + 0.138 * fish,
+          .default = 7.06 * hauls
         ), 0),
         fleet = paste0(unique(gear_groups), "-", unique(fleet_groups))
       ) |>
@@ -108,15 +109,17 @@ calc_comps <- function(
         vessels = length(unique(drvid)),
         ratio = fish / trips,
         nsamp = round(dplyr::case_when(
-          ratio < 44 ~ trips + 0.138 * fish, .default = 7.06 * hauls
+          ratio < 44 ~ trips + 0.138 * fish,
+          .default = 7.06 * hauls
         ), 0),
         fleet = paste0(unique(gear_groups), "-", unique(fleet_groups))
       ) |>
       data.frame()
 
-    comps_sexed <-  cbind(
+    comps_sexed <- cbind(
       comps[comps$sex == "F", 6:ncol(comps)],
-      comps[comps$sex == "M", 6:ncol(comps)])
+      comps[comps$sex == "M", 6:ncol(comps)]
+    )
     remove <- which(apply(comps_sexed, 1, sum) == 0)
     filter_comps <- comps_sexed[-remove, ]
 
@@ -134,7 +137,7 @@ calc_comps <- function(
   }
 
   if (comp_column == "age") {
-    if (!is.null(comps_out_unsexed)){
+    if (!is.null(comps_out_unsexed)) {
       comps_out_unsexed <- cbind(
         comps_out_unsexed[, 1:5],
         "age_error",
@@ -147,7 +150,7 @@ calc_comps <- function(
       colnames(comps_out_unsexed)[6:9] <- c("age_error", "age_low", "age_high", "input_n")
       out$unsexed <- comps_out_unsexed
     }
-    if (!is.null(comps_out_sexed)){
+    if (!is.null(comps_out_sexed)) {
       comps_out_sexed <- cbind(
         comps_out_sexed[, 1:5],
         "age_error",
@@ -171,24 +174,25 @@ calc_comps <- function(
       vessels = length(unique(drvid)),
       ratio = fish / trips,
       nsamp = round(dplyr::case_when(
-        ratio < 44 ~ trips + 0.138 * fish, .default = 7.06 * hauls
+        ratio < 44 ~ trips + 0.138 * fish,
+        .default = 7.06 * hauls
       ), 0)
     ) |>
     dplyr::select(-ratio) |>
     data.frame()
 
   if (!is.null(dir)) {
-    if (dim(sample_size)[1] > 0 ) {
+    if (dim(sample_size)[1] > 0) {
       write.csv(sample_size,
-                file = file.path(dir, paste0("biological_sample_sizes_", comp_column, ".csv")),
-                row.names = FALSE
+        file = file.path(dir, paste0("biological_sample_sizes_", comp_column, ".csv")),
+        row.names = FALSE
       )
     }
 
     if (!is.null(all_comps)) {
       write.csv(all_comps,
-                file = file.path(dir, paste0("biological_discard_", comp_column, "s.csv")),
-                row.names = FALSE
+        file = file.path(dir, paste0("biological_discard_", comp_column, "s.csv")),
+        row.names = FALSE
       )
     }
   }

R/get_biological_data.R

@@ -95,13 +95,16 @@ get_biological_data <- function(
     dplyr::mutate(
       exp1 = dplyr::case_when(
         !is.na(species_number) | !is.na(bio_specimen_count) ~ species_number / bio_specimen_count,
-        .default = 0),
+        .default = 0
+      ),
       exp_weight = dplyr::case_when(
         is.na(exp_sp_wt) ~ (species_weight / hooks_sampled) * total_hooks,
-        .default = exp_sp_wt),
+        .default = exp_sp_wt
+      ),
       exp2 = dplyr::case_when(
         !is.na(species_weight) ~ exp_weight / species_weight,
-        .default = 0),
+        .default = 0
+      ),
       wghtd_freq = frequency * exp1 * exp2
     )
 

R/run.R

@@ -26,9 +26,8 @@ run <- function(
     biological_data,
     em_catch_data = NULL,
     save_loc = NULL,
-    n_boot = 10000
-    ) {
-  if(!is.null(em_catch_data)) {
+    n_boot = 10000) {
+  if (!is.null(em_catch_data)) {
     do_em <- TRUE
   } else {
     do_em <- FALSE