Merge pull request #136 from pfmc-assessments/desgin_based

Desgin based

R/check_strata.R

@@ -74,7 +74,7 @@ check_strata <- function(
 
   if (!is.null(dir)) {
     write.csv(
-      x = out,
+      x = tows_by_strata,
       file = file.path(plotdir, "strata_observations.csv"),
       row.names = FALSE
     )

R/get_design_based.R

@@ -1,8 +1,9 @@
 #' Calculates design based estimates from survey data for West Coast surveys.
 #'
 #' @details
-#' The design based index is calculated based on the area of the strata and
-#' the mean catch by strata. This function returns a list of design-based
+#' The design based index is calculated based on the area of the strata with the
+#' output estimates representing the adjusted median estimates
+#' (e.g., est * exp(0.5*log(var)). This function returns a list of design-based
 #' estimates by strata and estimates combined across stratas by year. This
 #' function is designed to work with data frames pulled from the NWFSC
 #' data warehouse using [pull_catch()].
@@ -108,10 +109,7 @@ get_design_based <- function(
       mean_cpue = mean(cpue_mt_km2),
       var_cpue = var(cpue_mt_km2),
       est = area * mean_cpue,
-      var = var_cpue * (area * area) / ntows,
-      cv = sqrt(var_cpue) / (mean_cpue + 1e-09),
-      log_var = sqrt(log(cv^2 + 1)),
-      se = log(cv^2 + 1)
+      var = var_cpue * (area * area) / ntows
     ) |>
     dplyr::ungroup()
 
@@ -140,8 +138,8 @@ get_design_based <- function(
       year = biomass[, "year"],
       month = month,
       fleet = fleet,
-      est = est,
-      se_log = se_log
+      est = biomass[, "est"],
+      se_log = biomass[, "se_log"]
     )
     write.csv(
       biomass_out,

R/plot_index.R

@@ -19,7 +19,7 @@
 #'   2. Design based index by year and strata.
 #' @param width,height Numeric values for the figure width and height in
 #'   inches. The defaults are 7 by 7 inches.
-#' @param res The resolution to apply when saving figures.  Lower resolution values
+#' @param dpi The resolution to apply when saving figures.  Lower resolution values
 #'    can reduce file size which can be helpful when creating large documents
 #'    with many figures. The default is 300.
 #'
@@ -34,7 +34,7 @@ plot_index <- function(
     plot = 1:2,
     height = 7,
     width = 7,
-    res = 300) {
+    dpi = 300) {
 
   plotdir <- file.path(dir, "plots")
   check_dir(plotdir)
@@ -88,7 +88,7 @@ plot_index <- function(
     if (!is.null(dir)) {
       ggplot2::ggsave(
         filename = plot_names[1], plot = gg,
-        height = height, width = width, units = "in", res = res
+        height = height, width = width, units = "in", dpi = dpi
       )
     } else {
       print(gg)
@@ -117,7 +117,7 @@ plot_index <- function(
     if (!is.null(dir)) {
       ggplot2::ggsave(
         filename = plot_names[1], plot = g2,
-        height = height, width = width, units = "in", res = res
+        height = height, width = width, units = "in", dpi = dpi
       )
     } else {
       print(g2)