From 74aa50c3b47d2e9b7fb148a2a832f871ffda1dde Mon Sep 17 00:00:00 2001
From: Schiano-NOAA <samantha.schiano@noaa.gov>
Date: Fri, 15 Nov 2024 11:26:53 -0500
Subject: [PATCH] fix(bugs in fxns): minor adjustments to rec devs, SR, and SB
 plots

---
 R/plot_recruitment_deviations.R | 23 ++++++++++++++++++++--
 R/plot_spawn_recruitment.R      | 34 ++++++++++++++++-----------------
 R/plot_spawning_biomass.R       |  9 ++++++++-
 3 files changed, 46 insertions(+), 20 deletions(-)

diff --git a/R/plot_recruitment_deviations.R b/R/plot_recruitment_deviations.R
index 975c77b..fb30582 100644
--- a/R/plot_recruitment_deviations.R
+++ b/R/plot_recruitment_deviations.R
@@ -18,7 +18,7 @@ plot_recruitment_deviations <- function (
   } else {
     end_year <- end_year
   }
-  stryr <- min(as.numeric(dat$year), na.rm = TRUE)
+  start_year <- min(as.numeric(dat$year), na.rm = TRUE)
 
   rec_devs <- dat |>
     dplyr::filter(label == "recruitment_deviations" | label == "log_recruitment_deviations",
@@ -39,9 +39,22 @@ plot_recruitment_deviations <- function (
     stop("No recruitment deviations found in data.")
   }
 
+  # change plot breaks
+  x_n_breaks <- round(length(rec_devs[["year"]]) / 10)
+  if (x_n_breaks <= 5) {
+    x_n_breaks <- round(length(rec_devs[["year"]]) / 5)
+  } else if (x_n_breaks > 10) {
+   x_n_breaks <-  round(length(rec_devs[["year"]]) / 15)
+  }
+
   # Plot
   plt <- ggplot2::ggplot(data = rec_devs) +
-    ggplot2::geom_point(ggplot2::aes(x = year, y = estimate), shape = 1, size = 2.5) +
+    ggplot2::geom_point(
+      ggplot2::aes(
+        x = year,
+        y = estimate),
+      shape = 1,
+      size = 2.5) +
     # ggplot2::geom_pointrange(
     #   ggplot2::aes(
     #     x = year,
@@ -59,6 +72,12 @@ plot_recruitment_deviations <- function (
     ggplot2::labs(
       x = "Year",
       y = "Recruitment Deviations"
+      ) +
+    ggplot2::scale_x_continuous(
+      n.breaks = x_n_breaks,
+      guide = ggplot2::guide_axis(
+        minor.ticks = TRUE
       )
+    )
   suppressWarnings(add_theme(plt))
 }
diff --git a/R/plot_spawn_recruitment.R b/R/plot_spawn_recruitment.R
index 1d50de6..215b55b 100644
--- a/R/plot_spawn_recruitment.R
+++ b/R/plot_spawn_recruitment.R
@@ -13,16 +13,9 @@ plot_spawn_recruitment <- function(
     recruitment_label = "metric tons",
     end_year = NULL
 ) {
-  if (is.null(end_year)){
-    endyr <- max(rec$year)
-  } else {
-    endyr <- end_year
-  }
-  stryr <- min(rec$year)
-
-  # Extract spawning biomass
-  sb <- output |>
-    dplyr::filter(label == "spawning_biomass",
+  # Extract recruitment
+  rec <- dat |>
+    dplyr::filter(label == "recruitment",
                   module_name == "TIME_SERIES" | module_name == "t.series",
                   !is.na(year),
                   is.na(fleet) | length(unique(fleet)) <= 1,
@@ -33,12 +26,19 @@ plot_spawn_recruitment <- function(
     ) |> # SS3 and BAM target module names
     dplyr::mutate(estimate = as.numeric(estimate),
                   year = as.numeric(year)) |>
-    dplyr::rename(spawning_biomass = estimate) |>
+    dplyr::rename(recruitment = estimate) |>
     dplyr::select(-c(module_name, label))
 
-  # Extract recruitment
-  rec <- dat |>
-    dplyr::filter(label == "recruitment",
+  if (is.null(end_year)){
+    endyr <- max(rec$year)
+  } else {
+    endyr <- end_year
+  }
+  stryr <- min(rec$year)
+
+  # Extract spawning biomass
+  sb <- dat |>
+    dplyr::filter(label == "spawning_biomass",
                   module_name == "TIME_SERIES" | module_name == "t.series",
                   !is.na(year),
                   is.na(fleet) | length(unique(fleet)) <= 1,
@@ -49,7 +49,7 @@ plot_spawn_recruitment <- function(
     ) |> # SS3 and BAM target module names
     dplyr::mutate(estimate = as.numeric(estimate),
                   year = as.numeric(year)) |>
-    dplyr::rename(recruitment = estimate) |>
+    dplyr::rename(spawning_biomass = estimate) |>
     dplyr::select(-c(module_name, label))
 
   # merge DF
@@ -57,9 +57,9 @@ plot_spawn_recruitment <- function(
 
   # Plot
   plt <- ggplot2::ggplot(data = sr) +
-    ggplot2::geom_line(ggplot2::aes(x = spawning_biomass, y = recruitment/1000), linewidth = 1) +
+    ggplot2::geom_point(ggplot2::aes(x = spawning_biomass, y = recruitment/1000)) +
     ggplot2::labs(x = glue::glue("Spawning Biomass ({spawning_biomass_label})"),
                   y = glue::glue("Recruitment ({recruitment_label})")) +
     ggplot2::theme(legend.position = "none")
-  suppressWarnings(add_theme(sr_plt))
+  suppressWarnings(add_theme(plt))
 }
diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 1b3f74c..026a98f 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -21,7 +21,7 @@ plot_spawning_biomass <- function(
   dat,
   unit_label = "metric ton",
   scale_amount = 1,
-  ref_line = c("target", "unfished"),
+  ref_line = c("target", "unfished", "msy"),
   end_year = NULL,
   relative = FALSE,
   n_projected_years = 10
@@ -45,6 +45,8 @@ plot_spawning_biomass <- function(
   stopifnot(any(end_year >= all_years))
 
   # Select value for reference line and label
+  # TODO: add case if ref_line not indicated or hard to find - find one of the
+  # options and set as ref_line
   ref_line_val <- as.numeric(dat[
     grep(
       pattern = glue::glue("^spawning_biomass.*{tolower(ref_line)}"),
@@ -57,6 +59,11 @@ plot_spawning_biomass <- function(
       "The resulting reference value of `spawning_biomass_{ref_line}` was
       not found in `dat[[\"label\"]]`."
     ))
+  } else if (length(ref_line_val > 1)) {
+    warning(glue::glue(
+      "More than one of the resulting reference value of `spawning_biomass_{ref_line}` was
+      not in `dat[[\"label\"]]`."
+    ))
   }
   sb <- dat |>
     dplyr::filter(