From e912c0a6fa2603856bfbbfc1b8102fc2ed6facaa Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Tue, 21 Jul 2026 15:50:50 -0400
Subject: [PATCH 01/14] add note for where editing will occur

---
 R/plot_spawning_biomass.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 33a67fca..486a5d09 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -228,6 +228,7 @@ plot_spawning_biomass <- function(
         ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
         theme_noaa()
     } else {
+      # add apply/purrr/or for loop for reference lines -- not just the first anymore
       final <- reference_line(
         plot = plt,
         dat = rp_dat,

From c7acf3aa3113cf70dd97b5cbd2c8105ccbdc42d1 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Thu, 23 Jul 2026 17:09:11 -0400
Subject: [PATCH 02/14] update reference_line to use plus operator and remove
 calc ref point fron function; replace old ref line code with for loop for
 multiple lines

---
 R/plot_spawning_biomass.R | 85 +++++++++++++++++++++++++--------------
 R/utils_plot.R            | 69 ++++++++++++-------------------
 2 files changed, 80 insertions(+), 74 deletions(-)

diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 486a5d09..5c7e8af1 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -146,11 +146,11 @@ plot_spawning_biomass <- function(
     }
   )
   # Pull first df if in a list to find reference point
-  if (!is.data.frame(dat)) {
-    rp_dat <- dat[[1]]
-  } else {
-    rp_dat <- dat
-  }
+  # if (!is.data.frame(dat)) {
+  #   rp_dat <- dat[[1]]
+  # } else {
+  #   rp_dat <- dat
+  # }
 
   if (relative & scale_amount > 1) {
     cli::cli_alert_warning("Scale amount is not applicable when relative = TRUE. Resetting scale_amount to 1.")
@@ -206,38 +206,61 @@ plot_spawning_biomass <- function(
     ...
   )
   # Add reference line
+  # Conditions for ref line
+  # 1. all are comparing same value = msy, target, unfished...
+  # 2. custom input vector = c("sabe23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
+  # 3. input vector of labels = c("msy", "target")
   # getting data set - an ifelse statement in the fxn wasn't working
   if (relative) {
     # don't add any reference line here and just add theme for final plot
     final <- plt + theme_noaa()
   } else {
-    if ("unfished" %in% c(names(ref_line), ref_line)) {
-      # find the minimum x axis value from the plot
-      min_year <- min <- ggplot2::ggplot_build(plt)[["data"]][[2]] |>
-        as.data.frame() |>
-        dplyr::pull(x) |>
-        min() |>
-        round(digits = 2)
-      # find the reference point value for unfished
-      ref_point <- calculate_reference_point(
-        dat = rp_dat,
-        reference_name = "spawing_biomass_unfished"
-      ) / scale_amount
-      # add point to plot and add theme
-      final <- plt +
-        ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-        theme_noaa()
-    } else {
-      # add apply/purrr/or for loop for reference lines -- not just the first anymore
-      final <- reference_line(
-        plot = plt,
-        dat = rp_dat,
-        lbs = lbs,
-        label_name = "spawning_biomass",
-        reference = ref_line,
-        scale_amount = scale_amount
-      ) + theme_noaa()
+    plt2 <- plt
+    # Put into for loop and add lines sequentially to plt
+    for (i in 1:length(ref_line)) {
+      # find the reference point value
+      if (is.null(names(ref_line[i]))) {
+        ref_line_x <- calculate_reference_point(
+          dat = dat[[i]],
+          reference_name = i,
+          lbs = lbs
+        ) / scale_amount
+        ref_line_x <- setNames(ref_line_x, i)
+      } else {
+        ref_line_x <- ref_line[i] / scale_amount
+      }
+      
+        if ("unfished" %in% names(ref_line_x)) {
+        # find the minimum x axis value from the plot
+        min_year <- min <- ggplot2::ggplot_build(plt)[["data"]][[2]] |> # I think this was causing issues on linux
+          as.data.frame() |>
+          dplyr::pull(x) |>
+          min() |>
+          round(digits = 2)
+        # add point to plot and add theme
+        plt2 <- plt2 +
+          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
+          theme_noaa()
+      } else {
+        # add apply/purrr/or for loop for reference lines -- not just the first anymore
+        plt2 <- plt2 +
+          reference_line(
+            label_name = names(dat)[i], #"spawning_biomass",
+            ref_line = ref_line_x,
+            scale_amount = 1
+          )
+          
+        #   reference_line(
+        #   plot = plt,
+        #   dat = rp_dat,
+        #   lbs = lbs,
+        #   label_name = "spawning_biomass",
+        #   reference = ref_line,
+        #   scale_amount = scale_amount
+        # ) + theme_noaa()
+      }
     }
+    final <- plt2 + theme_noaa()
   }
 
   ### Make RDA ----
diff --git a/R/utils_plot.R b/R/utils_plot.R
index 44817291..458fc20c 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -529,11 +529,9 @@ cohort_line <- function(
 #' Preformatted reference line
 #'
 #' @inheritParams plot_spawning_biomass
-#' @param plot Plot object. A ggplot2 object where the reference line will be added
-#' @param dat Data frame. Standard data frame where reference point should be extracted
 #' @param label_name String. Name of the quantity that users want to
 #' extract the reference point from
-#' @param reference String of the reference point
+#' @param ref_line String of the reference point
 #'
 #' Options: Including, but not limited to: "msy", "unfished", "target"
 #'
@@ -546,49 +544,34 @@ cohort_line <- function(
 #' reference_line(dat, "biomass", "msy")
 #' }
 reference_line <- function(
-  plot,
-  dat,
   label_name,
-  reference,
-  scale_amount = 1,
-  lbs = FALSE
+  ref_line,
+  scale_amount = 1
 ) {
-  if (!is.null(names(reference))) {
-    ref_line_val <- reference[[1]]
-    reference <- names(reference)
-  } else {
-    # calculate reference point value
-    ref_line_val <- calculate_reference_point(
-      dat = dat,
-      reference_name = glue::glue("{label_name}_{reference}"),
-      lbs = lbs
-    )
-  }
+  # Extract reference line values and labels
+  ref_line_val <- ref_line[[1]]
+  reference <- names(ref_line)
 
-  # Add geom for ref line
-  if (is.null(ref_line_val)) {
-    plot
-  } else {
-    plot +
-      ggplot2::geom_hline(
-        # ggplot2::aes(
-        yintercept = ref_line_val / scale_amount,
-        # ),
-        color = "black",
-        linetype = "dashed"
-      ) +
-      ggplot2::annotate(
-        geom = "text",
-        # TODO: need to change this for general process
-        x = as.numeric(max(ggplot2::ggplot_build(plot)[["data"]][[2]][["x"]], na.rm = TRUE)), # - as.numeric(max(dat$year[dat$era == "time"], na.rm = TRUE))/200,
-        y = ref_line_val / scale_amount,
-        label = glue::glue("{stringr::str_replace_all(label_name, '_', '~')}[{reference}]"), # list(bquote(label_name[.(reference)])),
-        parse = TRUE,
-        hjust = 1,
-        vjust = 0,
-        size = 5 # this is not foolproof
-      )
-  }
+  list(
+    # Add geom for ref line
+    ggplot2::geom_hline(
+      yintercept = ref_line_val / scale_amount,
+      color = "black",
+      linetype = "dashed"
+    ),
+    # add line annotation
+    ggplot2::annotate(
+      geom = "text",
+      # TODO: need to change this for general process
+      x = Inf,
+      y = ref_line_val / scale_amount,
+      label = glue::glue("{stringr::str_replace_all(label_name, '_', '~')}[{reference}]"), # list(bquote(label_name[.(reference)])),
+      parse = TRUE,
+      hjust = 1.05, # slight offset so text doesn't hit border
+      vjust = -0.5, #slightly above line
+      size = 5 # this is not foolproof
+    )
+  )
 }
 
 #------------------------------------------------------------------------------

From 12348bc510eb2ab0bf0f6ddf4ba0d53babab3058 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 24 Jul 2026 10:15:27 -0400
Subject: [PATCH 03/14] add ifelse statement for single model ref line label

---
 R/plot_spawning_biomass.R | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 5c7e8af1..ed4084a0 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -245,19 +245,11 @@ plot_spawning_biomass <- function(
         # add apply/purrr/or for loop for reference lines -- not just the first anymore
         plt2 <- plt2 +
           reference_line(
-            label_name = names(dat)[i], #"spawning_biomass",
+            # conditionally add label name
+            label_name = ifelse(length(names(ref_line)) == 1, "spawning_biomass", names(dat)[i]), #"spawning_biomass",
             ref_line = ref_line_x,
             scale_amount = 1
           )
-          
-        #   reference_line(
-        #   plot = plt,
-        #   dat = rp_dat,
-        #   lbs = lbs,
-        #   label_name = "spawning_biomass",
-        #   reference = ref_line,
-        #   scale_amount = scale_amount
-        # ) + theme_noaa()
       }
     }
     final <- plt2 + theme_noaa()

From ed04eef040d649448a77c663dfce4fd93ff88aeb Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 24 Jul 2026 10:43:38 -0400
Subject: [PATCH 04/14] other adjustments to allow the use to make ref explicit
 or search for each model

---
 R/plot_spawning_biomass.R | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index ed4084a0..b5780df5 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -145,12 +145,6 @@ plot_spawning_biomass <- function(
       )
     }
   )
-  # Pull first df if in a list to find reference point
-  # if (!is.data.frame(dat)) {
-  #   rp_dat <- dat[[1]]
-  # } else {
-  #   rp_dat <- dat
-  # }
 
   if (relative & scale_amount > 1) {
     cli::cli_alert_warning("Scale amount is not applicable when relative = TRUE. Resetting scale_amount to 1.")
@@ -216,23 +210,26 @@ plot_spawning_biomass <- function(
     final <- plt + theme_noaa()
   } else {
     plt2 <- plt
+    # Check if length of ref_line = dat
+    # replicate value if not
+    if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
     # Put into for loop and add lines sequentially to plt
     for (i in 1:length(ref_line)) {
       # find the reference point value
       if (is.null(names(ref_line[i]))) {
         ref_line_x <- calculate_reference_point(
           dat = dat[[i]],
-          reference_name = i,
+          reference_name = glue::glue("spawning_biomass_{ref_line[i]}"),
           lbs = lbs
         ) / scale_amount
-        ref_line_x <- setNames(ref_line_x, i)
+        ref_line_x <- setNames(ref_line_x, ref_line[i])
       } else {
         ref_line_x <- ref_line[i] / scale_amount
       }
       
         if ("unfished" %in% names(ref_line_x)) {
         # find the minimum x axis value from the plot
-        min_year <- min <- ggplot2::ggplot_build(plt)[["data"]][[2]] |> # I think this was causing issues on linux
+        min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
           as.data.frame() |>
           dplyr::pull(x) |>
           min() |>

From 7b6170d9c58d3e82cd4b5e14d50c81073bf1e1f9 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 24 Jul 2026 11:11:02 -0400
Subject: [PATCH 05/14] update ref line fxn man

---
 man/reference_line.Rd | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/man/reference_line.Rd b/man/reference_line.Rd
index fbd71ec4..72ac2bd7 100644
--- a/man/reference_line.Rd
+++ b/man/reference_line.Rd
@@ -4,29 +4,19 @@
 \alias{reference_line}
 \title{Preformatted reference line}
 \usage{
-reference_line(plot, dat, label_name, reference, scale_amount = 1, lbs = FALSE)
+reference_line(label_name, ref_line, scale_amount = 1)
 }
 \arguments{
-\item{plot}{Plot object. A ggplot2 object where the reference line will be added}
-
-\item{dat}{Data frame. Standard data frame where reference point should be extracted}
-
 \item{label_name}{String. Name of the quantity that users want to
 extract the reference point from}
 
-\item{reference}{String of the reference point
+\item{ref_line}{String of the reference point
 
 Options: Including, but not limited to: "msy", "unfished", "target"}
 
 \item{scale_amount}{Number. A number to scale the y-axis values.
 
 Default: 1}
-
-\item{lbs}{Logical. TRUE/FALSE; indicate whether to convert the y-axis values from
-kilograms to pounds. The default units match the default in the
-unit_label argument - 'mt'.
-
-Default: `FALSE`}
 }
 \value{
 A ggplot2 geom_hline object for a reference point that can be added

From 711627cb59401d8605c14be867b75a6149f4d750 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 24 Jul 2026 11:33:52 -0400
Subject: [PATCH 06/14] make adjustment to reference lines for plot_biomass

---
 R/plot_biomass.R          | 69 +++++++++++++++++++++++++--------------
 R/plot_spawning_biomass.R |  2 +-
 2 files changed, 45 insertions(+), 26 deletions(-)

diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index 45dbf3f4..e12fddf4 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -141,37 +141,56 @@ plot_biomass <- function(
     ...
   )
   # Add reference line
+  # Conditions for ref line
+  # 1. all are comparing same value = msy, target, unfished...
+  # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
+  # 3. input vector of labels = c("msy", "target")
   # getting data set - an ifelse statement in the fxn wasn't working
   if (relative) {
     # don't add any reference line here and just add theme for final plot
     final <- plt + theme_noaa()
   } else {
-    if ("unfished" %in% c(names(ref_line), ref_line)) {
-      # find the minimum x axis value from the plot
-      min_year <- min <- ggplot2::ggplot_build(plt)[["data"]][[2]] |>
-        as.data.frame() |>
-        dplyr::pull(x) |>
-        min() |>
-        round(digits = 2)
-      # find the reference point value for unfished
-      ref_point <- calculate_reference_point(
-        dat = stockplotr::example_data,
-        reference_name = "biomass_unfished"
-      ) / scale_amount
-      # add point to plot and add theme
-      final <- plt +
-        ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-        theme_noaa()
-    } else {
-      final <- reference_line(
-        plot = plt,
-        dat = rp_dat,
-        label_name = "biomass",
-        reference = ref_line,
-        scale_amount = scale_amount
-      ) +
-        theme_noaa()
+    plt2 <- plt
+    # Check if length of ref_line = dat
+    # replicate value if not
+    if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
+    # Put into for loop and add lines sequentially to plt
+    for (i in 1:length(ref_line)) {
+      # find the reference point value
+      if (is.null(names(ref_line[i]))) {
+        ref_line_x <- calculate_reference_point(
+          dat = dat[[i]],
+          reference_name = glue::glue("biomass_{ref_line[i]}"),
+          lbs = lbs
+        ) / scale_amount
+        ref_line_x <- setNames(ref_line_x, ref_line[i])
+      } else {
+        ref_line_x <- ref_line[i] / scale_amount
+      }
+      
+      if ("unfished" %in% names(ref_line_x)) {
+        # find the minimum x axis value from the plot
+        min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
+          as.data.frame() |>
+          dplyr::pull(x) |>
+          min() |>
+          round(digits = 2)
+        # add point to plot and add theme
+        plt2 <- plt2 +
+          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
+          theme_noaa()
+      } else {
+        # add apply/purrr/or for loop for reference lines -- not just the first anymore
+        plt2 <- plt2 +
+          reference_line(
+            # conditionally add label name
+            label_name = ifelse(length(names(ref_line)) == 1, "biomass", names(dat)[i]), #"spawning_biomass",
+            ref_line = ref_line_x,
+            scale_amount = 1
+          )
+      }
     }
+    final <- plt2 + theme_noaa()
   }
 
   ### Make RDA ----
diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index b5780df5..187ca92e 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -202,7 +202,7 @@ plot_spawning_biomass <- function(
   # Add reference line
   # Conditions for ref line
   # 1. all are comparing same value = msy, target, unfished...
-  # 2. custom input vector = c("sabe23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
+  # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
   # 3. input vector of labels = c("msy", "target")
   # getting data set - an ifelse statement in the fxn wasn't working
   if (relative) {

From 98286c2238cc2b6ce2ca5b87975edc4374f11621 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Fri, 24 Jul 2026 11:36:41 -0400
Subject: [PATCH 07/14] add new ref line approach for plot F

---
 R/plot_fishing_mortality.R | 60 +++++++++++++++++++++++++++++++++-----
 1 file changed, 52 insertions(+), 8 deletions(-)

diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index 56b01401..aebda3ae 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -76,14 +76,58 @@ plot_fishing_mortality <- function(
     facet = facet,
     ...
   )
-  # Add reference line and theme
-  final <- reference_line(
-    plot = plt,
-    dat = dat,
-    label_name = "fishing_mortality",
-    reference = ref_line,
-    scale_amount = 1
-  ) + theme_noaa()
+  # Add reference line
+  # Conditions for ref line
+  # 1. all are comparing same value = msy, target, unfished...
+  # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
+  # 3. input vector of labels = c("msy", "target")
+  # getting data set - an ifelse statement in the fxn wasn't working
+  if (relative) {
+    # don't add any reference line here and just add theme for final plot
+    final <- plt + theme_noaa()
+  } else {
+    plt2 <- plt
+    # Check if length of ref_line = dat
+    # replicate value if not
+    if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
+    # Put into for loop and add lines sequentially to plt
+    for (i in 1:length(ref_line)) {
+      # find the reference point value
+      if (is.null(names(ref_line[i]))) {
+        ref_line_x <- calculate_reference_point(
+          dat = dat[[i]],
+          reference_name = glue::glue("fishing_mortality_{ref_line[i]}"),
+          lbs = lbs
+        ) / scale_amount
+        ref_line_x <- setNames(ref_line_x, ref_line[i])
+      } else {
+        ref_line_x <- ref_line[i] / scale_amount
+      }
+      
+      if ("unfished" %in% names(ref_line_x)) {
+        # find the minimum x axis value from the plot
+        min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
+          as.data.frame() |>
+          dplyr::pull(x) |>
+          min() |>
+          round(digits = 2)
+        # add point to plot and add theme
+        plt2 <- plt2 +
+          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
+          theme_noaa()
+      } else {
+        # add apply/purrr/or for loop for reference lines -- not just the first anymore
+        plt2 <- plt2 +
+          reference_line(
+            # conditionally add label name
+            label_name = ifelse(length(names(ref_line)) == 1, "fishing_mortality", names(dat)[i]), #"spawning_biomass",
+            ref_line = ref_line_x,
+            scale_amount = 1
+          )
+      }
+    }
+    final <- plt2 + theme_noaa()
+  }
 
   ### Make RDA ----
   if (make_rda) {

From 6cb15b456c5063486433928c08c79dd8700b760d Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Mon, 27 Jul 2026 16:24:50 -0400
Subject: [PATCH 08/14] move reference line code into own function for
 simplicity

---
 R/plot_biomass.R           | 76 +++++++++++++++++++-------------------
 R/plot_fishing_mortality.R | 76 +++++++++++++++++++-------------------
 R/plot_spawning_biomass.R  | 54 ++++++---------------------
 R/utils_plot.R             | 58 +++++++++++++++++++++++++++++
 4 files changed, 147 insertions(+), 117 deletions(-)

diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index e12fddf4..9652ac71 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -151,43 +151,45 @@ plot_biomass <- function(
     final <- plt + theme_noaa()
   } else {
     plt2 <- plt
-    # Check if length of ref_line = dat
-    # replicate value if not
-    if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
-    # Put into for loop and add lines sequentially to plt
-    for (i in 1:length(ref_line)) {
-      # find the reference point value
-      if (is.null(names(ref_line[i]))) {
-        ref_line_x <- calculate_reference_point(
-          dat = dat[[i]],
-          reference_name = glue::glue("biomass_{ref_line[i]}"),
-          lbs = lbs
-        ) / scale_amount
-        ref_line_x <- setNames(ref_line_x, ref_line[i])
-      } else {
-        ref_line_x <- ref_line[i] / scale_amount
-      }
-      
-      if ("unfished" %in% names(ref_line_x)) {
-        # find the minimum x axis value from the plot
-        min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
-          as.data.frame() |>
-          dplyr::pull(x) |>
-          min() |>
-          round(digits = 2)
-        # add point to plot and add theme
-        plt2 <- plt2 +
-          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-          theme_noaa()
-      } else {
-        # add apply/purrr/or for loop for reference lines -- not just the first anymore
-        plt2 <- plt2 +
-          reference_line(
-            # conditionally add label name
-            label_name = ifelse(length(names(ref_line)) == 1, "biomass", names(dat)[i]), #"spawning_biomass",
-            ref_line = ref_line_x,
-            scale_amount = 1
-          )
+    if (is.null(names(ref_line[i]))) {
+      # Check if length of ref_line = dat
+      # replicate value if not
+      if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
+      # Put into for loop and add lines sequentially to plt
+      for (i in 1:length(ref_line)) {
+        # find the reference point value
+        if (is.null(names(ref_line[i]))) {
+          ref_line_x <- calculate_reference_point(
+            dat = dat[[i]],
+            reference_name = glue::glue("biomass_{ref_line[i]}"),
+            lbs = lbs
+          ) / scale_amount
+          ref_line_x <- setNames(ref_line_x, ref_line[i])
+        } else {
+          ref_line_x <- ref_line[i] / scale_amount
+        }
+        
+        if ("unfished" %in% names(ref_line_x)) {
+          # find the minimum x axis value from the plot
+          min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
+            as.data.frame() |>
+            dplyr::pull(x) |>
+            min() |>
+            round(digits = 2)
+          # add point to plot and add theme
+          plt2 <- plt2 +
+            ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
+            theme_noaa()
+        } else {
+          # add apply/purrr/or for loop for reference lines -- not just the first anymore
+          plt2 <- plt2 +
+            reference_line(
+              # conditionally add label name
+              label_name = ifelse(length(names(ref_line)) == 1, "biomass", names(dat)[i]), #"spawning_biomass",
+              ref_line = ref_line_x,
+              scale_amount = 1
+            )
+        }
       }
     }
     final <- plt2 + theme_noaa()
diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index aebda3ae..82668e5c 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -87,43 +87,45 @@ plot_fishing_mortality <- function(
     final <- plt + theme_noaa()
   } else {
     plt2 <- plt
-    # Check if length of ref_line = dat
-    # replicate value if not
-    if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
-    # Put into for loop and add lines sequentially to plt
-    for (i in 1:length(ref_line)) {
-      # find the reference point value
-      if (is.null(names(ref_line[i]))) {
-        ref_line_x <- calculate_reference_point(
-          dat = dat[[i]],
-          reference_name = glue::glue("fishing_mortality_{ref_line[i]}"),
-          lbs = lbs
-        ) / scale_amount
-        ref_line_x <- setNames(ref_line_x, ref_line[i])
-      } else {
-        ref_line_x <- ref_line[i] / scale_amount
-      }
-      
-      if ("unfished" %in% names(ref_line_x)) {
-        # find the minimum x axis value from the plot
-        min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
-          as.data.frame() |>
-          dplyr::pull(x) |>
-          min() |>
-          round(digits = 2)
-        # add point to plot and add theme
-        plt2 <- plt2 +
-          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-          theme_noaa()
-      } else {
-        # add apply/purrr/or for loop for reference lines -- not just the first anymore
-        plt2 <- plt2 +
-          reference_line(
-            # conditionally add label name
-            label_name = ifelse(length(names(ref_line)) == 1, "fishing_mortality", names(dat)[i]), #"spawning_biomass",
-            ref_line = ref_line_x,
-            scale_amount = 1
-          )
+    if (is.null(names(ref_line[i]))) {
+      # Check if length of ref_line = dat
+      # replicate value if not
+      if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
+      # Put into for loop and add lines sequentially to plt
+      for (i in 1:length(ref_line)) {
+        # find the reference point value
+        if (is.null(names(ref_line[i]))) {
+          ref_line_x <- calculate_reference_point(
+            dat = dat[[i]],
+            reference_name = glue::glue("fishing_mortality_{ref_line[i]}"),
+            lbs = lbs
+          ) / scale_amount
+          ref_line_x <- setNames(ref_line_x, ref_line[i])
+        } else {
+          ref_line_x <- ref_line[i] / scale_amount
+        }
+        
+        if ("unfished" %in% names(ref_line_x)) {
+          # find the minimum x axis value from the plot
+          min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
+            as.data.frame() |>
+            dplyr::pull(x) |>
+            min() |>
+            round(digits = 2)
+          # add point to plot and add theme
+          plt2 <- plt2 +
+            ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
+            theme_noaa()
+        } else {
+          # add apply/purrr/or for loop for reference lines -- not just the first anymore
+          plt2 <- plt2 +
+            reference_line(
+              # conditionally add label name
+              label_name = ifelse(length(names(ref_line)) == 1, "fishing_mortality", names(dat)[i]), #"spawning_biomass",
+              ref_line = ref_line_x,
+              scale_amount = 1
+            )
+        }
       }
     }
     final <- plt2 + theme_noaa()
diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 187ca92e..2338fe6b 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -196,8 +196,8 @@ plot_spawning_biomass <- function(
     ylab = spawning_biomass_label,
     group = group,
     # add check in case facet is returned as character(0)
-    facet = if (length(facet) > 0) facet else NULL,
-    ...
+    facet = if (length(facet) > 0) facet else NULL#,
+    # ...
   )
   # Add reference line
   # Conditions for ref line
@@ -209,47 +209,15 @@ plot_spawning_biomass <- function(
     # don't add any reference line here and just add theme for final plot
     final <- plt + theme_noaa()
   } else {
-    plt2 <- plt
-    # Check if length of ref_line = dat
-    # replicate value if not
-    if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
-    # Put into for loop and add lines sequentially to plt
-    for (i in 1:length(ref_line)) {
-      # find the reference point value
-      if (is.null(names(ref_line[i]))) {
-        ref_line_x <- calculate_reference_point(
-          dat = dat[[i]],
-          reference_name = glue::glue("spawning_biomass_{ref_line[i]}"),
-          lbs = lbs
-        ) / scale_amount
-        ref_line_x <- setNames(ref_line_x, ref_line[i])
-      } else {
-        ref_line_x <- ref_line[i] / scale_amount
-      }
-      
-        if ("unfished" %in% names(ref_line_x)) {
-        # find the minimum x axis value from the plot
-        min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
-          as.data.frame() |>
-          dplyr::pull(x) |>
-          min() |>
-          round(digits = 2)
-        # add point to plot and add theme
-        plt2 <- plt2 +
-          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-          theme_noaa()
-      } else {
-        # add apply/purrr/or for loop for reference lines -- not just the first anymore
-        plt2 <- plt2 +
-          reference_line(
-            # conditionally add label name
-            label_name = ifelse(length(names(ref_line)) == 1, "spawning_biomass", names(dat)[i]), #"spawning_biomass",
-            ref_line = ref_line_x,
-            scale_amount = 1
-          )
-      }
-    }
-    final <- plt2 + theme_noaa()
+    final <- plt + 
+      add_reference_line(
+        dat = dat, 
+        ref_line = ref_line, 
+        label = "spawning_biomass", 
+        lbs = lbs,
+        scale_amount = scale_amount
+      ) + 
+      theme_noaa()
   }
 
   ### Make RDA ----
diff --git a/R/utils_plot.R b/R/utils_plot.R
index 458fc20c..d107848b 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -1045,3 +1045,61 @@ plot_obsvpred <- function(
   }
   final
 }
+
+#------------------------------------------------------------------------------
+
+add_reference_line <- function(
+    dat,
+    ref_line,
+    label,
+    lbs = FALSE,
+    scale_amount = 1
+) {
+  ref_lines_list <- list()
+  if (!is.null(ref_line)) {
+    # Check if length of ref_line = dat
+    # replicate value if not
+    if (!is.data.frame(dat) & length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
+    # Put into for loop and add lines sequentially to plt
+    for (i in 1:length(ref_line)) {
+      # find the reference point value
+      if (is.null(names(ref_line[i]))) {
+        ref_line_x <- calculate_reference_point(
+          dat = if (is.data.frame(dat)) { dat } else { dat[[i]] },
+          reference_name = glue::glue("{label}_{ref_line[i]}"),
+          lbs = lbs
+        ) / scale_amount
+        ref_line_x <- setNames(ref_line_x, ref_line[i])
+      } else {
+        ref_line_x <- ref_line[i] / scale_amount
+      }
+      
+      if ("unfished" %in% names(ref_line_x)) {
+        # find the minimum x axis value from the plot
+        min_year <- dat |> 
+          dplyr::filter(grepl(label, label)) |>
+          dplyr::pull(estimate) |>
+          min() |>
+          round(digits = 2)
+        # add point to plot and add theme
+        # plt2 <- plt2 +
+        ref_lines_list <- append(ref_lines_list,
+          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
+            theme_noaa()
+        )
+      } else {
+        # add apply/purrr/or for loop for reference lines -- not just the first anymore
+        # plt2 <- plt2 +
+        ref_lines_list <- append(ref_lines_list,
+          reference_line(
+            # conditionally add label name
+            label_name = ifelse(length(names(dat)[i]) == 1, "spawning_biomass", names(dat)[i]), #"spawning_biomass",
+            ref_line = ref_line_x,
+            scale_amount = scale_amount
+          )
+        )
+      }
+    } # close ref_line for loop
+  } # close if ref_line NULL
+  ref_lines_list
+}

From b47e247eab9a321ccce60b65095c19340e445bf0 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Mon, 27 Jul 2026 16:31:33 -0400
Subject: [PATCH 09/14] add new ref line function into other relevant fxns and
 replace code

---
 R/plot_biomass.R           | 57 ++++++--------------------------------
 R/plot_fishing_mortality.R | 52 ++++++----------------------------
 R/plot_spawning_biomass.R  |  5 ----
 R/utils_plot.R             |  6 ++++
 4 files changed, 24 insertions(+), 96 deletions(-)

diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index 9652ac71..5c7bcd01 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -141,58 +141,19 @@ plot_biomass <- function(
     ...
   )
   # Add reference line
-  # Conditions for ref line
-  # 1. all are comparing same value = msy, target, unfished...
-  # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
-  # 3. input vector of labels = c("msy", "target")
-  # getting data set - an ifelse statement in the fxn wasn't working
   if (relative) {
     # don't add any reference line here and just add theme for final plot
     final <- plt + theme_noaa()
   } else {
-    plt2 <- plt
-    if (is.null(names(ref_line[i]))) {
-      # Check if length of ref_line = dat
-      # replicate value if not
-      if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
-      # Put into for loop and add lines sequentially to plt
-      for (i in 1:length(ref_line)) {
-        # find the reference point value
-        if (is.null(names(ref_line[i]))) {
-          ref_line_x <- calculate_reference_point(
-            dat = dat[[i]],
-            reference_name = glue::glue("biomass_{ref_line[i]}"),
-            lbs = lbs
-          ) / scale_amount
-          ref_line_x <- setNames(ref_line_x, ref_line[i])
-        } else {
-          ref_line_x <- ref_line[i] / scale_amount
-        }
-        
-        if ("unfished" %in% names(ref_line_x)) {
-          # find the minimum x axis value from the plot
-          min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
-            as.data.frame() |>
-            dplyr::pull(x) |>
-            min() |>
-            round(digits = 2)
-          # add point to plot and add theme
-          plt2 <- plt2 +
-            ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-            theme_noaa()
-        } else {
-          # add apply/purrr/or for loop for reference lines -- not just the first anymore
-          plt2 <- plt2 +
-            reference_line(
-              # conditionally add label name
-              label_name = ifelse(length(names(ref_line)) == 1, "biomass", names(dat)[i]), #"spawning_biomass",
-              ref_line = ref_line_x,
-              scale_amount = 1
-            )
-        }
-      }
-    }
-    final <- plt2 + theme_noaa()
+    final <- plt +
+      add_reference_line(
+        dat = dat, 
+        ref_line = ref_line, 
+        label = "biomass", 
+        lbs = lbs,
+        scale_amount = scale_amount
+      ) +
+      theme_noaa()
   }
 
   ### Make RDA ----
diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index 82668e5c..2161f486 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -86,49 +86,15 @@ plot_fishing_mortality <- function(
     # don't add any reference line here and just add theme for final plot
     final <- plt + theme_noaa()
   } else {
-    plt2 <- plt
-    if (is.null(names(ref_line[i]))) {
-      # Check if length of ref_line = dat
-      # replicate value if not
-      if (length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
-      # Put into for loop and add lines sequentially to plt
-      for (i in 1:length(ref_line)) {
-        # find the reference point value
-        if (is.null(names(ref_line[i]))) {
-          ref_line_x <- calculate_reference_point(
-            dat = dat[[i]],
-            reference_name = glue::glue("fishing_mortality_{ref_line[i]}"),
-            lbs = lbs
-          ) / scale_amount
-          ref_line_x <- setNames(ref_line_x, ref_line[i])
-        } else {
-          ref_line_x <- ref_line[i] / scale_amount
-        }
-        
-        if ("unfished" %in% names(ref_line_x)) {
-          # find the minimum x axis value from the plot
-          min_year <- min <- ggplot2::ggplot_build(plt2)[["data"]][[2]] |> # I think this was causing issues on linux?
-            as.data.frame() |>
-            dplyr::pull(x) |>
-            min() |>
-            round(digits = 2)
-          # add point to plot and add theme
-          plt2 <- plt2 +
-            ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-            theme_noaa()
-        } else {
-          # add apply/purrr/or for loop for reference lines -- not just the first anymore
-          plt2 <- plt2 +
-            reference_line(
-              # conditionally add label name
-              label_name = ifelse(length(names(ref_line)) == 1, "fishing_mortality", names(dat)[i]), #"spawning_biomass",
-              ref_line = ref_line_x,
-              scale_amount = 1
-            )
-        }
-      }
-    }
-    final <- plt2 + theme_noaa()
+    final <- plt +
+      add_reference_line(
+        dat = dat, 
+        ref_line = ref_line, 
+        label = "fishing_mortality", 
+        lbs = lbs,
+        scale_amount = scale_amount
+      ) +
+      theme_noaa()
   }
 
   ### Make RDA ----
diff --git a/R/plot_spawning_biomass.R b/R/plot_spawning_biomass.R
index 2338fe6b..cc12c70c 100644
--- a/R/plot_spawning_biomass.R
+++ b/R/plot_spawning_biomass.R
@@ -200,11 +200,6 @@ plot_spawning_biomass <- function(
     # ...
   )
   # Add reference line
-  # Conditions for ref line
-  # 1. all are comparing same value = msy, target, unfished...
-  # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
-  # 3. input vector of labels = c("msy", "target")
-  # getting data set - an ifelse statement in the fxn wasn't working
   if (relative) {
     # don't add any reference line here and just add theme for final plot
     final <- plt + theme_noaa()
diff --git a/R/utils_plot.R b/R/utils_plot.R
index d107848b..6e406db8 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -1055,6 +1055,12 @@ add_reference_line <- function(
     lbs = FALSE,
     scale_amount = 1
 ) {
+  # Add reference line
+  # Conditions for ref line
+  # 1. all are comparing same value = msy, target, unfished...
+  # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
+  # 3. input vector of labels = c("msy", "target")
+  # getting data set - an ifelse statement in the fxn wasn't working
   ref_lines_list <- list()
   if (!is.null(ref_line)) {
     # Check if length of ref_line = dat

From 1ac2b748afe5f031b74dd975403ab6daabe2e817 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Tue, 28 Jul 2026 17:40:58 -0400
Subject: [PATCH 10/14] remove lbs from B and F plots in ref line; consolidate
 note in utils

---
 R/plot_biomass.R           |  3 +--
 R/plot_fishing_mortality.R | 11 ++---------
 R/utils_plot.R             | 26 +++++++++++++++++---------
 3 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/R/plot_biomass.R b/R/plot_biomass.R
index 5c7bcd01..725d3a36 100644
--- a/R/plot_biomass.R
+++ b/R/plot_biomass.R
@@ -149,8 +149,7 @@ plot_biomass <- function(
       add_reference_line(
         dat = dat, 
         ref_line = ref_line, 
-        label = "biomass", 
-        lbs = lbs,
+        label = "biomass",
         scale_amount = scale_amount
       ) +
       theme_noaa()
diff --git a/R/plot_fishing_mortality.R b/R/plot_fishing_mortality.R
index 2161f486..93b73e1f 100644
--- a/R/plot_fishing_mortality.R
+++ b/R/plot_fishing_mortality.R
@@ -82,20 +82,13 @@ plot_fishing_mortality <- function(
   # 2. custom input vector = c("sable23_msy"=30, "sable25_msy"=40) -- user must indicate which model in label otherwise it will assign in order of dat
   # 3. input vector of labels = c("msy", "target")
   # getting data set - an ifelse statement in the fxn wasn't working
-  if (relative) {
-    # don't add any reference line here and just add theme for final plot
-    final <- plt + theme_noaa()
-  } else {
-    final <- plt +
+  final <- plt +
       add_reference_line(
         dat = dat, 
         ref_line = ref_line, 
-        label = "fishing_mortality", 
-        lbs = lbs,
-        scale_amount = scale_amount
+        label = "fishing_mortality"
       ) +
       theme_noaa()
-  }
 
   ### Make RDA ----
   if (make_rda) {
diff --git a/R/utils_plot.R b/R/utils_plot.R
index 6e406db8..360f0dc3 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -1063,8 +1063,7 @@ add_reference_line <- function(
   # getting data set - an ifelse statement in the fxn wasn't working
   ref_lines_list <- list()
   if (!is.null(ref_line)) {
-    # Check if length of ref_line = dat
-    # replicate value if not
+    # Check if length of ref_line = dat -- replicate value if not
     if (!is.data.frame(dat) & length(ref_line) != length(dat)) ref_line <- rep(ref_line, length(dat))
     # Put into for loop and add lines sequentially to plt
     for (i in 1:length(ref_line)) {
@@ -1075,23 +1074,32 @@ add_reference_line <- function(
           reference_name = glue::glue("{label}_{ref_line[i]}"),
           lbs = lbs
         ) / scale_amount
+        if (length(ref_line_x) == 0) {
+          cli::cli_alert_warning("{label}_{ref_line[i]} not found for {ifelse(is.data.frame(dat), 'data', names(dat[i]))}")
+          next
+        }
         ref_line_x <- setNames(ref_line_x, ref_line[i])
       } else {
         ref_line_x <- ref_line[i] / scale_amount
       }
       
       if ("unfished" %in% names(ref_line_x)) {
+        if (is.data.frame(dat)) {
+          sel_dat <- dat
+        } else {
+          sel_dat <- dat[[i]]
+        }
+        plt_lab <- label
         # find the minimum x axis value from the plot
-        min_year <- dat |> 
-          dplyr::filter(grepl(label, label)) |>
-          dplyr::pull(estimate) |>
-          min() |>
+        min_year <- sel_dat |> 
+          dplyr::filter(grepl(plt_lab, label), year != 1) |>
+          dplyr::pull(year) |>
+          min(na.rm = TRUE) |>
           round(digits = 2)
         # add point to plot and add theme
         # plt2 <- plt2 +
         ref_lines_list <- append(ref_lines_list,
-          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_point)) + # should I keep -1 or set as first year?
-            theme_noaa()
+          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_line_x)) # should I keep -1 or set as first year?
         )
       } else {
         # add apply/purrr/or for loop for reference lines -- not just the first anymore
@@ -1099,7 +1107,7 @@ add_reference_line <- function(
         ref_lines_list <- append(ref_lines_list,
           reference_line(
             # conditionally add label name
-            label_name = ifelse(length(names(dat)[i]) == 1, "spawning_biomass", names(dat)[i]), #"spawning_biomass",
+            label_name = ifelse(length(names(dat)[i]) == 1, label, names(dat)[i]), #"spawning_biomass",
             ref_line = ref_line_x,
             scale_amount = scale_amount
           )

From 222f420754241228cb625647bd3f1b839ea61b1f Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Tue, 28 Jul 2026 17:49:15 -0400
Subject: [PATCH 11/14] add todo to adjust color of unfished ref pt

---
 R/utils_plot.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/utils_plot.R b/R/utils_plot.R
index 360f0dc3..d7b60615 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -1098,6 +1098,7 @@ add_reference_line <- function(
           round(digits = 2)
         # add point to plot and add theme
         # plt2 <- plt2 +
+        # TODO: set color for each point to match that of the line for the model
         ref_lines_list <- append(ref_lines_list,
           ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_line_x)) # should I keep -1 or set as first year?
         )

From 1f44495b98328af4b1b6a190e44662015354cf7f Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Wed, 29 Jul 2026 10:29:00 -0400
Subject: [PATCH 12/14] add missing pkg dependencies from used functions

---
 R/utils_plot.R | 2 +-
 R/utils_rda.R  | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/utils_plot.R b/R/utils_plot.R
index d7b60615..9defe9d8 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -1078,7 +1078,7 @@ add_reference_line <- function(
           cli::cli_alert_warning("{label}_{ref_line[i]} not found for {ifelse(is.data.frame(dat), 'data', names(dat[i]))}")
           next
         }
-        ref_line_x <- setNames(ref_line_x, ref_line[i])
+        ref_line_x <- utils::setNames(ref_line_x, ref_line[i])
       } else {
         ref_line_x <- ref_line[i] / scale_amount
       }
diff --git a/R/utils_rda.R b/R/utils_rda.R
index a5b84d2c..27721710 100644
--- a/R/utils_rda.R
+++ b/R/utils_rda.R
@@ -177,7 +177,7 @@ calc_kqs <- function(returned_kq,
   if (returned_kq == "F.min") {
     return(
       prepared_data$estimate |>
-        na.omit() |>
+        data.table::na.omit() |>
         min() |>
         round(digits = 3)
     )
@@ -186,7 +186,7 @@ calc_kqs <- function(returned_kq,
   if (returned_kq == "F.max") {
     return(
       prepared_data$estimate |>
-        na.omit() |>
+        data.table::na.omit() |>
         max() |>
         round(digits = 3)
     )

From 0ba22c43bfa44c48b905f8b30533a1b228ccd235 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Wed, 29 Jul 2026 16:31:57 -0400
Subject: [PATCH 13/14] set legends to show under certain conditions for
 elements of line plot and ref line

---
 R/utils_plot.R | 64 ++++++++++++++++++--------------------------------
 1 file changed, 23 insertions(+), 41 deletions(-)

diff --git a/R/utils_plot.R b/R/utils_plot.R
index 9defe9d8..bf9a14da 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -71,30 +71,19 @@ plot_timeseries <- function(
 ) {
   # Start plot
   plot <- ggplot2::ggplot()
-  # make into new geom?
-  # more defaults and fxnality for ggplot
 
   # Add geom
   plot <- switch(geom,
     "point" = {
-      # point_size = ifelse(
-      #   is.null(list(...)$size),
-      #   2.0,
-      #   list(...)$size
-      # )
       plot +
         ggplot2::geom_point(
           data = dat,
           ggplot2::aes(
             .data[[x]],
             .data[[y]],
-            # TODO: add more groupings
-            # shape = ifelse(any(grepl("shape", names(group))), .data[[group[[grep("shape", names(group))]]]], 1),
-            # color = ifelse(any(grepl("color", names(group))), .data[[group[[grep("color", names(group))]]]], "black")
             color = model,
             shape = group_var
           ),
-          # size = point_size,
           ...
         )
     },
@@ -119,7 +108,8 @@ plot_timeseries <- function(
               }
             }
           ),
-          alpha = 0.3
+          alpha = 0.3,
+          show.legend = ifelse(all(is.na(dat$estimate_lower)), FALSE, TRUE)
         ) +
         # }
         ggplot2::geom_line(
@@ -127,8 +117,6 @@ plot_timeseries <- function(
           ggplot2::aes(
             x = .data[[x]],
             y = .data[[y]],
-            # linetype = group_var,
-            # linetype = ifelse(!is.null(group), group_var, "solid"),
             color = {
               if (length(unique(.data[["model"]])) > 1) {
                 interaction(model, group_var)
@@ -137,7 +125,7 @@ plot_timeseries <- function(
               }
             }
           ),
-          # linewidth = 1.0,
+          show.legend = FALSE, #ifelse(all(is.na(dat$estimate_lower)), TRUE, FALSE),
           ...
         )
     },
@@ -148,7 +136,7 @@ plot_timeseries <- function(
           ggplot2::aes(
             x = .data[[x]],
             y = .data[[y]],
-            fill = model
+            fill = interaction(model, group_var) # model
           ),
           ...
         )
@@ -160,10 +148,6 @@ plot_timeseries <- function(
     labs <- plot + ggplot2::labs(
       x = xlab,
       y = ylab
-      # color = "Model",
-      # linetype = cap_first_letter(group),
-      # fill = cap_first_letter(group),
-      # shape = cap_first_letter(group)
     ) +
       ggplot2::theme(legend.title = ggplot2::element_blank())
   } else {
@@ -195,15 +179,7 @@ plot_timeseries <- function(
       # return plot if option beyond line and point for now
       labs
     )
-  } # else if (length(unique(dat$model)) == 1) {
-  #   labs <- switch(geom,
-  #     "line" = labs + ggplot2::guides(color = "none"),
-  #     "point" = labs + ggplot2::guides(color = "none"),
-  #     "area" = labs + ggplot2::guides(fill = "none"),
-  #     # return plot if option beyond line and point for now
-  #     labs
-  #   )
-  # }
+  }
 
   # Calc axis breaks
   x_n_breaks <- axis_breaks(dat[[x]])
@@ -546,7 +522,8 @@ cohort_line <- function(
 reference_line <- function(
   label_name,
   ref_line,
-  scale_amount = 1
+  scale_amount = 1,
+  model_name = "1"
 ) {
   # Extract reference line values and labels
   ref_line_val <- ref_line[[1]]
@@ -555,21 +532,25 @@ reference_line <- function(
   list(
     # Add geom for ref line
     ggplot2::geom_hline(
-      yintercept = ref_line_val / scale_amount,
-      color = "black",
-      linetype = "dashed"
+      data = data.frame(yintercept = ref_line_val, model = model_name, group_var = "1"),
+      ggplot2::aes(
+        yintercept = ref_line_val / scale_amount,
+        color = interaction(model, group_var) # model
+      ),
+      linetype = "dashed",
+      show.legend = FALSE
     ),
     # add line annotation
     ggplot2::annotate(
       geom = "text",
       # TODO: need to change this for general process
-      x = Inf,
+      x = -Inf,
       y = ref_line_val / scale_amount,
-      label = glue::glue("{stringr::str_replace_all(label_name, '_', '~')}[{reference}]"), # list(bquote(label_name[.(reference)])),
+      label = glue::glue("{reference}"), # glue::glue("{stringr::str_replace_all(label_name, '_', '~')}[{reference}]"), # list(bquote(label_name[.(reference)])),
       parse = TRUE,
-      hjust = 1.05, # slight offset so text doesn't hit border
-      vjust = -0.5, #slightly above line
-      size = 5 # this is not foolproof
+      hjust = -0.05, # slight offset so text doesn't hit border
+      vjust = -0.5 # , #slightly above line
+      # size = 5 # this is not foolproof
     )
   )
 }
@@ -1078,7 +1059,7 @@ add_reference_line <- function(
           cli::cli_alert_warning("{label}_{ref_line[i]} not found for {ifelse(is.data.frame(dat), 'data', names(dat[i]))}")
           next
         }
-        ref_line_x <- utils::setNames(ref_line_x, ref_line[i])
+        ref_line_x <- stats::setNames(ref_line_x, ref_line[i])
       } else {
         ref_line_x <- ref_line[i] / scale_amount
       }
@@ -1100,7 +1081,7 @@ add_reference_line <- function(
         # plt2 <- plt2 +
         # TODO: set color for each point to match that of the line for the model
         ref_lines_list <- append(ref_lines_list,
-          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_line_x)) # should I keep -1 or set as first year?
+          ggplot2::geom_point(ggplot2::aes(x = min_year - 1, y = ref_line_x, color = model)) # should I keep -1 or set as first year?
         )
       } else {
         # add apply/purrr/or for loop for reference lines -- not just the first anymore
@@ -1110,7 +1091,8 @@ add_reference_line <- function(
             # conditionally add label name
             label_name = ifelse(length(names(dat)[i]) == 1, label, names(dat)[i]), #"spawning_biomass",
             ref_line = ref_line_x,
-            scale_amount = scale_amount
+            scale_amount = scale_amount,
+            model_name = ifelse(is.data.frame(dat), "1", names(dat)[i])
           )
         )
       }

From 64b6e7b21f392f5ec71949736b89d39534730936 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Thu, 30 Jul 2026 10:18:58 -0400
Subject: [PATCH 14/14] comment out conditional removal of legend

---
 R/utils_plot.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/utils_plot.R b/R/utils_plot.R
index bf9a14da..eeaffbd1 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -108,8 +108,8 @@ plot_timeseries <- function(
               }
             }
           ),
-          alpha = 0.3,
-          show.legend = ifelse(all(is.na(dat$estimate_lower)), FALSE, TRUE)
+          alpha = 0.3 #,
+          # show.legend = ifelse(all(is.na(dat$estimate_lower)), FALSE, TRUE)
         ) +
         # }
         ggplot2::geom_line(
@@ -125,7 +125,7 @@ plot_timeseries <- function(
               }
             }
           ),
-          show.legend = FALSE, #ifelse(all(is.na(dat$estimate_lower)), TRUE, FALSE),
+          # show.legend = FALSE, #ifelse(all(is.na(dat$estimate_lower)), TRUE, FALSE),
           ...
         )
     },