From 10a1f2ca20a343b0a8a8a3a1068a4407554e9d33 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:02:14 -0500
Subject: [PATCH 1/3] add interaction to timeseries plot line

---
 R/utils_plot.R | 34 +++++++++++++++++++++++-----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/R/utils_plot.R b/R/utils_plot.R
index 87a500eb..8c4bd6b5 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -89,7 +89,7 @@ plot_timeseries <- function(
             x = .data[[x]],
             ymin = estimate_lower,
             ymax = estimate_upper,
-            fill = group_var
+            fill = interaction(model, group_var)
           ),
           alpha = 0.3
         ) +
@@ -99,9 +99,9 @@ plot_timeseries <- function(
           ggplot2::aes(
             x = .data[[x]],
             y = .data[[y]],
-            linetype = group_var,
+            # linetype = group_var,
             # linetype = ifelse(!is.null(group), group_var, "solid"),
-            color = model
+            color = interaction(model, group_var)
           ),
           # linewidth = 1.0,
           ...
@@ -122,14 +122,26 @@ plot_timeseries <- function(
   )
 
   # Add labels to axis and legend
-  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)
-  )
+  if (length(unique(dat$model)) > 1 & !is.null(group)) {
+    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 {
+    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)
+    )
+  }
 
   # Remove linetype or point when there is no grouping
   if (is.null(group) & length(unique(dat$model)) == 1) {

From 1fa996cfbc6bcf1149d57425710582d533aa03b2 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:53:16 -0500
Subject: [PATCH 2/3] remove duplicated plot_timeseries

---
 R/utils_plot.R | 178 -------------------------------------------------
 1 file changed, 178 deletions(-)

diff --git a/R/utils_plot.R b/R/utils_plot.R
index 8c4bd6b5..921df943 100644
--- a/R/utils_plot.R
+++ b/R/utils_plot.R
@@ -194,184 +194,6 @@ plot_timeseries <- function(
 
 #------------------------------------------------------------------------------
 
-#' Create plot with error
-#'
-#' @param dat filtered data frame from standard output file(s) preformatted for
-#'  the target label from \link[stockplotr]{filter_data}
-#' @param x a string of the column name of data used to plot on the x-axis (default
-#' is "year")
-#' @param y a string of the column name of data used to plot on the y-axis (default
-#' is "estimate")
-#' @param geom type of geom to use for plotting found in ggplot2 (e.g. "point",
-#' "line", etc.). Default is "line". Other options are "point" and "area".
-#' @param xlab a string of the x-axis label (default is "Year")
-#' @param ylab a string of the y-axis label. If NULL, it will be set to the name
-#'  of `y`.
-#' @param group a string of a single column that groups the data (e.g. "fleet",
-#' "sex", "area", etc.). Currently can only have one level of grouping.
-#' @param facet a string or vector of strings of a column that facets the data
-#' (e.g. "year", "area", etc.)
-#' @param ... inherited arguments from internal functions from ggplot2::geom_xx
-#'
-#'
-#' @returns Create a time series plot for a stock assessment report. The user
-#' has options to create a line, point, or area plot where the x-axis is year
-#' and Y can vary for any time series quantity. Currently, grouping is
-#' restricted to one group where faceting can be any number of facets.
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' plot_timeseries(dat,
-#'   x = "year",
-#'   y = "estimate",
-#'   geom = "line",
-#'   xlab = "Year",
-#'   ylab = "Biomass",
-#'   group = "fleet",
-#'   facet = "area"
-#' )
-#' }
-plot_timeseries <- function(
-  dat,
-  x = "year",
-  y = "estimate",
-  geom = "line",
-  xlab = "Year",
-  ylab = NULL,
-  group = NULL,
-  facet = NULL,
-  ...
-) {
-  # 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,
-          ...
-        )
-    },
-    "line" = {
-      plot +
-        ggplot2::geom_ribbon(
-          dat = dat |> dplyr::filter(!is.na(estimate_lower)),
-          ggplot2::aes(
-            x = .data[[x]],
-            ymin = estimate_lower,
-            ymax = estimate_upper
-          ),
-          colour = "grey",
-          alpha = 0.3
-        ) +
-        ggplot2::geom_line(
-          data = dat,
-          ggplot2::aes(
-            .data[[x]],
-            .data[[y]],
-            linetype = group_var,
-            # linetype = ifelse(!is.null(group), group_var, "solid"),
-            color = model
-          ),
-          # linewidth = 1.0,
-          ...
-        )
-    },
-    "area" = {
-      plot +
-        ggplot2::geom_area(
-          data = dat,
-          ggplot2::aes(
-            x = .data[[x]],
-            y = .data[[y]],
-            fill = model
-          ),
-          ...
-        )
-    }
-  )
-
-  # Add labels to axis and legend
-  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)
-  )
-
-  # Remove linetype or point when there is no grouping
-  if (is.null(group)) {
-    labs <- switch(geom,
-      "line" = labs + ggplot2::guides(linetype = "none"),
-      "point" = labs + ggplot2::guides(shape = "none"),
-      # return plot if option beyond line and point for now
-      labs
-    )
-  }
-  if (length(unique(dat$model)) == 1) {
-    labs <- switch(geom,
-      "line" = labs + ggplot2::guides(color = "none"),
-      "point" = labs + ggplot2::guides(color = "none"),
-      "area" = labs + ggplot2::guides(fill = "none"),
-      # return plot if option beyond line and point for now
-      labs
-    )
-  }
-
-  # Calc axis breaks
-  x_n_breaks <- axis_breaks(dat[[x]])
-  breaks <- ggplot2::scale_x_continuous(
-    breaks = x_n_breaks,
-    guide = ggplot2::guide_axis(
-      minor.ticks = TRUE
-    )
-  )
-
-  # Put together final plot
-  final <- labs + breaks + ggplot2::expand_limits(y = 0) +
-    ggplot2::scale_y_continuous(
-      labels = scales::label_comma()
-    )
-
-  # Remove legend if no group is selected
-  if (is.null(group) & is.data.frame(dat) & any(is.na(unique(dat$model)))) {
-    final <- final + ggplot2::theme(legend.position = "none")
-  }
-
-  # Check if facet(s) are desired
-  if (!is.null(facet)) {
-    facet <- paste("~", paste(facet, collapse = " + "))
-    facet_formula <- stats::reformulate(facet)
-
-    final <- final + ggplot2::facet_wrap(facet_formula)
-  }
-  final
-}
-
-#------------------------------------------------------------------------------
-
 #' Create plot with error
 #'
 #' @param dat filtered data frame from standard output file(s) preformatted for

From da2f2c021eacef89f12f816e85cb6327fa689ce1 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Thu, 26 Feb 2026 17:07:43 -0500
Subject: [PATCH 3/3] update documentation for plot timeseries

---
 man/plot_timeseries.Rd | 30 ------------------------------
 1 file changed, 30 deletions(-)

diff --git a/man/plot_timeseries.Rd b/man/plot_timeseries.Rd
index 089bb757..2a5fb8b3 100644
--- a/man/plot_timeseries.Rd
+++ b/man/plot_timeseries.Rd
@@ -4,18 +4,6 @@
 \alias{plot_timeseries}
 \title{Plot time series trends}
 \usage{
-plot_timeseries(
-  dat,
-  x = "year",
-  y = "estimate",
-  geom = "line",
-  xlab = "Year",
-  ylab = NULL,
-  group = NULL,
-  facet = NULL,
-  ...
-)
-
 plot_timeseries(
   dat,
   x = "year",
@@ -55,11 +43,6 @@ of `y`.}
 \item{...}{inherited arguments from internal functions from ggplot2::geom_xx}
 }
 \value{
-Create a time series plot for a stock assessment report. The user
-has options to create a line, point, or area plot where the x-axis is year
-and Y can vary for any time series quantity. Currently, grouping is
-restricted to one group where faceting can be any number of facets.
-
 Create a time series plot for a stock assessment report. The user
 has options to create a line, point, or area plot where the x-axis is year
 and Y can vary for any time series quantity. Currently, grouping is
@@ -67,8 +50,6 @@ restricted to one group where faceting can be any number of facets.
 }
 \description{
 Plot time series trends
-
-Create plot with error
 }
 \examples{
 \dontrun{
@@ -82,15 +63,4 @@ plot_timeseries(dat,
   facet = "area"
 )
 }
-\dontrun{
-plot_timeseries(dat,
-  x = "year",
-  y = "estimate",
-  geom = "line",
-  xlab = "Year",
-  ylab = "Biomass",
-  group = "fleet",
-  facet = "area"
-)
-}
 }