From 1e564eac853d5165041c30f1069f0a9cde36ab11 Mon Sep 17 00:00:00 2001
From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:47:47 -0400
Subject: [PATCH 01/10] fix(README): fix example so parameters are added into
 the YAML

The example had parameters = FALSE, but the default child documents contained a reference to a parameter as an example for use in-text. This will be fixed by setting parameters = TRUE (default), but also by removing the line in the file.

Future development will redesign this example and provide an example folder where users can see the product of create_template and rendering of the doc
---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 5b1b2fbd..7cc7ada7 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,6 @@ asar::create_template(
   year = 2010,
   author = c("John Snow", "Danny Phantom", "Patrick Star"),
   include_affiliation = TRUE,
-  parameters = FALSE,
   resdir = "C:/Users/Documents/Example_Files",
   model_results = "Report.sso",
   model = "SS3"

From 5f74433dda7dd7d5255abb13a801f053945d8d1a Mon Sep 17 00:00:00 2001
From: Schiano-NOAA <samantha.schiano@noaa.gov>
Date: Tue, 1 Oct 2024 16:56:16 -0400
Subject: [PATCH 02/10] feat(skeleton): add section tagging to default skeleton

---
 inst/templates/skeleton/acknowledgments.qmd   |  2 +-
 inst/templates/skeleton/appendix.qmd          |  2 +-
 inst/templates/skeleton/data.qmd              |  2 +-
 inst/templates/skeleton/discussion.qmd        |  2 +-
 inst/templates/skeleton/executive_summary.qmd |  6 +++---
 inst/templates/skeleton/introduction.qmd      | 10 +++++-----
 inst/templates/skeleton/modeling_approach.qmd | 14 +++++++-------
 inst/templates/skeleton/projections.qmd       |  2 +-
 inst/templates/skeleton/references.qmd        |  8 +-------
 inst/templates/skeleton/results.qmd           | 12 ++++++------
 10 files changed, 27 insertions(+), 33 deletions(-)

diff --git a/inst/templates/skeleton/acknowledgments.qmd b/inst/templates/skeleton/acknowledgments.qmd
index 8fa8c479..c2f08519 100644
--- a/inst/templates/skeleton/acknowledgments.qmd
+++ b/inst/templates/skeleton/acknowledgments.qmd
@@ -1 +1 @@
-## Acknowledgements
+## Acknowledgements {#sec-acknowledgements}
diff --git a/inst/templates/skeleton/appendix.qmd b/inst/templates/skeleton/appendix.qmd
index c4ab246d..db68a12e 100644
--- a/inst/templates/skeleton/appendix.qmd
+++ b/inst/templates/skeleton/appendix.qmd
@@ -1 +1 @@
-## Appendices
+## Appendices {#sec-appendix}
diff --git a/inst/templates/skeleton/data.qmd b/inst/templates/skeleton/data.qmd
index 194f2ae4..208bd248 100644
--- a/inst/templates/skeleton/data.qmd
+++ b/inst/templates/skeleton/data.qmd
@@ -1,4 +1,4 @@
-## Data
+## Data {#sec-data}
 
 <!---
 Include the following:
diff --git a/inst/templates/skeleton/discussion.qmd b/inst/templates/skeleton/discussion.qmd
index 2f9cd945..d10684ab 100644
--- a/inst/templates/skeleton/discussion.qmd
+++ b/inst/templates/skeleton/discussion.qmd
@@ -1,4 +1,4 @@
-## Discussion
+## Discussion {#sec-discussion}
 
 <!---
 There are no specified guidelines to structure this section; however, please include subsections discussing ecosystem considerations (if applicable) and research recommendations/improvements to the assessment.
diff --git a/inst/templates/skeleton/executive_summary.qmd b/inst/templates/skeleton/executive_summary.qmd
index c23a669e..f6cd6695 100644
--- a/inst/templates/skeleton/executive_summary.qmd
+++ b/inst/templates/skeleton/executive_summary.qmd
@@ -1,10 +1,10 @@
-## Executive Summary
+## Executive Summary {#sec-executive-summary}
 
 <!---
 Table of updates among the current stock assessment report
 --->
 
-### Assessment Methods
+### Assessment Methods {#sec-assessment-methods}
 
 <!---
 - Current Assessment
@@ -12,7 +12,7 @@ Table of updates among the current stock assessment report
 - Major changes
 --->
 
-### Stock Status
+### Stock Status {#sec-stock-status}
 
 <!---
 Short description followed by a tables with reference points, stock status, and projections
diff --git a/inst/templates/skeleton/introduction.qmd b/inst/templates/skeleton/introduction.qmd
index fbe8a1dd..aa9f28ac 100644
--- a/inst/templates/skeleton/introduction.qmd
+++ b/inst/templates/skeleton/introduction.qmd
@@ -1,27 +1,27 @@
-## Introduction
+## Introduction {#sec-introduction}
 
 Testing adding in an introduction for `r params$species`. There is currently no read of parameters for child documents.
 
-### Management and Assessment History
+### Management and Assessment History {#sec-history}
 
 <!---
 - Provide a brief description of management history of the stock and status (including change in fishery behavior).
 - History of assessment approaches.
 --->
 
-### Stock Structure and ID
+### Stock Structure and ID {#sec-stock-id}
 
 <!---
 Provide a short description (a longer explanation will be included in the data section if applicable)
 --->
 
-### Fishery Descriptions
+### Fishery Descriptions {#sec-fishery-desscriptions}
 
 <!---
 Short summary of fleet composition (i.e. boat types), gear types, species targeted, and fishing grounds (one paragraph).
 --->
 
-### Ecosystem Considerations or climate indicators
+### Ecosystem Considerations or climate indicators {#sec-eco-indicators}
 
 <!---
 If this section is not relevant, please state "Ecosystem considerations and/or climate indicators were not included in this assessment."
diff --git a/inst/templates/skeleton/modeling_approach.qmd b/inst/templates/skeleton/modeling_approach.qmd
index d0eb5425..cfaaae74 100644
--- a/inst/templates/skeleton/modeling_approach.qmd
+++ b/inst/templates/skeleton/modeling_approach.qmd
@@ -1,6 +1,6 @@
-## Modeling Approach
+## Modeling Approach {#sec-modeling-approach}
 
-### Current Approach
+### Current Approach {#sec-current-approach}
 
 <!---
 This is a potential automated subsection which will dynamically changed according to the assessment model used to perform the analysis. 
@@ -8,7 +8,7 @@ This is a potential automated subsection which will dynamically changed accordin
 Please provide a short, general overview of platform including reference to the model's paper or online reference.
 --->
 
-### Configuration
+### Configuration {#sec-configuration}
 
 <!---
 - Time blocks
@@ -22,25 +22,25 @@ Please provide a short, general overview of platform including reference to the
 - Likelihood (penalty, reweighting, ect.)
 --->
 
-### Sensitivity Analyses
+### Sensitivity Analyses {#sec-model-sensitivity-analyses}
 
 <!---
 Descriptions of which sensitivity analysis to be performed. (i.e. which parameters or data input streams changed in different setups of the model and why)
 --->
 
-### Management Benchmarks
+### Management Benchmarks {#sec-management-benchmarks}
 
 <!---
 Description decisions on management metrics/benchmarks.
 --->
 
-### Diagnostics
+### Diagnostics {#sec-diagnostics}
 
 <!---
 Description of which diagnostics will be used.
 --->
 
-### Projection Scenarios
+### Projection Scenarios {#sec-projection-scenarios}
 
 <!---
 Description of which projection scenarios will be run and how the projections will be set up.
diff --git a/inst/templates/skeleton/projections.qmd b/inst/templates/skeleton/projections.qmd
index 2eea8437..c1966c93 100644
--- a/inst/templates/skeleton/projections.qmd
+++ b/inst/templates/skeleton/projections.qmd
@@ -1,4 +1,4 @@
-## Projections
+## Projections {#sec-projections}
 
 <!---
 Description of stock status, biological reference points (BRPs), and trends for each scenario; include rebuilding times
diff --git a/inst/templates/skeleton/references.qmd b/inst/templates/skeleton/references.qmd
index dce1c488..0b060605 100644
--- a/inst/templates/skeleton/references.qmd
+++ b/inst/templates/skeleton/references.qmd
@@ -1,7 +1 @@
-## References
-
-\begingroup
-\raggedright
-::: {#refs}
-:::
-\endgroup
+## References {#sec-references}
diff --git a/inst/templates/skeleton/results.qmd b/inst/templates/skeleton/results.qmd
index 5a6e3bdd..d7a81e3c 100644
--- a/inst/templates/skeleton/results.qmd
+++ b/inst/templates/skeleton/results.qmd
@@ -1,18 +1,18 @@
-## Results
+## Results {#sec-results}
 
-### Parameter Estimates
+### Parameter Estimates {#sec-parameter-estimates}
 
 <!---
 Table of the parameters that were estimated and text interpretation as needed; includes Bayesian parameter fit values.
 --->
 
-### Recruitment Estimates and Deviations
+### Recruitment Estimates and Deviations {#recruitment-estimates}
 
 <!---
 Interpretation of the spawner-recruit curve estimation, challenges or issues, and any interpretation of recruitment deviations (i.e. if there is a pattern indicating regime shift, ect.)
 --->
 
-### Model Fits
+### Model Fits {#sec-model-fits}
 
 <!---
 - Indices
@@ -23,7 +23,7 @@ Interpretation of the spawner-recruit curve estimation, challenges or issues, an
 - Other metrics (if applicable) - discards, environmental data, ect.
 --->
 
-### Model Diagnostics
+### Model Diagnostics {#sec-model-diagnostics}
 
 <!---
 Where applicable:
@@ -34,7 +34,7 @@ Where applicable:
 - Retrospective analysis
 --->
 
-### Sensitivity Analysis
+### Sensitivity Analysis {#sec-res-sensitivity-analyses}
 
 <!---
 Results and comparison with the base model; each scenario result and what was changed; please include key metrics from each scenario such as steepness (h), R0, Bcurrent, Fcurrent, F/Fmsy, B/Bmsy, ect.

From 605638931644d4c9621f93985c671c0163258fce Mon Sep 17 00:00:00 2001
From: Schiano-NOAA <samantha.schiano@noaa.gov>
Date: Wed, 2 Oct 2024 11:38:57 -0400
Subject: [PATCH 03/10] Fix(create_template): edit name to remove spaces when
 species name is more than 1 word when converting output within fxn

---
 R/create_template.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/create_template.R b/R/create_template.R
index 70f07598..6bee258f 100644
--- a/R/create_template.R
+++ b/R/create_template.R
@@ -478,7 +478,7 @@ create_template <- function(
                          model = model,
                          fleet_names = fleet_names,
                          savedir = subdir,
-                         save_name = paste(species, "_std_res_", year, sep = ""))
+                         save_name = paste(sub(" ", "_", species), "_std_res_", year, sep = ""))
         } else {
           convert_output(output_file = model_results,
                          outdir = resdir,

From ceecaf9fce933a33dcb71c13fdce3b0763cf38d1 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Fri, 27 Sep 2024 16:49:20 -0400
Subject: [PATCH 04/10] Added code to add_theme.R to use the nmfs color palette
 in plots

---
 R/add_theme.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/add_theme.R b/R/add_theme.R
index 0c760545..3bc25637 100644
--- a/R/add_theme.R
+++ b/R/add_theme.R
@@ -36,7 +36,12 @@ add_theme <- function(x) {
         panel.grid = ggplot2::element_blank(),
         panel.border = ggplot2::element_rect(colour = "black", fill = NA, linewidth = 0.5)
         # text = ggplot2::element_text(size = 12, family = "Cambria")
-      )
+      ) +
+      # add nmfs color palette (palette will be default)
+      # I believe including both functions is fine and will
+      # works regardless of the type of plot (one won't be used)
+      nmfspalette::scale_color_nmfs() +
+      nmfspalette::scale_fill_nmfs()
     # Determining how to treat a legend if there is one
     # check if one is present
     # check_for_legend <- function(x) {

From f84e571a999efbf07f766a0e3d756b830b034f9d Mon Sep 17 00:00:00 2001
From: Bai-Li-NOAA <bai.li@noaa.gov>
Date: Wed, 2 Oct 2024 15:12:11 -0400
Subject: [PATCH 05/10] test: add tests to test add_theme()

---
 R/add_theme.R                   |  2 +-
 tests/testthat/test-add_theme.R | 98 +++++++++++++++++++++++++++++++++
 2 files changed, 99 insertions(+), 1 deletion(-)

diff --git a/R/add_theme.R b/R/add_theme.R
index 3bc25637..d01e40c4 100644
--- a/R/add_theme.R
+++ b/R/add_theme.R
@@ -37,7 +37,7 @@ add_theme <- function(x) {
         panel.border = ggplot2::element_rect(colour = "black", fill = NA, linewidth = 0.5)
         # text = ggplot2::element_text(size = 12, family = "Cambria")
       ) +
-      # add nmfs color palette (palette will be default)
+      # add nmfs color palette "ocean" (palette will be default)
       # I believe including both functions is fine and will
       # works regardless of the type of plot (one won't be used)
       nmfspalette::scale_color_nmfs() +
diff --git a/tests/testthat/test-add_theme.R b/tests/testthat/test-add_theme.R
index 5e94a52e..994e62da 100644
--- a/tests/testthat/test-add_theme.R
+++ b/tests/testthat/test-add_theme.R
@@ -33,3 +33,101 @@
 #
 #   expect_equal(2 * 2, 4)
 # })
+test_that("add_theme applies NOAA formatting correctly", {
+  
+  # Test with a ggplot object
+  ggplot_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist)) +
+    ggplot2::geom_point()
+  result_ggplot <- add_theme(ggplot_obj)
+  
+  expect_true(inherits(result_ggplot, "ggplot"))
+  expect_true(ggplot2::is.ggplot(result_ggplot))
+  
+  # Test with a flextable object
+  flex_obj <- flextable::flextable(head(cars))
+  result_flextable <- add_theme(flex_obj)
+  
+  expect_true(inherits(result_flextable, "flextable"))
+  expect_true("flextable" %in% class(result_flextable))
+  
+  # Test with a gt table object
+  gt_obj <- gt::gt(head(cars))
+  result_gt <- add_theme(gt_obj)
+  
+  expect_true(inherits(result_gt, "gt_tbl"))
+  
+  # Test with a kableExtra object
+  kable_obj <- knitr::kable(head(cars), format = "html") %>%
+    kableExtra::kable_styling()
+  result_kable <- add_theme(kable_obj)
+  
+  expect_true("kableExtra" %in% class(result_kable))
+  
+  # Test with an unsupported object
+  unsupported_obj <- data.frame(a = 1, b = 2)
+  expect_message(add_theme(unsupported_obj), "NOAA formatting cannot be applied to this object.")
+})
+
+test_that("nmfspalette returns correct scales", {
+  
+  # Test 1: Ensure nmfspalette integrates with ggplot color scales
+  ggplot_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist, color = speed)) +
+    ggplot2::geom_point() +
+    nmfspalette::scale_color_nmfs()
+  
+  # Check if the correct scale is added
+  expect_true("ScaleDiscrete" %in% class(ggplot_obj$scales$scales[[1]]))
+  expect_true(ggplot_obj$scales$scales[[1]]$aesthetics == "colour")
+  
+  # Test 2: Ensure fill scale works with ggplot
+  ggplot_fill_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = factor(speed), fill = factor(speed))) +
+    ggplot2::geom_bar() +
+    nmfspalette::scale_fill_nmfs()
+  
+  # Check if the correct fill scale is applied
+  expect_true("ScaleDiscrete" %in% class(ggplot_fill_obj$scales$scales[[1]]))
+  expect_true(ggplot_fill_obj$scales$scales[[1]]$aesthetics == "fill")
+  
+})
+
+test_that("nmfspalette scales are applied to ggplot object", {
+  p <- ggplot(mtcars, aes(x = wt, y = mpg, color = as.factor(cyl))) +
+    geom_point()
+  formatted_plot <- add_theme(p)
+
+  # Extract the color and fill scales from the plot
+  scales <- formatted_plot$scales$scales
+
+  # Check if the color scale is from nmfspalette
+  color_scale <- scales[[1]]
+  expect_true("ScaleDiscrete" %in% class(color_scale)) # It's a discrete scale
+  expect_true(grepl("nmfs", deparse(color_scale$call))) # Check if nmfspalette scale is used
+
+  # Ensure the color scale is the "default"ocean" nmfspalette scale
+  default_nmfs_colors <- nmfspalette::nmfs_palette("oceans")(3)
+  plot_colors <- color_scale$palette(3) # Extract applied colors
+  expect_equal(plot_colors, default_nmfs_colors) # Check if the colors match
+
+  default_nmfs_colors <- nmfspalette::nmfs_palette("oceans")(6)
+  plot_colors <- color_scale$palette(6) # Extract applied colors
+  expect_equal(plot_colors, default_nmfs_colors) # Check if the colors match
+
+})
+
+# Test for both color and fill scales
+test_that("nmfspalette scales apply both color and fill scales", {
+  p <- ggplot(mtcars, aes(x = wt, y = mpg, color = as.factor(cyl), fill = as.factor(cyl))) +
+    geom_point()
+  formatted_plot <- add_theme(p)
+
+  # Extract the scales from the plot
+  scales <- formatted_plot$scales$scales
+
+  # Check color scale
+  color_scale <- scales[[1]]
+  expect_true(grepl("nmfs", deparse(color_scale$call))) # Color scale from nmfspalette
+
+  # Check fill scale
+  fill_scale <- scales[[2]]
+  expect_true(grepl("nmfs", deparse(fill_scale$call))) # Fill scale from nmfspalette
+})

From c597ae86a688a1d31466f9a5ca5513a6ed9e2ea2 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Fri, 27 Sep 2024 16:49:20 -0400
Subject: [PATCH 06/10] Added code to add_theme.R to use the nmfs color palette
 in plots

---
 R/add_theme.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/add_theme.R b/R/add_theme.R
index 0c760545..3bc25637 100644
--- a/R/add_theme.R
+++ b/R/add_theme.R
@@ -36,7 +36,12 @@ add_theme <- function(x) {
         panel.grid = ggplot2::element_blank(),
         panel.border = ggplot2::element_rect(colour = "black", fill = NA, linewidth = 0.5)
         # text = ggplot2::element_text(size = 12, family = "Cambria")
-      )
+      ) +
+      # add nmfs color palette (palette will be default)
+      # I believe including both functions is fine and will
+      # works regardless of the type of plot (one won't be used)
+      nmfspalette::scale_color_nmfs() +
+      nmfspalette::scale_fill_nmfs()
     # Determining how to treat a legend if there is one
     # check if one is present
     # check_for_legend <- function(x) {

From 40fa5792c386a94e36be60c5c8a5443dfad82e67 Mon Sep 17 00:00:00 2001
From: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Date: Thu, 3 Oct 2024 11:23:59 -0400
Subject: [PATCH 07/10] add_theme.R: -Removed the explicit choice of "ocean"
 color palette because, if "ocean" is indicated and the object being themed
 has only one color (e.g., a basic scatterplot), there will be an error.
 Indicating "ocean" in nmfspalette::scale_color_nmfs() will succeed only when
 the object being themed has >1 color. -Added a comment to clearly state that
 the palette's default "ocean" palette will be applied.

-Changed else if statements to fix bugs/more accurately identify object before assigning else if statements

test-add_theme.R:
-Updated code testing that the default nmfspalette palette was "oceans".
-Fixed bug to enable error messages to be sent for inappropriate function argument types
---
 R/add_theme.R                   |  19 ++++--
 tests/testthat/test-add_theme.R | 102 ++++++++++++++------------------
 2 files changed, 58 insertions(+), 63 deletions(-)

diff --git a/R/add_theme.R b/R/add_theme.R
index 6274ea70..b32627c1 100644
--- a/R/add_theme.R
+++ b/R/add_theme.R
@@ -16,6 +16,11 @@ add_theme <- function(x) {
   #     )
   # )
   # this is bad coding practice, but what I have for now
+
+
+  # Initialize theme_obj to NULL
+  theme_obj <- NULL
+
   if (class(x)[1] == "flextable") {
     theme_obj <- x |>
       flextable::merge_h(i = 1, part = "header") |>
@@ -26,9 +31,10 @@ add_theme <- function(x) {
   } else if (class(x)[1] == "gt_tbl") {
     theme_obj <- x
     # gt object
-  } else if (class(x)[1] == "kableExtra" | as.character(class(x)[2]) == "knitr_kable") {
+  } else if ("kableExtra" %in% class(x) ||
+             (length(class(x)) > 1 && class(x)[2] == "knitr_kable")) {
     theme_obj <- x
-  } else if (class(x)[1] == "gg" | class(x)[2] == "ggplot") { #  - removed bc wouldn't work with only 1 entry in the class for other object classes
+  } else if ("gg" %in% class(x) || "ggplot" %in% class(x)) {
     theme_obj <- x +
       ggplot2::theme(
         plot.background = ggplot2::element_rect(fill = "transparent"),
@@ -37,9 +43,9 @@ add_theme <- function(x) {
         panel.border = ggplot2::element_rect(colour = "black", fill = NA, linewidth = 0.5)
         # text = ggplot2::element_text(size = 12, family = "Cambria")
       ) +
-      # add nmfs color palette "ocean" (palette will be default)
-      nmfspalette::scale_color_nmfs("ocean") +
-      nmfspalette::scale_fill_nmfs("ocean")
+      # add default nmfs color palette (palette will be "ocean")
+      nmfspalette::scale_color_nmfs() +
+      nmfspalette::scale_fill_nmfs()
     # Determining how to treat a legend if there is one
     # check if one is present
     # check_for_legend <- function(x) {
@@ -49,7 +55,8 @@ add_theme <- function(x) {
     #   move_legend <- theme_obj +
     #     ggplot2::theme()
     # }
-  } else {
+
+    } else {
     message("NOAA formatting cannot be applied to this object.")
   }
 
diff --git a/tests/testthat/test-add_theme.R b/tests/testthat/test-add_theme.R
index 994e62da..b99a0959 100644
--- a/tests/testthat/test-add_theme.R
+++ b/tests/testthat/test-add_theme.R
@@ -1,93 +1,61 @@
-# test_that("formatting applied to ggplot", {
-#   test_fig <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist)) +
-#     ggplot2::geom_point()+
-#     ggplot2::theme_classic()
-#   test_fxn <- add_theme(
-#                 ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist)) +
-#                 ggplot2::geom_point()
-#               )
-#
-#   expect_equal(2 * 2, 4)
-# })
-#
-# test_that("formatting applied to base R plotting", {
-#   test_fig <- plot(x = cars$speed, y= cars$dist)
-#
-#   expect_equal(2 * 2, 4)
-# })
-#
-# test_that("formatting applied to flextable", {
-#   test_tab <- flextable::flextable(head(cars))
-#
-#   expect_equal(2 * 2, 4)
-# })
-#
-# test_that("formatting applied to gt table", {
-#   test_tab <- gt::gt(head(cars))
-#
-#   expect_equal(2 * 2, 4)
-# })
-#
-# test_that("formatting applied to kable table", {
-#   test_tab <- kableExtra::kbl(head(cars))
-#
-#   expect_equal(2 * 2, 4)
-# })
 test_that("add_theme applies NOAA formatting correctly", {
-  
+
   # Test with a ggplot object
   ggplot_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist)) +
     ggplot2::geom_point()
   result_ggplot <- add_theme(ggplot_obj)
-  
+
   expect_true(inherits(result_ggplot, "ggplot"))
   expect_true(ggplot2::is.ggplot(result_ggplot))
-  
+
   # Test with a flextable object
   flex_obj <- flextable::flextable(head(cars))
   result_flextable <- add_theme(flex_obj)
-  
+
   expect_true(inherits(result_flextable, "flextable"))
   expect_true("flextable" %in% class(result_flextable))
-  
+
   # Test with a gt table object
   gt_obj <- gt::gt(head(cars))
   result_gt <- add_theme(gt_obj)
-  
+
   expect_true(inherits(result_gt, "gt_tbl"))
-  
+
   # Test with a kableExtra object
   kable_obj <- knitr::kable(head(cars), format = "html") %>%
     kableExtra::kable_styling()
   result_kable <- add_theme(kable_obj)
-  
+
   expect_true("kableExtra" %in% class(result_kable))
-  
-  # Test with an unsupported object
+
+  # Test with unsupported objects
   unsupported_obj <- data.frame(a = 1, b = 2)
   expect_message(add_theme(unsupported_obj), "NOAA formatting cannot be applied to this object.")
+
+  unsupported_obj2 <- list(1,3,4)
+  expect_message(add_theme(unsupported_obj2), "NOAA formatting cannot be applied to this object.")
 })
 
 test_that("nmfspalette returns correct scales", {
-  
+
   # Test 1: Ensure nmfspalette integrates with ggplot color scales
   ggplot_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist, color = speed)) +
     ggplot2::geom_point() +
     nmfspalette::scale_color_nmfs()
-  
+
   # Check if the correct scale is added
   expect_true("ScaleDiscrete" %in% class(ggplot_obj$scales$scales[[1]]))
   expect_true(ggplot_obj$scales$scales[[1]]$aesthetics == "colour")
-  
+
   # Test 2: Ensure fill scale works with ggplot
   ggplot_fill_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = factor(speed), fill = factor(speed))) +
     ggplot2::geom_bar() +
     nmfspalette::scale_fill_nmfs()
-  
+
   # Check if the correct fill scale is applied
   expect_true("ScaleDiscrete" %in% class(ggplot_fill_obj$scales$scales[[1]]))
   expect_true(ggplot_fill_obj$scales$scales[[1]]$aesthetics == "fill")
-  
+
 })
 
 test_that("nmfspalette scales are applied to ggplot object", {
@@ -103,14 +71,33 @@ test_that("nmfspalette scales are applied to ggplot object", {
   expect_true("ScaleDiscrete" %in% class(color_scale)) # It's a discrete scale
   expect_true(grepl("nmfs", deparse(color_scale$call))) # Check if nmfspalette scale is used
 
-  # Ensure the color scale is the "default"ocean" nmfspalette scale
-  default_nmfs_colors <- nmfspalette::nmfs_palette("oceans")(3)
-  plot_colors <- color_scale$palette(3) # Extract applied colors
-  expect_equal(plot_colors, default_nmfs_colors) # Check if the colors match
+  # Ensure the color scale is the default "oceans" nmfspalette scale
+  test_plot <- ggplot(Orange,
+                        aes(
+                          x = age,
+                          y = circumference,
+                          color = Tree)) +
+    geom_smooth(se = F,
+                method = "loess",
+                formula = "y ~ x")
+
+  ## use default color palette
+  plot_default <- test_plot +
+    nmfspalette::scale_color_nmfs()
+
+  ## use oceans color palette
+  plot_oceans <- test_plot +
+    nmfspalette::scale_color_nmfs("oceans", 5)
+
+  ## extract colors used for both plots
+  plot_default_build <- ggplot_build(plot_default)
+  colors_default <- unique(plot_default_build$data[[1]]["colour"])
 
-  default_nmfs_colors <- nmfspalette::nmfs_palette("oceans")(6)
-  plot_colors <- color_scale$palette(6) # Extract applied colors
-  expect_equal(plot_colors, default_nmfs_colors) # Check if the colors match
+  plot_oceans_build <- ggplot_build(plot_oceans)
+  colors_oceans <- unique(plot_oceans_build$data[[1]]["colour"])
+
+  ## test if plots' colors are identical
+  expect_equal(colors_default, colors_oceans) # Check if the colors match
 
 })
 
@@ -131,3 +118,4 @@ test_that("nmfspalette scales apply both color and fill scales", {
   fill_scale <- scales[[2]]
   expect_true(grepl("nmfs", deparse(fill_scale$call))) # Fill scale from nmfspalette
 })
+

From 0006a6804cc608cead44b09d4f25f3bb76ced749 Mon Sep 17 00:00:00 2001
From: Bai-Li-NOAA <bai.li@noaa.gov>
Date: Mon, 7 Oct 2024 09:36:35 -0400
Subject: [PATCH 08/10] fix failed GHA tests on main branch

- add gt to the Imports section in DESCRIPTION and reorder package listings
- use ggplot2:: to access specific functions from ggplot2
- update the path the assessment reports for testing purposes
---
 DESCRIPTION                           |  5 +++--
 man/create_template.Rd                |  6 ++++++
 tests/testthat/test-add_theme.R       | 18 +++++++++---------
 tests/testthat/test-create_template.R | 13 +++++++++----
 4 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8e3b0e99..7e24106e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,6 +16,7 @@ Imports:
     fs,
     ggplot2,
     gridExtra,
+    gt,
     naniar,
     officer,
     openxlsx,
@@ -30,10 +31,10 @@ Imports:
     utils
 Suggests: 
     knitr,
-    rmarkdown,
     parallel,
-    snowfall, 
     r4ss,
+    rmarkdown,
+    snowfall, 
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
diff --git a/man/create_template.Rd b/man/create_template.Rd
index 501654a4..afe78218 100644
--- a/man/create_template.Rd
+++ b/man/create_template.Rd
@@ -23,6 +23,8 @@ create_template(
   parameters = TRUE,
   param_names = NULL,
   param_values = NULL,
+  convert_output = FALSE,
+  fleet_names = NULL,
   resdir = NULL,
   model_results = NULL,
   model = NULL,
@@ -79,6 +81,10 @@ and species listed in function parameters}
 \item{param_values}{List of values associated with the order of parameter names; parameters automatically included are office, region,
 and species listed in function parameters}
 
+\item{convert_output}{TRUE/FALSE convert output file to standard while creating report template}
+
+\item{fleet_names}{list of fleet names as seen in BAM output file (abbreviations)}
+
 \item{resdir}{Directory where the model results file(s) are located}
 
 \item{model_results}{Name of the model results file}
diff --git a/tests/testthat/test-add_theme.R b/tests/testthat/test-add_theme.R
index b99a0959..83d16339 100644
--- a/tests/testthat/test-add_theme.R
+++ b/tests/testthat/test-add_theme.R
@@ -59,8 +59,8 @@ test_that("nmfspalette returns correct scales", {
 })
 
 test_that("nmfspalette scales are applied to ggplot object", {
-  p <- ggplot(mtcars, aes(x = wt, y = mpg, color = as.factor(cyl))) +
-    geom_point()
+  p <- ggplot2::ggplot(mtcars, ggplot2::aes(x = wt, y = mpg, color = as.factor(cyl))) +
+    ggplot2::geom_point()
   formatted_plot <- add_theme(p)
 
   # Extract the color and fill scales from the plot
@@ -72,12 +72,12 @@ test_that("nmfspalette scales are applied to ggplot object", {
   expect_true(grepl("nmfs", deparse(color_scale$call))) # Check if nmfspalette scale is used
 
   # Ensure the color scale is the default "oceans" nmfspalette scale
-  test_plot <- ggplot(Orange,
-                        aes(
+  test_plot <- ggplot2::ggplot(Orange,
+                               ggplot2::aes(
                           x = age,
                           y = circumference,
                           color = Tree)) +
-    geom_smooth(se = F,
+    ggplot2::geom_smooth(se = F,
                 method = "loess",
                 formula = "y ~ x")
 
@@ -90,10 +90,10 @@ test_that("nmfspalette scales are applied to ggplot object", {
     nmfspalette::scale_color_nmfs("oceans", 5)
 
   ## extract colors used for both plots
-  plot_default_build <- ggplot_build(plot_default)
+  plot_default_build <- ggplot2::ggplot_build(plot_default)
   colors_default <- unique(plot_default_build$data[[1]]["colour"])
 
-  plot_oceans_build <- ggplot_build(plot_oceans)
+  plot_oceans_build <- ggplot2::ggplot_build(plot_oceans)
   colors_oceans <- unique(plot_oceans_build$data[[1]]["colour"])
 
   ## test if plots' colors are identical
@@ -103,8 +103,8 @@ test_that("nmfspalette scales are applied to ggplot object", {
 
 # Test for both color and fill scales
 test_that("nmfspalette scales apply both color and fill scales", {
-  p <- ggplot(mtcars, aes(x = wt, y = mpg, color = as.factor(cyl), fill = as.factor(cyl))) +
-    geom_point()
+  p <- ggplot2::ggplot(mtcars, ggplot2::aes(x = wt, y = mpg, color = as.factor(cyl), fill = as.factor(cyl))) +
+    ggplot2::geom_point()
   formatted_plot <- add_theme(p)
 
   # Extract the scales from the plot
diff --git a/tests/testthat/test-create_template.R b/tests/testthat/test-create_template.R
index 955149b0..dfaa07f0 100644
--- a/tests/testthat/test-create_template.R
+++ b/tests/testthat/test-create_template.R
@@ -196,13 +196,17 @@ test_that("file_dir works", {
     FALSE
   )
 
+  office <- "NWFSC"
+  species <- "Dover sole"
+  year <- 2010
+
   create_template(
     new_template = TRUE,
     format = "pdf",
-    office = "NWFSC",
-    species = "Dover sole",
+    office = office,
+    species = species,
     spp_latin = "Pomatomus saltatrix",
-    year = 2010,
+    year = year,
     author = c("John Snow", "Danny Phantom", "Patrick Star"),
     include_affiliation = TRUE,
     parameters = FALSE,
@@ -212,6 +216,7 @@ test_that("file_dir works", {
     file_dir = dir
   )
 
-  expect_gt(length(list.files(dir)), 1)
+  file_path <- file.path(dir, "stock_assessment_reports", office, species, year)
+  expect_gt(length(list.files(file_path)), 1)
   on.exit(unlink(dir, recursive = TRUE), add = TRUE)
 })

From 47db2201e6c6c1b4e8949b76577e23125f16ccb6 Mon Sep 17 00:00:00 2001
From: Bai-Li-NOAA <bai.li@noaa.gov>
Date: Thu, 3 Oct 2024 11:15:34 -0400
Subject: [PATCH 09/10] add issue templates

- add bug report template
- add feature request template
- add question template
- add pull request tempate
- add PR checklist
---
 .github/ISSUE_TEMPLATE/bug_report.yml      | 69 ++++++++++++++++++++++
 .github/ISSUE_TEMPLATE/feature_request.yml | 43 ++++++++++++++
 .github/ISSUE_TEMPLATE/question.yml        | 23 ++++++++
 .github/pull_request_template.md           | 12 ++++
 .github/workflows/pr-checklist.yml         | 44 ++++++++++++++
 5 files changed, 191 insertions(+)
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml
 create mode 100644 .github/ISSUE_TEMPLATE/question.yml
 create mode 100644 .github/pull_request_template.md
 create mode 100644 .github/workflows/pr-checklist.yml

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 00000000..6faba655
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,69 @@
+name: Bug Report
+description: Report asar not working as expected.
+title: "[Bug]: "
+labels: ["bug", "triage_needed"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report! Before
+        filling out this report please search the existing issues to see
+        if the problem has already been reported. If it has, please add a
+        comment to the open issue or link to the related, but closed, issue in
+        this report.
+  - type: textarea
+    id: describe
+    attributes:
+      label: Describe the bug
+      description: Please provide a description of the bug.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Describe how to reproduce the bug
+      description: |
+        Please include a minimal reproducible example (i.e., a
+        [reprex]((https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html))).
+        If you have not heard of a [reprex](http://reprex.tidyverse.org/)
+        before, you can start by reading about them on the [tidyverse
+        blog](https://www.tidyverse.org/help/#reprex). Feel free to copy, paste,
+        and edit the [demo
+        vignette](https://github.com/NOAA-FIMS/FIMS/blob/4539fc4b6e65b901231c4fb66a113bb5b5d54d22/vignettes/fims-demo.Rmd)
+        for your reprex.
+      placeholder: |
+        # insert reprex here
+    validations:
+      required: false
+  - type: textarea
+    id: screenshots
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots to help explain your problem.
+    validations:
+      required: false
+  - type: dropdown
+    id: os
+    attributes:
+      label: Which OS are you seeing the problem on?
+      multiple: true
+      options:
+        - Windows
+        - Mac
+        - Linux
+        - Other
+    validations:
+      required: false
+  - type: input
+    id: version
+    attributes:
+      label: Which version of asar are you seeing the problem on?
+    validations:
+      required: false
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: Add any other context about the problem here.
+    validations:
+      required: false
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 00000000..edf174f5
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,43 @@
+name: Feature Request
+description: Request new features or changes to features
+title: "[Feature]: "
+labels: ["enhancement", "triage_needed"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this feature request! Before
+        filling out this report please search the existing issues to see
+        if the problem has already been reported. If it has, please add a
+        comment to the open issue or link to the related, but closed, issue in
+        this report.
+  - type: textarea
+    id: problem
+    attributes:
+      label: Is your feature request related to a problem? Please describe.
+      description: A clear and concise description of what the problem is.
+      placeholder: I'm always frustrated when...
+    validations:
+      required: true
+  - type: textarea
+    id: solution
+    attributes:
+      label: Describe the solution you would like.
+      description: A clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Describe alternatives you have considered
+      description: A clear and concise description of any alternative solutions or features you have considered.
+      placeholder: Other solutions include ...
+    validations:
+      required: true
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Add any other context or screenshots about the feature request here.
+    validations:
+      required: false
diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml
new file mode 100644
index 00000000..678fd1fd
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/question.yml
@@ -0,0 +1,23 @@
+name: Question about asar
+description: Ask a question about asar
+title: "[Question]: "
+labels: ["question", "triage_needed"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to ask a question!
+  - type: textarea
+    id: question
+    attributes:
+      label: What is your question?
+      placeholder: Please ask a clear and concise question about asar.
+    validations:
+      required: true
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional context
+      description: Add any other context or screenshots here.
+    validations:
+      required: false
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
new file mode 100644
index 00000000..22a35abc
--- /dev/null
+++ b/.github/pull_request_template.md
@@ -0,0 +1,12 @@
+<!---
+Thanks for opening a PR. This commented text will **NOT** appear in the final PR. Toggle between Write and Preview to see what your PR will look like without the comments.
+-->
+
+# What is the feature?
+*
+
+# How have you implemented the solution?
+*
+
+# Does the PR impact any other area of the project, maybe another repo?
+*
diff --git a/.github/workflows/pr-checklist.yml b/.github/workflows/pr-checklist.yml
new file mode 100644
index 00000000..6f258dfd
--- /dev/null
+++ b/.github/workflows/pr-checklist.yml
@@ -0,0 +1,44 @@
+# This workflow automatically adds a comment containing a reviewer checklist
+# when a new pull request is opened.
+name: Add a comment with reviewer checklist when PR opened
+on:
+  pull_request:
+    types: [opened]
+jobs:
+  pr-checklist:
+    runs-on: ubuntu-latest
+    name: pr-checklist
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: 'Comment PR'
+        uses: actions/github-script@0.3.0
+        if: github.event_name == 'pull_request'
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            var msg = `# Instructions for code reviewer
+
+            Hello reviewer, thanks for taking the time to review this PR!
+
+            - Please use this checklist during your review, checking off items that you have verified are complete!
+            - For PRs that don't make changes to code (e.g., changes to README.md or Github actions workflows), feel free to skip over items on the checklist that are not relevant. Remember it is still important to do a thorough review.
+            - Then, comment on the pull request with your review indicating where you have questions or changes need to be made before merging.
+            - Remember to review **every line of code** you’ve been asked to review, look at the context, make sure you’re improving code health, and compliment developers on good things that they do.
+            - PR reviews are a great way to learn, so feel free to share your tips and tricks. However, for optional changes (i.e., not required for merging), please include \`nit:\` (for nitpicking) before making the suggestion. For example, \`nit:\` I prefer using a \`data.frame()\` instead of a \`matrix\` because...
+            - Engage with the developer when they respond to comments and check off additional boxes as they become complete so the PR can be merged in when all the tasks are fulfilled. Make it clear when this has been reached by commenting on the PR with something like \`This PR is now ready to be merged, no changes needed\`.
+
+            ## Checklist
+
+            - [ ] The PR is requested to be merged into the appropriate branch (typically main)
+            - [ ] The code is well-designed.
+            - [ ] The functionality is good for the users of the code.
+            - [ ] Any User Interface changes are sensible and look good.
+            - [ ] The code isn’t more complex than it needs to be.
+            - [ ] Code coverage remains high, indicating the new code is tested.
+            - [ ] The developer used clear names for everything.
+            - [ ] Comments are clear and useful, and mostly explain why instead of what.
+            - [ ] Code is appropriately documented (doxygen and roxygen).
+            `
+            const { issue: { number: issue_number }, repo: { owner, repo }  } = context;
+            github.issues.createComment({ issue_number, owner, repo, body: msg });

From f92cbe959a8dacad2bb9fab34928ea71b635125d Mon Sep 17 00:00:00 2001
From: Bai-Li-NOAA <Bai-Li-NOAA@users.noreply.github.com>
Date: Mon, 7 Oct 2024 15:50:37 +0000
Subject: [PATCH 10/10] style and docs: run devtools::document() and
 styler::style_pkg()

---
 DESCRIPTION                                   |  2 +-
 R/add_theme.R                                 |  5 ++-
 R/create_template.R                           | 32 +++++++++++--------
 .../fixtures/prepare_ss3_output_files.R       |  6 ++--
 tests/testthat/test-add_theme.R               | 28 ++++++++--------
 tests/testthat/test-convert_output.R          |  5 +--
 6 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7e24106e..9958ccf4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,7 @@ Suggests:
     parallel,
     r4ss,
     rmarkdown,
-    snowfall, 
+    snowfall,
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
diff --git a/R/add_theme.R b/R/add_theme.R
index b32627c1..7ea07dfa 100644
--- a/R/add_theme.R
+++ b/R/add_theme.R
@@ -32,7 +32,7 @@ add_theme <- function(x) {
     theme_obj <- x
     # gt object
   } else if ("kableExtra" %in% class(x) ||
-             (length(class(x)) > 1 && class(x)[2] == "knitr_kable")) {
+    (length(class(x)) > 1 && class(x)[2] == "knitr_kable")) {
     theme_obj <- x
   } else if ("gg" %in% class(x) || "ggplot" %in% class(x)) {
     theme_obj <- x +
@@ -55,8 +55,7 @@ add_theme <- function(x) {
     #   move_legend <- theme_obj +
     #     ggplot2::theme()
     # }
-
-    } else {
+  } else {
     message("NOAA formatting cannot be applied to this object.")
   }
 
diff --git a/R/create_template.R b/R/create_template.R
index 6bee258f..eea7e802 100644
--- a/R/create_template.R
+++ b/R/create_template.R
@@ -469,23 +469,27 @@ create_template <- function(
       # Convert output file if TRUE
       if (convert_output) {
         print("__________Converting output file__________")
-        if(tolower(model) == "bam" & is.null(fleet_names)) {
+        if (tolower(model) == "bam" & is.null(fleet_names)) {
           warning("Fleet names not defined.")
         } else if (tolower(model) == "bam") {
-          convert_output(output_file = model_results,
-                         outdir = resdir,
-                         file_save = TRUE,
-                         model = model,
-                         fleet_names = fleet_names,
-                         savedir = subdir,
-                         save_name = paste(sub(" ", "_", species), "_std_res_", year, sep = ""))
+          convert_output(
+            output_file = model_results,
+            outdir = resdir,
+            file_save = TRUE,
+            model = model,
+            fleet_names = fleet_names,
+            savedir = subdir,
+            save_name = paste(sub(" ", "_", species), "_std_res_", year, sep = "")
+          )
         } else {
-          convert_output(output_file = model_results,
-                         outdir = resdir,
-                         file_save = TRUE,
-                         model = model,
-                         savedir = subdir,
-                         save_name = paste(species, "_std_res_", year, sep = ""))
+          convert_output(
+            output_file = model_results,
+            outdir = resdir,
+            file_save = TRUE,
+            model = model,
+            savedir = subdir,
+            save_name = paste(species, "_std_res_", year, sep = "")
+          )
         }
       }
 
diff --git a/tests/testthat/fixtures/prepare_ss3_output_files.R b/tests/testthat/fixtures/prepare_ss3_output_files.R
index 49640b09..5980c359 100644
--- a/tests/testthat/fixtures/prepare_ss3_output_files.R
+++ b/tests/testthat/fixtures/prepare_ss3_output_files.R
@@ -9,7 +9,7 @@ ss3_exe <- r4ss::get_ss3_exe(
 )
 
 # Function to run a specific SS3 model
-run_ss3_models <- function(model_id, model_dir, exe_dir){
+run_ss3_models <- function(model_id, model_dir, exe_dir) {
   # Define the working directory for the model
   working_dir <- model_dir[model_id]
 
@@ -23,8 +23,8 @@ run_ss3_models <- function(model_id, model_dir, exe_dir){
 # List all the model directories to be processed
 all_models <- list.dirs(
   file.path(test_path("fixtures", "ss3_models"), "models"),
-                      full.names = TRUE,
-                      recursive = FALSE
+  full.names = TRUE,
+  recursive = FALSE
 )
 
 # Detect the number of available CPU cores, leaving one free
diff --git a/tests/testthat/test-add_theme.R b/tests/testthat/test-add_theme.R
index 83d16339..b84508e3 100644
--- a/tests/testthat/test-add_theme.R
+++ b/tests/testthat/test-add_theme.R
@@ -1,5 +1,4 @@
 test_that("add_theme applies NOAA formatting correctly", {
-
   # Test with a ggplot object
   ggplot_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist)) +
     ggplot2::geom_point()
@@ -32,12 +31,11 @@ test_that("add_theme applies NOAA formatting correctly", {
   unsupported_obj <- data.frame(a = 1, b = 2)
   expect_message(add_theme(unsupported_obj), "NOAA formatting cannot be applied to this object.")
 
-  unsupported_obj2 <- list(1,3,4)
+  unsupported_obj2 <- list(1, 3, 4)
   expect_message(add_theme(unsupported_obj2), "NOAA formatting cannot be applied to this object.")
 })
 
 test_that("nmfspalette returns correct scales", {
-
   # Test 1: Ensure nmfspalette integrates with ggplot color scales
   ggplot_obj <- ggplot2::ggplot(data = cars, ggplot2::aes(x = speed, y = dist, color = speed)) +
     ggplot2::geom_point() +
@@ -55,7 +53,6 @@ test_that("nmfspalette returns correct scales", {
   # Check if the correct fill scale is applied
   expect_true("ScaleDiscrete" %in% class(ggplot_fill_obj$scales$scales[[1]]))
   expect_true(ggplot_fill_obj$scales$scales[[1]]$aesthetics == "fill")
-
 })
 
 test_that("nmfspalette scales are applied to ggplot object", {
@@ -72,14 +69,19 @@ test_that("nmfspalette scales are applied to ggplot object", {
   expect_true(grepl("nmfs", deparse(color_scale$call))) # Check if nmfspalette scale is used
 
   # Ensure the color scale is the default "oceans" nmfspalette scale
-  test_plot <- ggplot2::ggplot(Orange,
-                               ggplot2::aes(
-                          x = age,
-                          y = circumference,
-                          color = Tree)) +
-    ggplot2::geom_smooth(se = F,
-                method = "loess",
-                formula = "y ~ x")
+  test_plot <- ggplot2::ggplot(
+    Orange,
+    ggplot2::aes(
+      x = age,
+      y = circumference,
+      color = Tree
+    )
+  ) +
+    ggplot2::geom_smooth(
+      se = F,
+      method = "loess",
+      formula = "y ~ x"
+    )
 
   ## use default color palette
   plot_default <- test_plot +
@@ -98,7 +100,6 @@ test_that("nmfspalette scales are applied to ggplot object", {
 
   ## test if plots' colors are identical
   expect_equal(colors_default, colors_oceans) # Check if the colors match
-
 })
 
 # Test for both color and fill scales
@@ -118,4 +119,3 @@ test_that("nmfspalette scales apply both color and fill scales", {
   fill_scale <- scales[[2]]
   expect_true(grepl("nmfs", deparse(fill_scale$call))) # Fill scale from nmfspalette
 })
-
diff --git a/tests/testthat/test-convert_output.R b/tests/testthat/test-convert_output.R
index 617f7611..df505474 100644
--- a/tests/testthat/test-convert_output.R
+++ b/tests/testthat/test-convert_output.R
@@ -1,5 +1,4 @@
 test_that("convert_output works for SS3", {
-
   # Get a list of directories containing SS3 models
   all_models <- list.dirs(
     file.path(test_path("fixtures", "ss3_models"), "models"),
@@ -8,8 +7,7 @@ test_that("convert_output works for SS3", {
   )
 
   # Loop through each model directory and check convert_output function
-  for (i in seq_along(all_models)){
-
+  for (i in seq_along(all_models)) {
     # Ensure no errors occur while converting SS3 output
     expect_no_error(result <- convert_output(
       output_file = "Report.sso",
@@ -40,5 +38,4 @@ test_that("convert_output works for SS3", {
 
   # Ensure the CSV file was created successfully
   expect_true(file.exists(file.path(tempdir(), "std_model_output.csv")))
-
 })