diff --git a/DESCRIPTION b/DESCRIPTION
index ec9b52e0..91d966c4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -4,13 +4,10 @@ Version: 0.0.0.9000
 Authors@R: 
     person("Samantha", "Schiano", , "samantha.schiano@noaa.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0003-3744-6428"))
-Description: Build a full or update stock assessment report for any stock 
-             assessment model. Parameterization allows the user to call a 
-             template based on their regional science center, species, area, ect.
+Description: Build a full or update stock assessment report for any stock
+    assessment model. Parameterization allows the user to call a template
+    based on their regional science center, species, area, ect.
 License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
 Imports: 
     dplyr,
     flextable,
@@ -22,3 +19,6 @@ Imports:
     openxlsx,
     purrr,
     readr
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
diff --git a/R/add_section.R b/R/add_section.R
index 7796314f..e4ed6236 100644
--- a/R/add_section.R
+++ b/R/add_section.R
@@ -20,28 +20,25 @@
 #' @export
 #'
 #' @examples add_section(title = "Ecosystem Considerations", location = "after-discussion")
-
 add_section <- function(
     title = NULL,
     location = NULL,
-    multi = FALSE
-){
+    multi = FALSE) {
   # Location options
-    # before-section
-    # after-section
-    # in-section (will always apend to the end of the section)
+  # before-section
+  # after-section
+  # in-section (will always apend to the end of the section)
   section_name <- forstringr::str_extract_part(location, "-", before = FALSE)
 
-  if(grepl("before-", location)){
+  if (grepl("before-", location)) {
 
   }
 
-  if(grepl("in-", location)){
+  if (grepl("in-", location)) {
 
   }
 
-  if(grepl("after-", location)){
+  if (grepl("after-", location)) {
 
   }
-
 }
diff --git a/R/chunkr.R b/R/chunkr.R
index f81181aa..544ec63b 100644
--- a/R/chunkr.R
+++ b/R/chunkr.R
@@ -19,18 +19,19 @@ chunkr <- function(
     warnings = "false",
     eval = "true",
     add_option = FALSE,
-    chunk_op = NULL){
+    chunk_op = NULL) {
   chunk <- paste0(
     "```{r} \n",
     # Add output options
     "#| echo: ", echo, " \n",
     "#| warning: ", warnings, " \n",
-    "#| eval: ", eval, " \n")
-    if(add_option==TRUE){
-      for (i in 1:length(chunk_op)) {
-        chunk <- paste0(chunk, "#| ", chunk_op[i], " \n")
-      }
+    "#| eval: ", eval, " \n"
+  )
+  if (add_option == TRUE) {
+    for (i in 1:length(chunk_op)) {
+      chunk <- paste0(chunk, "#| ", chunk_op[i], " \n")
     }
-    chunk <- paste0(chunk, x, "\n", "``` \n")
-    return(chunk)
+  }
+  chunk <- paste0(chunk, x, "\n", "``` \n")
+  return(chunk)
 }
diff --git a/R/convert_output.R b/R/convert_output.R
index f97ae52a..d82dbd9b 100644
--- a/R/convert_output.R
+++ b/R/convert_output.R
@@ -14,32 +14,27 @@
 #'         adapt results among regional assessments.
 #'
 #' @examples
-#' convert_output(output.file = "CumReport.sso", outdir = "~", model = 'ss', file.format = 'multi', multi.file = FALSE)
+#' convert_output(output.file = "CumReport.sso", outdir = "~", model = "ss", file.format = "multi", multi.file = FALSE)
 #'
 #' @export
 #'
 convert_output <- function(
     output.file = NULL,
     outdir = NULL,
-    model = NULL){
-
-  if(model=="ss"){
+    model = NULL) {
+  if (model == "ss") {
     # Fxn adapted from r4ss::SS_output
-
   }
 
-  if(model=='bam'){
-      dat <- dget(output.file)
+  if (model == "bam") {
+    dat <- dget(output.file)
   }
 
-  if(model=='asap'){
-
+  if (model == "asap") {
     # This is how Bai read the ASAP output
     # asap_output conversion written by Bai Li
-    asap_output <- dget(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep=""), "asap3.rdat"))
-    setwd(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep="")))
+    asap_output <- dget(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep = ""), "asap3.rdat"))
+    setwd(file.path(casedir, "output", subdir, paste("s", keep_sim_id[om_sim], sep = "")))
     asap_std <- readRep("asap3", suffix = ".std")
-
   }
-
 }
diff --git a/R/create_style_css.R b/R/create_style_css.R
index 910898e4..2ca0646d 100644
--- a/R/create_style_css.R
+++ b/R/create_style_css.R
@@ -1,18 +1,17 @@
 create_styles_css <- function(
     species = NULL,
-    savedir = NULL
-){
-  #Add species image to title
+    savedir = NULL) {
+  # Add species image to title
   spp_name <- sub(" ", "_", species)
-  spp_image <- list.files(path = here::here('inst', 'resources', 'spp_img'), pattern = spp_name)
+  spp_image <- list.files(path = here::here("inst", "resources", "spp_img"), pattern = spp_name)
   styles_css <- paste(
     ".quarto-title-block .quarto-title-banner {", "\n",
-      "  ", "background-image: ", spp_image, ";", "\n",
-      "  ", "background-size: 300px;", "\n",
-      "  ", "background-position: left;", "\n",
-      "  ", "background-repeat: no-repeat;", "\n",
-      "  ", "padding-left: 10px;", "\n",
-      "  ", "background-origin: content-box;", "\n",
+    "  ", "background-image: ", spp_image, ";", "\n",
+    "  ", "background-size: 300px;", "\n",
+    "  ", "background-position: left;", "\n",
+    "  ", "background-repeat: no-repeat;", "\n",
+    "  ", "padding-left: 10px;", "\n",
+    "  ", "background-origin: content-box;", "\n",
     "}", "\n"
   )
 
diff --git a/R/create_template.R b/R/create_template.R
index 93b87b4c..caaa1ac2 100644
--- a/R/create_template.R
+++ b/R/create_template.R
@@ -41,18 +41,19 @@
 #'         each of the child documents should be edited separately.
 #' @export
 #'
-#' @examples create_template(new_template = TRUE, format = "pdf",
-#' office = "NEFSC", region = "GB", species = "Bluefish",spp_latin = "bluishfihesi",
-#' year = 2024, author = c("John Snow", "Danny Phantom", "Patrick Star"),
-#' include_affiliation = TRUE, parameters = TRUE, param_names = c("fleet1", "fleet2", "model"),
-#' param_values = c("Commercial", "Recreational", "Woods Hole Assessment Model"),
-#' type = "RT")
-
+#' @examples create_template(
+#'   new_template = TRUE, format = "pdf",
+#'   office = "NEFSC", region = "GB", species = "Bluefish", spp_latin = "bluishfihesi",
+#'   year = 2024, author = c("John Snow", "Danny Phantom", "Patrick Star"),
+#'   include_affiliation = TRUE, parameters = TRUE, param_names = c("fleet1", "fleet2", "model"),
+#'   param_values = c("Commercial", "Recreational", "Woods Hole Assessment Model"),
+#'   type = "RT"
+#' )
 create_template <- function(
     new_template = TRUE,
     tempdir = here::here(),
-    format = c("pdf","docx","html", NULL),
-    office = c("AFSC","PIFSC","NEFSC","NWFSC","SEFSC","SWFSC"),
+    format = c("pdf", "docx", "html", NULL),
+    office = c("AFSC", "PIFSC", "NEFSC", "NWFSC", "SEFSC", "SWFSC"),
     region = NULL,
     complex = "NO",
     species = NULL,
@@ -73,338 +74,371 @@ create_template <- function(
     secdir = NULL,
     new_section = NULL,
     section_location = NULL,
-    type = c("OA","UP","RT","FULL","MT"),
+    type = c("OA", "UP", "RT", "FULL", "MT"),
     prev_year = NULL,
     custom = FALSE,
-    custom_sections = NULL
-    ){
-
+    custom_sections = NULL) {
   # If analyst forgets to add year, default will be the current year report is being produced
-  if(is.null(year)){
-    year <- format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"),"%Y")
+  if (is.null(year)) {
+    year <- format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y")
   }
 
   # Name report
-  report_name <- paste0(type,
-                        "_")
-  if(!is.null(region)){
-    report_name <- paste0(report_name,
-                          gsub("(\\b[A-Z])[^A-Z]+", "\\1", region))
+  report_name <- paste0(
+    type,
+    "_"
+  )
+  if (!is.null(region)) {
+    report_name <- paste0(
+      report_name,
+      gsub("(\\b[A-Z])[^A-Z]+", "\\1", region)
+    )
   }
-  report_name <- paste0(report_name, "_",
-                        gsub(" ", "_", species),
-                        "_skeleton.qmd")
+  report_name <- paste0(
+    report_name, "_",
+    gsub(" ", "_", species),
+    "_skeleton.qmd"
+  )
 
   # Select parameter from list
   format <- match.arg(format, several.ok = FALSE)
   office <- match.arg(office, several.ok = FALSE)
   type <- match.arg(type, several.ok = FALSE)
 
-  if(!is.null(region)){
-    subdir <- here::here('inst', 'templates', 'archive', office, species, region, year)
-    subdir <- system.file('inst', 'templates', 'archive', office, species, region, year, package = 'ASAR')
+  if (!is.null(region)) {
+    subdir <- here::here("inst", "templates", "archive", office, species, region, year)
+    subdir <- system.file("inst", "templates", "archive", office, species, region, year, package = "ASAR")
   } else {
-    subdir <- here::here('inst', 'templates', 'archive', office, species, year)
+    subdir <- here::here("inst", "templates", "archive", office, species, year)
   }
   # Always creating new directory for each assessment since they will each change
   # Allow NOAA to keep a record of each assessment file
   # These will need to be cataloged into a cloud system somehow
-  if(!dir.exists(here::here('inst','templates', 'archive', office, species))){
-    dir.create(here::here('inst','templates', 'archive', office, species))
+  if (!dir.exists(here::here("inst", "templates", "archive", office, species))) {
+    dir.create(here::here("inst", "templates", "archive", office, species))
   }
 
-  if(!is.null(region)){
-    if(!dir.exists(here::here('inst','templates', 'archive', office, species, region))){
-      dir.create(here::here('inst','templates', 'archive', office, species, region))
+  if (!is.null(region)) {
+    if (!dir.exists(here::here("inst", "templates", "archive", office, species, region))) {
+      dir.create(here::here("inst", "templates", "archive", office, species, region))
     }
     # Create new folder for current year
-    if(!dir.exists(here::here('inst','templates', 'archive', office, species, region, year))){
-      dir.create(here::here('inst','templates', 'archive', office, species, region, year))
+    if (!dir.exists(here::here("inst", "templates", "archive", office, species, region, year))) {
+      dir.create(here::here("inst", "templates", "archive", office, species, region, year))
     }
   } else {
     # Create new folder for current year
-    if(!dir.exists(here::here('inst','templates', 'archive', office, species, year))){
-      dir.create(here::here('inst','templates', 'archive', office, species, year))
+    if (!dir.exists(here::here("inst", "templates", "archive", office, species, year))) {
+      dir.create(here::here("inst", "templates", "archive", office, species, year))
     }
   }
 
-  if(new_template==TRUE){
-  # Pull skeleton for sections
-  current_folder <- here::here('inst','templates','skeleton')
-  new_folder <- subdir
-  files_to_copy <- list.files(current_folder)
-  file.copy(file.path(current_folder, files_to_copy), new_folder)
-
-  # Part I
-  # Create a report template file to render for the region and species
-  # Create YAML header for document
-  # Write title based on report type and region
-  if(alt_title==FALSE){
-    title <- write_title(office = office, species = species, spp_latin = spp_latin, region = region, type = type)
-  } else if (alt_title==TRUE){
-    if(!exists(title)){
-      stop("Alternate title not defined. Please define an alternative title in the parameter 'title'.")
-    } else {
-      title <- paste(title)
+  if (new_template == TRUE) {
+    # Pull skeleton for sections
+    current_folder <- here::here("inst", "templates", "skeleton")
+    new_folder <- subdir
+    files_to_copy <- list.files(current_folder)
+    file.copy(file.path(current_folder, files_to_copy), new_folder)
+
+    # Part I
+    # Create a report template file to render for the region and species
+    # Create YAML header for document
+    # Write title based on report type and region
+    if (alt_title == FALSE) {
+      title <- write_title(office = office, species = species, spp_latin = spp_latin, region = region, type = type)
+    } else if (alt_title == TRUE) {
+      if (!exists(title)) {
+        stop("Alternate title not defined. Please define an alternative title in the parameter 'title'.")
+      } else {
+        title <- paste(title)
+      }
     }
-  }
 
-  # Pull authors and affiliations from national db
-  # Parameters to add authorship to YAML
-  # Read authorship file
-  authors <- utils::read.csv(here::here('inst', 'resources', 'authorship.csv')) |>
-    dplyr::mutate(mi = dplyr::case_when(mi=="" ~ NA,
-                                        TRUE ~ mi),
-                  name = dplyr::case_when(is.na(mi) ~ paste0(first," ", last),
-                                          TRUE ~ paste(first, mi, last, sep = " "))) |>
-    dplyr::select(name, office) |>
-    dplyr::filter(name %in% author)
-  if(include_affiliation==TRUE){
-    affil <- read.csv(here::here('inst', 'resources', 'affiliation_info.csv'))
-  }
-  author_list <- list()
-
-  if(include_affiliation==TRUE & simple_affiliation==FALSE){
-    for(i in 1:nrow(authors)){
-      auth <- authors[i,]
-      aff <- affil |>
-        dplyr::filter(affiliation==auth$office)
-      paste0("  ", "- name: ", "'", auth$name, "'", "\n",
-             "  ", "  ", "affiliations:", "\n",
-             "  ", "  ", "  ", "- name: ", "'", "NOAA Fisheries ", aff$name, "'", "\n",
-             "  ", "  ", "  ", "  ", "address: ", "'", aff$address, "'","\n",
-             "  ", "  ", "  ", "  ", "city: ", "'", aff$city, "'","\n",
-             "  ", "  ", "  ", "  ", "state: ", "'", aff$state, "'","\n",
-             "  ", "  ", "  ", "  ", "postal-code: ", "'", aff$postal.code, "'","\n"
-             # sep = " "
-      ) -> author_list[[i]]
-    }
-  } else if(include_affiliation==TRUE & simple_affiliation==TRUE){
-    for(i in 1:nrow(authors)){
-      auth <- authors[i,]
-      aff <- affil |>
-        dplyr::filter(affiliation==auth$office)
-      paste0("  ", "- name: ", "'", auth$name, "'", "\n",
-             "  ", "  ", "affiliations: ", "'", aff$name, "'", "\n"
-      ) -> author_list[[i]]
-    }
-  } else {
-    for(i in 1:nrow(authors)){
-      auth <- authors[i,]
-      paste0("  ", "- ", "'", auth$name, "'", "\n") -> author_list[[i]]
+    # Pull authors and affiliations from national db
+    # Parameters to add authorship to YAML
+    # Read authorship file
+    authors <- utils::read.csv(here::here("inst", "resources", "authorship.csv")) |>
+      dplyr::mutate(
+        mi = dplyr::case_when(
+          mi == "" ~ NA,
+          TRUE ~ mi
+        ),
+        name = dplyr::case_when(
+          is.na(mi) ~ paste0(first, " ", last),
+          TRUE ~ paste(first, mi, last, sep = " ")
+        )
+      ) |>
+      dplyr::select(name, office) |>
+      dplyr::filter(name %in% author)
+    if (include_affiliation == TRUE) {
+      affil <- read.csv(here::here("inst", "resources", "affiliation_info.csv"))
     }
-  }
-
-  # Creating YAML
-  yaml <- paste0(
-    # start YAML notation
-    "---", "\n",
-
-    # Tile
-    "title: ", "'", title, "'", "\n",
-
-    # Author
-    "author:", "\n")
-  # Add authors
-  add_authors <- NULL
-  for (i in 1:length(author_list)) {
-    toad <- paste(author_list[[i]], sep =",")
-    add_authors <- paste0(add_authors, toad) # -> add_authors
-  }
-  yaml <- paste0(yaml, add_authors)
-
-  # Add other parts
-  yaml <- paste0(yaml,
-                 # Date
-                 "date: today", "\n"
-                 )
-
-  # Formating
-
-  if(include_affiliation==TRUE){
-
-    yaml <- paste(yaml, "format: \n",
-                  "  " , format, ": \n",
-                  "  ", "  ", "keep-tex: ", "true \n",
-                  "  " , "  ", "template-partials: \n",
-                  "  ", "  ", "  ", " - graphics.tex \n",
-                  "  ", "  ", "  ", " - title.tex \n",
-                  "  ", "  ", "include-in-header: \n",
-                  "  ", "  ", "  ", " - in-header.tex \n",
-                  sep = "")
-
-  } else if(include_affiliation==FALSE){
-
-    yaml <- paste0(yaml, "format: \n",
-                   "  ", format, ": \n",
-                   "  ", "  ", "template-partials: \n",
-                   "  ", "  ", "  ", "- sadraft.tex \n",
-                   "  ", "  ", "keep-tex: true \n"
-                   )
-
-  }
-
-  # Parameters
-  # office, region, and species are default parameters
-  yaml <- paste0(yaml, "params:", "\n",
-                 "  ", " ", "office: ", "'", office, "'", "\n",
-                 "  ", " ", "species: ", "'", species, "'", "\n",
-                 "  ", " ", "spp_latin: ", "'", spp_latin, "'", "\n"
-                 )
-  if(!is.null(region)){
-    yaml <- paste0(yaml, "  ", " ", "region: ", "'", region, "'", "\n")
-  }
-  if(parameters==TRUE){
-    if(!is.null(param_names) & !is.null(param_values)){
-      add_params <- NULL
-      for (i in 1:length(param_names)) {
-        toad <- paste("  ", " ", param_names[i], ": ", "'",param_values[i], "'", "\n", sep="")
-        add_params <- paste0(add_params, toad)
+    author_list <- list()
+
+    if (include_affiliation == TRUE & simple_affiliation == FALSE) {
+      for (i in 1:nrow(authors)) {
+        auth <- authors[i, ]
+        aff <- affil |>
+          dplyr::filter(affiliation == auth$office)
+        paste0(
+          "  ", "- name: ", "'", auth$name, "'", "\n",
+          "  ", "  ", "affiliations:", "\n",
+          "  ", "  ", "  ", "- name: ", "'", "NOAA Fisheries ", aff$name, "'", "\n",
+          "  ", "  ", "  ", "  ", "address: ", "'", aff$address, "'", "\n",
+          "  ", "  ", "  ", "  ", "city: ", "'", aff$city, "'", "\n",
+          "  ", "  ", "  ", "  ", "state: ", "'", aff$state, "'", "\n",
+          "  ", "  ", "  ", "  ", "postal-code: ", "'", aff$postal.code, "'", "\n"
+          # sep = " "
+        ) -> author_list[[i]]
+      }
+    } else if (include_affiliation == TRUE & simple_affiliation == TRUE) {
+      for (i in 1:nrow(authors)) {
+        auth <- authors[i, ]
+        aff <- affil |>
+          dplyr::filter(affiliation == auth$office)
+        paste0(
+          "  ", "- name: ", "'", auth$name, "'", "\n",
+          "  ", "  ", "affiliations: ", "'", aff$name, "'", "\n"
+        ) -> author_list[[i]]
       }
     } else {
-        print("Please define parameter names (param_names) and values (param_values).")
+      for (i in 1:nrow(authors)) {
+        auth <- authors[i, ]
+        paste0("  ", "- ", "'", auth$name, "'", "\n") -> author_list[[i]]
+      }
     }
 
-    yaml <- paste0(yaml, add_params)
-  }
-
-  # Add style guide
-  create_style_css(species = species, savedir = subdir)
-
-  yaml <- paste0(yaml,
-                 "css: styles.css", "\n")
-
-  # Close yaml
-  yaml <- paste0(yaml, "---")
-
-  print("__________Built YAML Header______________")
-  # yaml_save <- capture.output(cat(yaml))
-  # cat(yaml, file = here('template','yaml_header.qmd'))
-
-  # Add chunk to load in assessment data
-  ass_output <- chunkr(
-    "convert_output( output.file=", model_results, ", model=", model, ")",
-    eval = "false" # set false for testing this function in the template for now
-  )
-
-  # print("_______Standardized output data________")
-
-  # Add page for citation of assessment report
-  citation <- generate_citation(author = author,
-                                title = title,
-                                year = year,
-                                office = office)
+    # Creating YAML
+    yaml <- paste0(
+      # start YAML notation
+      "---", "\n",
+
+      # Tile
+      "title: ", "'", title, "'", "\n",
+
+      # Author
+      "author:", "\n"
+    )
+    # Add authors
+    add_authors <- NULL
+    for (i in 1:length(author_list)) {
+      toad <- paste(author_list[[i]], sep = ",")
+      add_authors <- paste0(add_authors, toad) # -> add_authors
+    }
+    yaml <- paste0(yaml, add_authors)
+
+    # Add other parts
+    yaml <- paste0(
+      yaml,
+      # Date
+      "date: today", "\n"
+    )
+
+    # Formating
+
+    if (include_affiliation == TRUE) {
+      yaml <- paste(yaml, "format: \n",
+        "  ", format, ": \n",
+        "  ", "  ", "keep-tex: ", "true \n",
+        "  ", "  ", "template-partials: \n",
+        "  ", "  ", "  ", " - graphics.tex \n",
+        "  ", "  ", "  ", " - title.tex \n",
+        "  ", "  ", "include-in-header: \n",
+        "  ", "  ", "  ", " - in-header.tex \n",
+        sep = ""
+      )
+    } else if (include_affiliation == FALSE) {
+      yaml <- paste0(
+        yaml, "format: \n",
+        "  ", format, ": \n",
+        "  ", "  ", "template-partials: \n",
+        "  ", "  ", "  ", "- sadraft.tex \n",
+        "  ", "  ", "keep-tex: true \n"
+      )
+    }
 
-  print("_______Generate Report Citaiton________")
+    # Parameters
+    # office, region, and species are default parameters
+    yaml <- paste0(
+      yaml, "params:", "\n",
+      "  ", " ", "office: ", "'", office, "'", "\n",
+      "  ", " ", "species: ", "'", species, "'", "\n",
+      "  ", " ", "spp_latin: ", "'", spp_latin, "'", "\n"
+    )
+    if (!is.null(region)) {
+      yaml <- paste0(yaml, "  ", " ", "region: ", "'", region, "'", "\n")
+    }
+    if (parameters == TRUE) {
+      if (!is.null(param_names) & !is.null(param_values)) {
+        add_params <- NULL
+        for (i in 1:length(param_names)) {
+          toad <- paste("  ", " ", param_names[i], ": ", "'", param_values[i], "'", "\n", sep = "")
+          add_params <- paste0(add_params, toad)
+        }
+      } else {
+        print("Please define parameter names (param_names) and values (param_values).")
+      }
 
-  # Create report template
+      yaml <- paste0(yaml, add_params)
+    }
 
-  if(custom==FALSE){
-    if(type=="OA" | type=="UP" | type=="MT"){
-      sections <- paste_child(
-        c("01_executive_summary.qmd",
-          "02_introduction.qmd"),
-        label = c("executive_summary",
-                  "introduction")
+    # Add style guide
+    create_style_css(species = species, savedir = subdir)
+
+    yaml <- paste0(
+      yaml,
+      "css: styles.css", "\n"
+    )
+
+    # Close yaml
+    yaml <- paste0(yaml, "---")
+
+    print("__________Built YAML Header______________")
+    # yaml_save <- capture.output(cat(yaml))
+    # cat(yaml, file = here('template','yaml_header.qmd'))
+
+    # Add chunk to load in assessment data
+    ass_output <- chunkr(
+      "convert_output( output.file=", model_results, ", model=", model, ")",
+      eval = "false" # set false for testing this function in the template for now
+    )
+
+    # print("_______Standardized output data________")
+
+    # Add page for citation of assessment report
+    citation <- generate_citation(
+      author = author,
+      title = title,
+      year = year,
+      office = office
+    )
+
+    print("_______Generate Report Citaiton________")
+
+    # Create report template
+
+    if (custom == FALSE) {
+      if (type == "OA" | type == "UP" | type == "MT") {
+        sections <- paste_child(
+          c(
+            "01_executive_summary.qmd",
+            "02_introduction.qmd"
+          ),
+          label = c(
+            "executive_summary",
+            "introduction"
+          )
         )
-    } else if (type=="RT" | type=="FULL"){
-      sections <- paste_child(c(
-          "01_executive_summary.qmd",
-          "02_introduction.qmd",
-          "03_data.qmd",
-          "04_model.qmd",
-          "05_results.qmd",
-          "06_discussion.qmd",
-          "07_acknowledgements.qmd",
-          "08_references.qmd",
-          "09_tables.qmd",
-          "10_figures.qmd",
-          "11_appendix.qmd"
-        ),
-        label = c("executive_summary",
-                  "introduction",
-                  "data",
-                  "model",
-                  "results",
-                  "discussion",
-                  "acknowlesgements",
-                  "references",
-                  "tables",
-                  "figures",
-                  "appendix"
-                  )
+      } else if (type == "RT" | type == "FULL") {
+        sections <- paste_child(
+          c(
+            "01_executive_summary.qmd",
+            "02_introduction.qmd",
+            "03_data.qmd",
+            "04_model.qmd",
+            "05_results.qmd",
+            "06_discussion.qmd",
+            "07_acknowledgements.qmd",
+            "08_references.qmd",
+            "09_tables.qmd",
+            "10_figures.qmd",
+            "11_appendix.qmd"
+          ),
+          label = c(
+            "executive_summary",
+            "introduction",
+            "data",
+            "model",
+            "results",
+            "discussion",
+            "acknowlesgements",
+            "references",
+            "tables",
+            "figures",
+            "appendix"
+          )
         )
-    } else {
-      print("Type of assessment report is not defined")
-    }
-  } else {
-    # Option for building custom template
-    # Create custom template from existing skeleton sections
-    if(add_section==FALSE){
-      section_list <- list()
-      for(i in 1:length(custom_sections)){
-        grep(
-          x = list.files(here::here('inst', 'templates', 'skeleton')),
-          pattern = custom_sections[i],
-          value = TRUE) -> section_list[i]
+      } else {
+        print("Type of assessment report is not defined")
       }
-      sections <- paste_child(section_list,
-                              label = custom_sections)
     } else {
-      # Create custom template using existing sections and new sections from analyst
-      # Add sections from package options
-      if(is.null(customs_sections)){stop("Custom sectioning not defined.")}
-      section_list <- list()
-      if(custom==TRUE){
-        for(i in 1:length(custom_sections)){
+      # Option for building custom template
+      # Create custom template from existing skeleton sections
+      if (add_section == FALSE) {
+        section_list <- list()
+        for (i in 1:length(custom_sections)) {
           grep(
-            x = list.files(here::here('inst', 'templates', 'skeleton')),
+            x = list.files(here::here("inst", "templates", "skeleton")),
             pattern = custom_sections[i],
-            value = TRUE) -> section_list[i]
+            value = TRUE
+          ) -> section_list[i]
+        }
+        sections <- paste_child(section_list,
+          label = custom_sections
+        )
+      } else {
+        # Create custom template using existing sections and new sections from analyst
+        # Add sections from package options
+        if (is.null(customs_sections)) {
+          stop("Custom sectioning not defined.")
+        }
+        section_list <- list()
+        if (custom == TRUE) {
+          for (i in 1:length(custom_sections)) {
+            grep(
+              x = list.files(here::here("inst", "templates", "skeleton")),
+              pattern = custom_sections[i],
+              value = TRUE
+            ) -> section_list[i]
+          }
         }
-      }
         # Add new sections
-      if(is.null(new_section) | is.null(section_location)){stop("New sections and locations not defined.")}
+        if (is.null(new_section) | is.null(section_location)) {
+          stop("New sections and locations not defined.")
+        }
 
         for (i in 1:length(new_section)) {
           add_sec_new[i] <- paste0(secdir, "/", new_section[i])
         }
 
-      append(section_list, add_sec_new)
+        append(section_list, add_sec_new)
 
         sections <- paste_child(section_list,
-                                label = section_list)
+          label = section_list
+        )
+      }
     }
-  }
-
-  # Combine template sections
-  report_template <- paste(yaml,
-                           ass_output,
-                           citation,
-                           sections,
-                           sep = "\n")
 
-  print("___Created desired report template______")
+    # Combine template sections
+    report_template <- paste(yaml,
+      ass_output,
+      citation,
+      sections,
+      sep = "\n"
+    )
 
-  # Save template as .qmd to render
-  utils::capture.output(cat(report_template), file = paste0(subdir, "/", report_name), append = FALSE)
+    print("___Created desired report template______")
 
-  print(cat(paste0("Saved report template in directory: ", subdir, "\n",
-        "To proceeed, please edit sections within the report template in order to produce a completed stock assessment report.")))
+    # Save template as .qmd to render
+    utils::capture.output(cat(report_template), file = paste0(subdir, "/", report_name), append = FALSE)
 
+    print(cat(paste0(
+      "Saved report template in directory: ", subdir, "\n",
+      "To proceeed, please edit sections within the report template in order to produce a completed stock assessment report."
+    )))
   } else {
     # Copy old template and rename for new year
     # Create copy of previous assessment
-    if(!is.null(region)){
-      olddir <- here::here('inst', 'templates', 'archive', office, species, region, prev_year)
-      invisible(file.copy(file.path(here::here('inst', 'templates', 'archive', office, species, region, prev_year), list.files(olddir)), subdir, recursive = FALSE))
+    if (!is.null(region)) {
+      olddir <- here::here("inst", "templates", "archive", office, species, region, prev_year)
+      invisible(file.copy(file.path(here::here("inst", "templates", "archive", office, species, region, prev_year), list.files(olddir)), subdir, recursive = FALSE))
     } else {
-      olddir <- here::here('inst', 'templates', 'archive', office, species, prev_year)
-      invisible(file.copy(file.path(here::here('inst', 'templates', 'archive', office, species, prev_year), list.files(olddir)), subdir, recursive = FALSE))
+      olddir <- here::here("inst", "templates", "archive", office, species, prev_year)
+      invisible(file.copy(file.path(here::here("inst", "templates", "archive", office, species, prev_year), list.files(olddir)), subdir, recursive = FALSE))
     }
 
     # Open previous skeleton
     skeleton <- list.files(subdir, pattern = "skeleton.qmd")
-    file.show(file.path(paste0(subdir,"/",report_name))) # this opens the new file, but also restarts the session
+    file.show(file.path(paste0(subdir, "/", report_name))) # this opens the new file, but also restarts the session
   }
 }
diff --git a/R/export_object.R b/R/export_object.R
index 6df5ae40..f0047d6a 100644
--- a/R/export_object.R
+++ b/R/export_object.R
@@ -12,50 +12,41 @@
 #' @export
 #'
 #' @examples
-#' source <- c("NMFS Groundfish Survey","","U.S. Trawl Fisheries", "", "")
-#' data <- c("Survey biomass","Age Composition","Catch","Age Composition","Length Composition")
-#' years <- c("1984-1999 (triennial), 2001-2013 (biennial)","1984, 1987, 1990, 1993, 1996, 1999, 2003, 2005, 2007, 2009, 2011","1961-2013", "1990,1998-2002, 2004, 2005, 2006, 2008, 2010","1963-1977, 1991-1997")
+#' source <- c("NMFS Groundfish Survey", "", "U.S. Trawl Fisheries", "", "")
+#' data <- c("Survey biomass", "Age Composition", "Catch", "Age Composition", "Length Composition")
+#' years <- c("1984-1999 (triennial), 2001-2013 (biennial)", "1984, 1987, 1990, 1993, 1996, 1999, 2003, 2005, 2007, 2009, 2011", "1961-2013", "1990,1998-2002, 2004, 2005, 2006, 2008, 2010", "1963-1977, 1991-1997")
 #' test_obj <- data.frame(source, data, years)
 #'
 #' export_object(object = test_obj, file_format = "csv")
 #'
-
-
 export_object <- function(
     object = NULL,
-    file_format = "docx"){
-
-  if(file_format=="pdf"){
-
-    grDevices::pdf(file = paste0(here::here('exported'),"/",sprintf(deparse(substitute(object))),".pdf")) # pdf fxn in base r
+    file_format = "docx") {
+  if (file_format == "pdf") {
+    grDevices::pdf(file = paste0(here::here("exported"), "/", sprintf(deparse(substitute(object))), ".pdf")) # pdf fxn in base r
     gridExtra::grid.table(object)
     grDevices::dev.off()
     # Doesn't fit to page
-
-  } else if(file_format=="docx"){
-
+  } else if (file_format == "docx") {
     doc_exp <- officer::read_docx()
     doc_exp <- officer::body_add_table(object)
     print(doc_exp,
-          target = paste0(here::here('exported'),"/", sprintf(deparse(substitute(object))),".docx")) # %>% invisible()
-
-  } else if(file_format=="xlsx"){
-
+      target = paste0(here::here("exported"), "/", sprintf(deparse(substitute(object))), ".docx")
+    ) # %>% invisible()
+  } else if (file_format == "xlsx") {
     openxlsx::write.xlsx(object,
-                         file = paste0(here::here('exported'),"/", sprintf(deparse(substitute(object))), ".xlsx"),
-                         overwrite = FALSE)
-
-  } else if(file_format=="csv"){
-
+      file = paste0(here::here("exported"), "/", sprintf(deparse(substitute(object))), ".xlsx"),
+      overwrite = FALSE
+    )
+  } else if (file_format == "csv") {
     utils::write.csv(object,
-              file = paste0(here::here('exported'),"/", sprintf(deparse(substitute(object))), ".csv"),
-              row.names = FALSE)
-
-  } else if(file_format=="rdata"){
-
+      file = paste0(here::here("exported"), "/", sprintf(deparse(substitute(object))), ".csv"),
+      row.names = FALSE
+    )
+  } else if (file_format == "rdata") {
     save(object,
-         file = paste0(here::here('exported'), "/", sprintf(deparse(substitute(object))), ".Rdata"))
-
+      file = paste0(here::here("exported"), "/", sprintf(deparse(substitute(object))), ".Rdata")
+    )
   } else {
     stop("File format is not currently available for output. Please open an issue in the GitHub repository to request the addition.")
   }
diff --git a/R/generate_citation.R b/R/generate_citation.R
index c64c6d79..316908ef 100644
--- a/R/generate_citation.R
+++ b/R/generate_citation.R
@@ -9,79 +9,82 @@
 #'         the stock assessment report generated in the ASAR package.
 #' @export
 #'
-#' @examples generate_citation(title = "SA Report for Jellyfish",
-#' author = c("John Snow", "Danny Phantom", "Patrick Star"),
-#' year = 2024, office = "NEFSC")
+#' @examples generate_citation(
+#'   title = "SA Report for Jellyfish",
+#'   author = c("John Snow", "Danny Phantom", "Patrick Star"),
+#'   year = 2024, office = "NEFSC"
+#' )
 #'
 generate_citation <- function(
     author = NULL,
     title = NULL,
     year = NULL,
-    office = NULL
-    ){
-
-  if(office %in% c('NEFSC','SEFSC','NWFSC','SWFSC','PIFSC','AFSC')){
+    office = NULL) {
+  if (office %in% c("NEFSC", "SEFSC", "NWFSC", "SWFSC", "PIFSC", "AFSC")) {
     off_title <- "NOAA Fisheries Science Center"
   }
 
   office1 <- office
-  office_loc <- utils::read.csv(here::here('inst', 'resources', 'affiliation_info.csv')) |>
-    dplyr::filter(affiliation==office1)
+  office_loc <- utils::read.csv(here::here("inst", "resources", "affiliation_info.csv")) |>
+    dplyr::filter(affiliation == office1)
   # Check
-  if(nrow(office_loc)>1){stop("There is more than one office being selected in this function. Please review 'generate_ciation.R'.")}
+  if (nrow(office_loc) > 1) {
+    stop("There is more than one office being selected in this function. Please review 'generate_ciation.R'.")
+  }
 
   loc_city <- office_loc$city
   loc_state <- office_loc$state
 
   # Author naming convention formatting
-  if(length(author)>1){
+  if (length(author) > 1) {
     author1 <- unlist(strsplit(author[1], split = " "))
     author1 <- paste0(
-      ifelse(length(author1)==3, author1[3], author1[2]), ", ",
+      ifelse(length(author1) == 3, author1[3], author1[2]), ", ",
       substring(author1[1], 1, 1), ".",
-      ifelse(length(author1)==3, author1[2], "")
+      ifelse(length(author1) == 3, author1[2], "")
     )
-  author_list <- paste0(author1)
-    for(i in 2:length(author)){
+    author_list <- paste0(author1)
+    for (i in 2:length(author)) {
       auth_extract <- unlist(strsplit(author[i], split = " "))
       auth_extract2 <- paste0(
         substring(auth_extract[1], 1, 1), ".",
-        ifelse(length(auth_extract)==3, auth_extract[2], ""), " ",
-        ifelse(length(auth_extract)==3, auth_extract[3], auth_extract[2])
-        )
+        ifelse(length(auth_extract) == 3, auth_extract[2], ""), " ",
+        ifelse(length(auth_extract) == 3, auth_extract[3], auth_extract[2])
+      )
       author_list <- paste0(author_list, ", ", auth_extract2)
     }
   } else {
     author_spl <- unlist(strsplit(author, split = " "))
     author_list <- paste0(
-      ifelse(length(author_spl)==3, author_spl[3], author_spl[2]), ", ",
+      ifelse(length(author_spl) == 3, author_spl[3], author_spl[2]), ", ",
       substring(author_spl[[1]][1], 1, 1), ".",
-      ifelse(length(author_spl)==3, author_spl[2], "")
+      ifelse(length(author_spl) == 3, author_spl[2], "")
     )
   }
 
   # Create citation string
-  if(office!="SEFSC"){
-  cit <- paste0("{{< pagebreak >}} \n",
-                "\n",
-                "Please cite this publication as \n",
-                "\n",
-                author_list, ". ", year, ". ",
-                title, ". ", off_title, ", ",
-                loc_city, ", ", loc_state, ". "
-                )
+  if (office != "SEFSC") {
+    cit <- paste0(
+      "{{< pagebreak >}} \n",
+      "\n",
+      "Please cite this publication as \n",
+      "\n",
+      author_list, ". ", year, ". ",
+      title, ". ", off_title, ", ",
+      loc_city, ", ", loc_state, ". "
+    )
   } else {
-    cit <- paste0("'{{< pagebreak >}}' \n",
-                  "\n",
-                  "Please cite this publication as \n",
-                  "\n",
-                  "SEDAR. ", year, ". ", title,
-                  "SEDAR, North Charleston SC. XXpp. ",
-                  "available online at: http://sedarweb.org/"
-                 )
+    cit <- paste0(
+      "'{{< pagebreak >}}' \n",
+      "\n",
+      "Please cite this publication as \n",
+      "\n",
+      "SEDAR. ", year, ". ", title,
+      "SEDAR, North Charleston SC. XXpp. ",
+      "available online at: http://sedarweb.org/"
+    )
   }
 
   # Add citation as .qmd to add into template
   return(cit)
-
 }
diff --git a/R/paste_child.R b/R/paste_child.R
index 9ad1104c..172c6235 100644
--- a/R/paste_child.R
+++ b/R/paste_child.R
@@ -8,11 +8,10 @@
 #' @export
 #'
 #' @examples paste_child("test_quarto.qmd", label = "test_doc")
-
 paste_child <- function(x,
-                        label = NULL){
+                        label = NULL) {
   child <- c()
-  for(i in 1:length(x)){
+  for (i in 1:length(x)) {
     sec_num <- x[i]
     child_loop <- paste0(
       "\n",
@@ -25,7 +24,7 @@ paste_child <- function(x,
       "a <- knitr::knit_child(", "'", sec_num, "'", ", quiet = TRUE)", "\n",
       "cat(a, sep = '\\n')", "\n",
       "```", "\n"
-      )
+    )
     child <- paste(child, child_loop, sep = "\n {{< pagebreak >}} \n")
   }
   return(child)
diff --git a/R/report_format.R b/R/report_format.R
index 62ff29bf..33a2f071 100644
--- a/R/report_format.R
+++ b/R/report_format.R
@@ -1,41 +1,41 @@
 report_format <- function(
     type = NULL,
-    office = NULL){
+    office = NULL) {
   # This may need to be changed bc not every region has different format - maybe just different format based on report type (OA vs RT)
   # Add report formatting based on report type (operational/research)
-  if(type=="OA" | type=="UP" | type=="MT"){
+  if (type == "OA" | type == "UP" | type == "MT") {
     # Add report formatting based on region
-    if(office=="AFSC"){
+    if (office == "AFSC") {
 
-    } else if(office=="NEFSC"){
+    } else if (office == "NEFSC") {
 
-    } else if(office=="NWFSC"){
+    } else if (office == "NWFSC") {
       template <- paste0(
         "output: ",
         "  ", "sa"
       )
-    } else if(office=="PIFSC"){
+    } else if (office == "PIFSC") {
 
-    } else if(office=="SEFSC"){
+    } else if (office == "SEFSC") {
 
-    } else if(office=="SWFSC"){
+    } else if (office == "SWFSC") {
 
     } else {
       print("office (FSC) is not defined. Please define which office you are associated with.")
     }
-  } else if (type=="RT" | type=="FULL"){
+  } else if (type == "RT" | type == "FULL") {
     # Add report formatting based on region
-    if(office=="AFSC"){
+    if (office == "AFSC") {
 
-    } else if(office=="NEFSC"){
+    } else if (office == "NEFSC") {
 
-    } else if(office=="NWFSC"){
+    } else if (office == "NWFSC") {
 
-    } else if(office=="PIFSC"){
+    } else if (office == "PIFSC") {
 
-    } else if(office=="SEFSC"){
+    } else if (office == "SEFSC") {
 
-    } else if(office=="SWFSC"){
+    } else if (office == "SWFSC") {
 
     } else {
       print("office (FSC) is not defined. Please define which office you are associated with.")
diff --git a/R/write_harv_proj_table.R b/R/write_harv_proj_table.R
index 42234881..776f538e 100644
--- a/R/write_harv_proj_table.R
+++ b/R/write_harv_proj_table.R
@@ -13,7 +13,6 @@
 #' @export
 #'
 #' @examples write_harv_proj_table(tier = 3)
-
 write_harv_proj_table <- function(
     results_last = 9999,
     results_lastp1 = 9999,
@@ -21,25 +20,23 @@ write_harv_proj_table <- function(
     results_currp1 = 9999,
     tier = NULL,
     overfishing_last = "NO",
-    overfishing_curr = "NO"
-    ){
-
+    overfishing_curr = "NO") {
   # Pull current projection results
   # Need to update function to pull these results after converter is finished
-    # proj_last <- results_last |>
-    #   dplyr::select(M)
-    #
-    # proj_lastp1 <- results_lastp1 |>
-    #   dplyr::select(M)
-    #
-    # proj_curr <- results_lastp1 |>
-    #   dplyr::select(M)
-    #
-    # proj_currp1 <- results_lastp1 |>
-    #   dplyr::select(M)
-    #
-    # proj_res <- list(results_last, results_lastp1, results_curr, results_currp1) |>
-    #   purrr::map(dplyr::select(M))
+  # proj_last <- results_last |>
+  #   dplyr::select(M)
+  #
+  # proj_lastp1 <- results_lastp1 |>
+  #   dplyr::select(M)
+  #
+  # proj_curr <- results_lastp1 |>
+  #   dplyr::select(M)
+  #
+  # proj_currp1 <- results_lastp1 |>
+  #   dplyr::select(M)
+  #
+  # proj_res <- list(results_last, results_lastp1, results_curr, results_currp1) |>
+  #   purrr::map(dplyr::select(M))
 
   # Temporary fill
   proj_last <- 9999
@@ -49,10 +46,14 @@ write_harv_proj_table <- function(
   proj_res <- 9999
 
   # Write table contents
-  quantity <- c("M (natural mortality rate", "Tier", "Biomass (t)", "F OFL", "maxF ABC", "F ABC","OFL (t)",
-                "maxABC (t)", "ABC (t)")
-  status <- c("Status", "As determined last year for: current year - 2", "As determined last year for: current year - 1",
-              "As determined this year for: current year - 1", "As determined this year for: current year")
+  quantity <- c(
+    "M (natural mortality rate", "Tier", "Biomass (t)", "F OFL", "maxF ABC", "F ABC", "OFL (t)",
+    "maxABC (t)", "ABC (t)"
+  )
+  status <- c(
+    "Status", "As determined last year for: current year - 2", "As determined last year for: current year - 1",
+    "As determined this year for: current year - 1", "As determined this year for: current year"
+  )
   overfishing <- c("Overfishing", overfishing_last, NA, overfishing_curr, NA)
 
   # Build table
@@ -75,11 +76,10 @@ write_harv_proj_table <- function(
       proj_currp1 = "As estimated or recommended this year for:"
     ) |>
     flextable::merge_h(part = "header") |>
-    flextable::vline(j = c(1,3), part = "body") |>
+    flextable::vline(j = c(1, 3), part = "body") |>
     flextable::vline(j = c(1), part = "header") |>
     flextable::hline(part = "header") |>
     flextable::align(part = "header", align = "center")
 
   return(proj_tab)
-
 }
diff --git a/R/write_title.R b/R/write_title.R
index 125ec709..b694bfbc 100644
--- a/R/write_title.R
+++ b/R/write_title.R
@@ -22,70 +22,65 @@ write_title <- function(
     year = NULL,
     complex = NULL,
     type = NULL,
-    spp_latin = NULL
-){
-  if(is.null(year)){
-    year = format(Sys.Date(), "%Y")
+    spp_latin = NULL) {
+  if (is.null(year)) {
+    year <- format(Sys.Date(), "%Y")
   }
 
   # Create title dependent on regional language
-  if(office=="AFSC"){
-    if(is.null(complex)){
-      title = paste0("Assessment of the ", species, " Stock in the ", region)
+  if (office == "AFSC") {
+    if (is.null(complex)) {
+      title <- paste0("Assessment of the ", species, " Stock in the ", region)
     } else {
-      title = paste0("Assessment of the ", species, " Stock Complex in the ", region)
+      title <- paste0("Assessment of the ", species, " Stock Complex in the ", region)
     }
-  } else if(office=="NEFSC"){
-    if(as.numeric(format(Sys.Date(), "%m")) %in% c(3,4,5)){
-      season = "Spring"
-    } else if(as.numeric(format(Sys.Date(), "%m")) %in% c(6,7,8)){
-      season = "Summer"
-    } else if(as.numeric(format(Sys.Date(), "%m")) %in% c(9,10,11)){
-      season = "Fall"
-    } else if(as.numeric(format(Sys.Date(), "%m")) %in% c(12,1,2)){
-      season = "Winter"
+  } else if (office == "NEFSC") {
+    if (as.numeric(format(Sys.Date(), "%m")) %in% c(3, 4, 5)) {
+      season <- "Spring"
+    } else if (as.numeric(format(Sys.Date(), "%m")) %in% c(6, 7, 8)) {
+      season <- "Summer"
+    } else if (as.numeric(format(Sys.Date(), "%m")) %in% c(9, 10, 11)) {
+      season <- "Fall"
+    } else if (as.numeric(format(Sys.Date(), "%m")) %in% c(12, 1, 2)) {
+      season <- "Winter"
     }
-    if(type=="RT"){
-      title = paste0("Research Track Assessment for ", species, " (", spp_latin, ") ", season, " ", year)
+    if (type == "RT") {
+      title <- paste0("Research Track Assessment for ", species, " (", spp_latin, ") ", season, " ", year)
     } else {
-      title = paste0("Management Track Assessment of ", species, " (", spp_latin, ") ", season, " ", year)
+      title <- paste0("Management Track Assessment of ", species, " (", spp_latin, ") ", season, " ", year)
     }
-
-  } else if(office=="NWFSC"){
-    if(is.null(region)){
-      title = paste0("Status of the ", species, " stock along the U.S. West Coast in ", year)
+  } else if (office == "NWFSC") {
+    if (is.null(region)) {
+      title <- paste0("Status of the ", species, " stock along the U.S. West Coast in ", year)
     } else {
       # region in NW should be specified as a state
-      title = paste0("Status of the ", species, " stock in U.S. waters off the coast of ", region, " in ", year)
+      title <- paste0("Status of the ", species, " stock in U.S. waters off the coast of ", region, " in ", year)
     }
-
-  } else if(office=="PIFSC"){
-    if(is.null(region)){
-      title = paste0("Stock Assessment for ", species, " (", spp_latin, ") along the main Hawaiian Islands in ", year)
+  } else if (office == "PIFSC") {
+    if (is.null(region)) {
+      title <- paste0("Stock Assessment for ", species, " (", spp_latin, ") along the main Hawaiian Islands in ", year)
     } else {
-      title = paste0("Stock Assessment for ", species, " (", spp_latin, ") on ", region, " in ", year)
+      title <- paste0("Stock Assessment for ", species, " (", spp_latin, ") on ", region, " in ", year)
     }
-  } else if(office=="SEFSC"){
-    title = paste0("SEDAR XX Assessment Report for ", species, " (", spp_latin, ") in the ", region, " in ", year)
-
-  } else if(office=="SWFSC"){
-    if(is.null(region)){
-      title = paste0("Status of the ", species, " stock along the U.S. West Coast in ", year)
+  } else if (office == "SEFSC") {
+    title <- paste0("SEDAR XX Assessment Report for ", species, " (", spp_latin, ") in the ", region, " in ", year)
+  } else if (office == "SWFSC") {
+    if (is.null(region)) {
+      title <- paste0("Status of the ", species, " stock along the U.S. West Coast in ", year)
     } else {
       # region in NW should be specified as a state
-      title = paste0("Status of the ", species, " stock in U.S. waters off the coast of ", region, " in ", year)
+      title <- paste0("Status of the ", species, " stock in U.S. waters off the coast of ", region, " in ", year)
     }
   } else {
     print("office (FSC) is not defined. Please define which office you are associated with.")
   }
 
   # Cohesive title for any stock assessment
-    # if(type %in% c('OA', 'UP')){
-    #    title = paste0("Stock Assessment Update for the ", species, " Stock in the ", region, " ", year)
-    # } else {
-    #   title = paste0("Stock Assessment Report for the ", species, " Stock in the ", region, " ", year)
-    # }
+  # if(type %in% c('OA', 'UP')){
+  #    title = paste0("Stock Assessment Update for the ", species, " Stock in the ", region, " ", year)
+  # } else {
+  #   title = paste0("Stock Assessment Report for the ", species, " Stock in the ", region, " ", year)
+  # }
 
   return(title)
 }
-
diff --git a/inst/templates/skeleton/01_executive_summary.qmd b/inst/templates/skeleton/01_executive_summary.qmd
index 1fb9a5ec..4e6bb764 100644
--- a/inst/templates/skeleton/01_executive_summary.qmd
+++ b/inst/templates/skeleton/01_executive_summary.qmd
@@ -8,9 +8,9 @@
 #| eval: true
 #| warning: false
 #| echo: false
-if(params$office=="NEFSC"){
+if (params$office == "NEFSC") {
   a <- knitr::knit_child("01a_proj_table.qmd", quiet = TRUE)
-  cat(a, sep='\n')
+  cat(a, sep = "\n")
 }
 ```
 
@@ -21,5 +21,5 @@ if(params$office=="NEFSC"){
 #| warning: false
 #| echo: false
 a <- knitr::knit_child("01b_refpt_table.qmd", quiet = TRUE)
-cat(a, sep='\n')
+cat(a, sep = "\n")
 ```
diff --git a/inst/templates/skeleton/01a_proj_table.qmd b/inst/templates/skeleton/01a_proj_table.qmd
index 85e5928a..6d50b3cc 100644
--- a/inst/templates/skeleton/01a_proj_table.qmd
+++ b/inst/templates/skeleton/01a_proj_table.qmd
@@ -3,8 +3,8 @@
 ```{r}
 #| echo: false
 #| warning: false
-a <- seq(1,10,1)
-b <- seq(2,20,2)
-data.frame(a,b) |>
+a <- seq(1, 10, 1)
+b <- seq(2, 20, 2)
+data.frame(a, b) |>
   flextable::flextable()
 ```
diff --git a/man/add_section.Rd b/man/add_section.Rd
index 472922bd..c7d26fbb 100644
--- a/man/add_section.Rd
+++ b/man/add_section.Rd
@@ -31,3 +31,6 @@ as a child document.
 \description{
 Add New Section to Template
 }
+\examples{
+add_section(title = "Ecosystem Considerations", location = "after-discussion")
+}
diff --git a/man/convert_output.Rd b/man/convert_output.Rd
index 73c29751..900bb55a 100644
--- a/man/convert_output.Rd
+++ b/man/convert_output.Rd
@@ -23,7 +23,7 @@ adapt results among regional assessments.
 Format stock assessment output files. Function is unfinished
 }
 \examples{
-convert_output(output.file = "CumReport.sso", outdir = "~", model = 'ss', file.format = 'multi', multi.file = FALSE)
+convert_output(output.file = "CumReport.sso", outdir = "~", model = "ss", file.format = "multi", multi.file = FALSE)
 
 }
 \author{
diff --git a/man/create_template.Rd b/man/create_template.Rd
index de34b420..9d1d379b 100644
--- a/man/create_template.Rd
+++ b/man/create_template.Rd
@@ -108,10 +108,12 @@ each of the child documents should be edited separately.
 Create Stock Assessment Report Template
 }
 \examples{
-create_template(new_template = TRUE, format = "pdf",
-office = "NEFSC", region = "GB", species = "Bluefish",spp_latin = "bluishfihesi",
-year = 2024, author = c("John Snow", "Danny Phantom", "Patrick Star"),
-include_affiliation = TRUE, parameters = TRUE, param_names = c("fleet1", "fleet2", "model"),
-param_values = c("Commercial", "Recreational", "Woods Hole Assessment Model"),
-type = "RT")
+create_template(
+  new_template = TRUE, format = "pdf",
+  office = "NEFSC", region = "GB", species = "Bluefish", spp_latin = "bluishfihesi",
+  year = 2024, author = c("John Snow", "Danny Phantom", "Patrick Star"),
+  include_affiliation = TRUE, parameters = TRUE, param_names = c("fleet1", "fleet2", "model"),
+  param_values = c("Commercial", "Recreational", "Woods Hole Assessment Model"),
+  type = "RT"
+)
 }
diff --git a/man/export_object.Rd b/man/export_object.Rd
index 56ef6d26..1c8fd301 100644
--- a/man/export_object.Rd
+++ b/man/export_object.Rd
@@ -21,9 +21,9 @@ Function to export specified object from R environment found in the
 stock assessment report.
 }
 \examples{
-source <- c("NMFS Groundfish Survey","","U.S. Trawl Fisheries", "", "")
-data <- c("Survey biomass","Age Composition","Catch","Age Composition","Length Composition")
-years <- c("1984-1999 (triennial), 2001-2013 (biennial)","1984, 1987, 1990, 1993, 1996, 1999, 2003, 2005, 2007, 2009, 2011","1961-2013", "1990,1998-2002, 2004, 2005, 2006, 2008, 2010","1963-1977, 1991-1997")
+source <- c("NMFS Groundfish Survey", "", "U.S. Trawl Fisheries", "", "")
+data <- c("Survey biomass", "Age Composition", "Catch", "Age Composition", "Length Composition")
+years <- c("1984-1999 (triennial), 2001-2013 (biennial)", "1984, 1987, 1990, 1993, 1996, 1999, 2003, 2005, 2007, 2009, 2011", "1961-2013", "1990,1998-2002, 2004, 2005, 2006, 2008, 2010", "1963-1977, 1991-1997")
 test_obj <- data.frame(source, data, years)
 
 export_object(object = test_obj, file_format = "csv")
diff --git a/man/generate_citation.Rd b/man/generate_citation.Rd
index bbfb7572..fdaf6f8f 100644
--- a/man/generate_citation.Rd
+++ b/man/generate_citation.Rd
@@ -23,8 +23,10 @@ the stock assessment report generated in the ASAR package.
 Generate Citation for Stock Assessment Report
 }
 \examples{
-generate_citation(title = "SA Report for Jellyfish",
-author = c("John Snow", "Danny Phantom", "Patrick Star"),
-year = 2024, office = "NEFSC")
+generate_citation(
+  title = "SA Report for Jellyfish",
+  author = c("John Snow", "Danny Phantom", "Patrick Star"),
+  year = 2024, office = "NEFSC"
+)
 
 }