diff --git a/R/count.R b/R/count.R
index afb2f8c..1e17b11 100644
--- a/R/count.R
+++ b/R/count.R
@@ -112,25 +112,24 @@ record_counts <- function(unique_citations, citations, db_colname) {
 #'
 #' @return A dataframe with counts of distinct records, imported records, and unique records for each source, including total counts and several calculated ratios and percentages.
 #' @examples
-# unique_citations <- data.frame(
-#   db_source = c("Database1", "Database1", "Database2", "Database3", "Database3", "Database3"),
-#   other_data = 1:6
-# )
-# 
-# citations <- data.frame(
-#   db_source = c("Database1", "Database1", "Database1", "Database2", "Database2", "Database3"),
-#   other_data = 7:12
-# )
-# 
-# n_unique <- data.frame(
-#   cite_source = c("Database1", "Database2", "Database2", "Database3", "Database3", "Database3"),
-#   cite_label = c("search", "final", "search", "search", "search", "final"),
-#   unique = c(1, 0, 1, 1, 1, 0)
-# )
-# 
-# result <- calculate_record_counts(unique_citations, citations, n_unique, "db_source")
-# result
-
+#' unique_citations <- data.frame(
+#'   db_source = c("Database1", "Database1", "Database2", "Database3", "Database3", "Database3"),
+#'   other_data = 1:6
+#' )
+#' 
+#' citations <- data.frame(
+#'   db_source = c("Database1", "Database1", "Database1", "Database2", "Database2", "Database3"),
+#'   other_data = 7:12
+#' )
+#'
+#' n_unique <- data.frame(
+#'   cite_source = c("Database1", "Database2", "Database2", "Database3", "Database3", "Database3"),
+#'  cite_label = c("search", "final", "search", "search", "search", "final"),
+#'   unique = c(1, 0, 1, 1, 1, 0)
+#' )
+#' 
+#' result <- calculate_record_counts(unique_citations, citations, n_unique, "db_source")
+#' print(result)
 
 calculate_record_counts <- function(unique_citations, citations, n_unique, db_colname) {
   
@@ -222,21 +221,21 @@ calculate_record_counts <- function(unique_citations, citations, n_unique, db_co
 #' and recall for each source, as well as totals.
 #'
 #' @examples
-# unique_citations <- data.frame(
-#   db_source = c("Database1", "Database1", "Database2", "Database3", "Database3", "Database3"),
-#   cite_label = c("screened", "final", "screened", "final", "screened", "final"),
-#   duplicate_id = c(102, 102, 103, 103, 104, 104),
-#   other_data = 1:6
-# )
-# 
-# citations <- data.frame(
-#   db_source = c("Database1", "Database1", "Database1", "Database2", "Database2", "Database3"),
-#   cite_label = c("screened", "final", "screened", "final", "screened", "final"),
-#   other_data = 7:12
-# )
-# 
-# result <- calculate_phase_count(unique_citations, citations, "db_source")
-# result
+#' unique_citations <- data.frame(
+#' db_source = c("Database1", "Database1", "Database2", "Database3", "Database3", "Database3"),
+#' cite_label = c("screened", "final", "screened", "final", "screened", "final"),
+#' duplicate_id = c(102, 102, 103, 103, 104, 104),
+#' other_data = 1:6
+#' )
+#' 
+#' citations <- data.frame(
+#' db_source = c("Database1", "Database1", "Database1", "Database2", "Database2", "Database3"),
+#' cite_label = c("screened", "final", "screened", "final", "screened", "final"),
+#' other_data = 7:12
+#' )
+#' 
+#' result <- calculate_phase_count(unique_citations, citations, "db_source")
+#' result
 
 
 calculate_phase_count <- function(unique_citations, citations, db_colname) {
diff --git a/R/dedup.R b/R/dedup.R
index c8fb35e..c4af832 100644
--- a/R/dedup.R
+++ b/R/dedup.R
@@ -6,7 +6,7 @@
 #' @export
 #' @param raw_citations Citation dataframe with relevant columns
 #' @param manual logical. If TRUE, manually specify pairs of duplicates to merge. Default is FALSE.
-#' @param shiny_progress logical. If TRUE, show a progress bar in the Shiny app. Default is FALSE.
+#' @param show_unknown_tags When a label, source, or other merged field is missing, do you want this to show as "unknown"?
 #' @return unique citations formatted for CiteSource
 #' @examples
 #' # Load example data from the package
@@ -17,7 +17,7 @@
 #' dedup_results <- dedup_citations(examplecitations)
 #' 
 
-dedup_citations <- function(raw_citations, manual=FALSE, shiny_progress=FALSE, show_unknown_tags=FALSE){
+dedup_citations <- function(raw_citations, manual=FALSE, show_unknown_tags=FALSE){
   
   # rename or coalesce columns
   targets <- c("journal", "number", "pages", "isbn", "record_id")
@@ -37,7 +37,7 @@ dedup_citations <- function(raw_citations, manual=FALSE, shiny_progress=FALSE, s
   raw_citations$source <- raw_citations$cite_source
   raw_citations$label <- raw_citations$cite_label
   
-  dedup_results <- ASySD::dedup_citations(raw_citations, merge_citations = TRUE, extra_merge_fields = "cite_string", shiny_progress=shiny_progress, show_unknown_tags = show_unknown_tags)
+  dedup_results <- ASySD::dedup_citations(raw_citations, merge_citations = TRUE, extra_merge_fields = "cite_string", show_unknown_tags = show_unknown_tags)
   
   if(manual == FALSE){
     
diff --git a/inst/shiny-app/CiteSource/app.R b/inst/shiny-app/CiteSource/app.R
index 1680863..06138ad 100644
--- a/inst/shiny-app/CiteSource/app.R
+++ b/inst/shiny-app/CiteSource/app.R
@@ -1,4 +1,6 @@
 library(DT)
+library(CiteSource)
+library(dplyr)
 
 # Set background colour
 shiny::tags$head(shiny::tags$style(
@@ -342,7 +344,7 @@ server <- function(input, output, session) {
       suggested_source <- stringr::str_replace_all(input$file$name, ".ris", "")
       suggested_source <- stringr::str_replace_all(suggested_source, ".bib", "")
       suggested_source <- stringr::str_replace_all(suggested_source, ".txt", "")
-      upload_df <- read_citations(
+      upload_df <- CiteSource::read_citations(
         files = input$file$datapath,
         cite_sources = suggested_source,
         cite_labels = rep("", length(input$file$datapath)),
@@ -479,10 +481,22 @@ server <- function(input, output, session) {
     rv$upload_df <- rv$upload_df %>% dplyr::mutate(record_id = as.character(1000 + dplyr::row_number()))
     
     # results of auto dedup
-    dedup_results <- dedup_citations(rv$upload_df, manual = TRUE, shiny_progress = TRUE, show_unknown_tags=TRUE)
+    dedup_results <- CiteSource::dedup_citations(rv$upload_df, manual = TRUE, show_unknown_tags=TRUE)
 
-    # unique and pairs to check sent to reactive values
-    rv$pairs_to_check <- dedup_results$manual_dedup 
+    # Possible way of PRIORITISING manual dedup 
+    # priority_df <- rv$upload_df %>%
+    #   filter(cite_label %in% c("final", "screened")) %>%
+    #   select(record_id)
+    
+    # manual_to_review <- dedup_results$manual_dedup %>%
+    #   mutate(match_score_ls = RecordLinkage::levenshteinSim(title1, title2)) %>%
+    #   arrange(desc(match_score_ls)) %>%
+    #   mutate(priority = ifelse(record_id1 %in% priority_df$record_id, "Yes", "No")) %>%
+    #   mutate(priority = ifelse(record_id2 %in% priority_df$record_id, "Yes", priority)) %>%
+    #   arrange(desc(priority)) %>%
+    #   filter(priority == "Yes")
+    
+    rv$pairs_to_check <- dedup_results$manual_dedup
     rv$latest_unique <- dedup_results$unique
 
     # generate shiny alert with dedup results
@@ -597,9 +611,8 @@ server <- function(input, output, session) {
     
     datatable(data,
               options = list(
-                dom = "t",
-                pageLength = 10,
-                lengthMenu = c(10, 20, 30, 40),
+                pageLength = 100, info = FALSE,
+                               lengthMenu = list(c(100, -1), c("100", "All")),
                 columnDefs =
                   list(
                     list(visible = FALSE, 
diff --git a/man/calculate_phase_count.Rd b/man/calculate_phase_count.Rd
index 098d8ab..c262240 100644
--- a/man/calculate_phase_count.Rd
+++ b/man/calculate_phase_count.Rd
@@ -29,3 +29,20 @@ will give a warning if these labels are not present in the input dataframes.
 The function will give a warning if 'screened' and 'final' labels are not present
 in the 'cite_label' column of the input dataframes.
 }
+\examples{
+unique_citations <- data.frame(
+db_source = c("Database1", "Database1", "Database2", "Database3", "Database3", "Database3"),
+cite_label = c("screened", "final", "screened", "final", "screened", "final"),
+duplicate_id = c(102, 102, 103, 103, 104, 104),
+other_data = 1:6
+)
+
+citations <- data.frame(
+db_source = c("Database1", "Database1", "Database1", "Database2", "Database2", "Database3"),
+cite_label = c("screened", "final", "screened", "final", "screened", "final"),
+other_data = 7:12
+)
+
+result <- calculate_phase_count(unique_citations, citations, "db_source")
+result
+}
diff --git a/man/calculate_record_counts.Rd b/man/calculate_record_counts.Rd
index 518df56..fbd38b2 100644
--- a/man/calculate_record_counts.Rd
+++ b/man/calculate_record_counts.Rd
@@ -24,3 +24,23 @@ This function calculates the counts of distinct records, records imported, and u
 It combines these counts into one dataframe and calculates several ratios and percentages related to the unique and distinct counts.
 It also calculates the total for each count type.
 }
+\examples{
+unique_citations <- data.frame(
+  db_source = c("Database1", "Database1", "Database2", "Database3", "Database3", "Database3"),
+  other_data = 1:6
+)
+
+citations <- data.frame(
+  db_source = c("Database1", "Database1", "Database1", "Database2", "Database2", "Database3"),
+  other_data = 7:12
+)
+
+n_unique <- data.frame(
+  cite_source = c("Database1", "Database2", "Database2", "Database3", "Database3", "Database3"),
+ cite_label = c("search", "final", "search", "search", "search", "final"),
+  unique = c(1, 0, 1, 1, 1, 0)
+)
+
+result <- calculate_record_counts(unique_citations, citations, n_unique, "db_source")
+print(result)
+}
diff --git a/man/dedup_citations.Rd b/man/dedup_citations.Rd
index 75f2608..2a2f459 100644
--- a/man/dedup_citations.Rd
+++ b/man/dedup_citations.Rd
@@ -4,19 +4,14 @@
 \alias{dedup_citations}
 \title{Deduplicate citations - ASySD wrapper}
 \usage{
-dedup_citations(
-  raw_citations,
-  manual = FALSE,
-  shiny_progress = FALSE,
-  show_unknown_tags = FALSE
-)
+dedup_citations(raw_citations, manual = FALSE, show_unknown_tags = FALSE)
 }
 \arguments{
 \item{raw_citations}{Citation dataframe with relevant columns}
 
 \item{manual}{logical. If TRUE, manually specify pairs of duplicates to merge. Default is FALSE.}
 
-\item{shiny_progress}{logical. If TRUE, show a progress bar in the Shiny app. Default is FALSE.}
+\item{show_unknown_tags}{When a label, source, or other merged field is missing, do you want this to show as "unknown"?}
 }
 \value{
 unique citations formatted for CiteSource