EIvimeyCook · EIvimeyCook · Jul 3, 2025 · Jul 3, 2025 · Jul 8, 2025 · Jul 8, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,7 @@ Description: The metRscreen shiny app allows you to screen papers via their abst
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     bslib,
     dplyr,

diff --git a/R/runApp.R b/R/runApp.R
@@ -2,14 +2,14 @@
 #' @description The metRscreen shiny app allows you to screen papers via their abstracts and titles and allows for highlighting of keywords in multiple colours.
 #' @return A dataframe of decisioned papers
 #' @param screen.file path to the csv file containing references you wish to screen.
-#' @param reject.vec vector of rejection reasons to be added to metRscreen, can be left empty
+#' @param reject.list list of rejection reasons to be added to metRscreen, can be left empty
 #' @param collab.names vector of names to identify screeners to be added to metRscreen, can be left empty
 #' @export
 
-metRscreen <- function(screen.file, reject.vec = NULL, collab.names = NULL) {
+metRscreen <- function(screen.file, reject.list = NULL, collab.names = NULL) {
   # if data.str if missing, assign an empty data.frame
   if (missing(screen.file)) cat("\nError: Please provide a .csv file to screen\n")
-  if (missing(reject.vec)) reject.vec <- NULL
+  if (missing(reject.list)) reject.list <- NULL
   if (missing(collab.names)) collab.names <- NULL
 
   if (file.exists(screen.file)) {
@@ -25,7 +25,7 @@ metRscreen <- function(screen.file, reject.vec = NULL, collab.names = NULL) {
     shiny_env <- 1
     envir <- as.environment(shiny_env)
     assign("screen.file", screen.file, envir = envir)
-    assign("reject.vec", reject.vec, envir = envir)
+    assign("reject.list", reject.list, envir = envir)
     assign("collab.names", collab.names, envir = envir)
     assign("screen.history", screen.history, envir = envir)
 

diff --git a/README.md b/README.md
@@ -34,10 +34,10 @@ metRscreen(screen.file = "~/Desktop/Example.csv")
 ```
 
 ## metRscreen arguments
-You can give specific rejection reasons as a vector with "reject.vec = c()".
+You can give specific rejection reasons as a vector with "reject.list = c()".
 
 ```{r}
-metRscreen(screen.file = "~/Desktop/Example.csv", reject.vec = c("no control", "wrong study system"))
+metRscreen(screen.file = "~/Desktop/Example.csv", reject.list = c("no control", "wrong study system"))
 ```
 
 The .rds file that's produced allows for reloading of previous screening decisions. This will be automatically reloaded the next instance metRscreen is run and will return screening to the same state (i.e. with the same reject list, hidden or showing paper components, and any previous screening decisions). 

diff --git a/inst/metRscreen/server.R b/inst/metRscreen/server.R
@@ -4,7 +4,7 @@ server <- function(input, output, session) {
 
   # settings object
   settings.store <- shiny::reactiveValues(
-    reject.vec = NULL,
+    reject.list = NULL,
     counter = NULL,
     datapath = NULL,
     new.data = NULL,
@@ -29,6 +29,9 @@ server <- function(input, output, session) {
 
   # create a new dataframe based on the old data in a reactive ovject
   original <- shiny::reactiveValues(new.data = NULL)
+
+  # create a new dataframe for hcecking
+  check_dat <- shiny::reactiveValues(check = NULL)
 
   # create a temp data file
   temp <- shiny::reactiveValues(import.data = NULL)
@@ -77,6 +80,7 @@ server <- function(input, output, session) {
 
   # input dataframe and create saving empty template#######
   shiny::observe({
+
     if (is.null(screen.history) & import$first.load == TRUE) {
       original$new.data <- cbind(
         read.csv(screen.file),
@@ -85,17 +89,51 @@ server <- function(input, output, session) {
         Comment = "No comments given",
         Screen.Name = "No screener name given"
       )
+
       import$first.load <- FALSE
+      countertot$total <- nrow(original$new.data)
       cat("\nReading in new screening file and creating new screening output(s)\n")
+
     } else if (!is.null(screen.history) & import$first.load == TRUE) {
+
       settings.store <<- do.call("reactiveValues", readRDS(screen.history))
-      original$new.data <- settings.store$new.data
-      cat("\nReading in saved screening file and using existing screening output\n")
-      import$first.load <- FALSE
-      import$first.import <- TRUE
+      check_dat$check <- read.csv(screen.file)
+      countertot$total <- nrow(settings.store$new.data)
       counter$countervalue <- settings.store$counter
+
+
+      if (isTRUE(all.equal(settings.store$new.data$Title, check_dat$check$Title))) {
+
+        original$new.data <- settings.store$new.data
+
+        import$first.load <- FALSE
+        import$first.import <- TRUE
+        cat("\nReading in saved screening file and using existing screening output\n")
+
+
+      } else if(!isTRUE(all.equal(settings.store$new.data$Title, check_dat$check$Title))) {
+
+        cat("\nData frame inconsistencies between saved and loaded data frames - please revert to previous version\n")
+        shinyalert::shinyalert(
+          title = "Warning",
+          text = "Data frame inconsistencies between saved and loaded data frames - please revert to previous version",
+          size = "m",
+          closeOnClickOutside = FALSE,
+          html = TRUE,
+          type = "warning",
+          showConfirmButton = TRUE,
+          showCancelButton = FALSE,
+          confirmButtonText = "OK",
+          confirmButtonCol = "#AEDEF4",
+          animation = TRUE,
+          imageHeight = "88",
+          imageWidth = "80"
+        )
+        shiny::stopApp()
+      }
     }
 
+
     # save a temp output
     settings.store$counter <- counter$countervalue
     settings.store$new.data <- original$new.data
@@ -114,10 +152,10 @@ server <- function(input, output, session) {
   shiny::observe({
     if (!is.null(screen.history) & import$first.import == "TRUE") {
       # update params
-      if (!identical(reject.vec, settings.store$reject.vec) & !is.null(reject.vec)) {
-        reject.vec <<- reject.vec
+      if (!identical(reject.list, settings.store$reject.list) & !is.null(reject.list)) {
+        reject.list <<- reject.list
       } else {
-        reject.vec <<- settings.store$reject.vec
+        reject.list <<- settings.store$reject.list
       }
 
       if (!identical(collab.names, settings.store$collab.names) & !is.null(collab.names)) {
@@ -196,12 +234,12 @@ server <- function(input, output, session) {
 
   # update radiogroup with imported reasons####
   shiny::observe({
-    if (length(reject.vec > 0)) {
+    if (length(reject.list > 0)) {
       shinyjs::show("reject.reason")
       shinyWidgets::updatePrettyRadioButtons(
         session = session,
         inputId = "reject.reason",
-        choices = reject.vec,
+        choices = reject.list,
         selected = character(0),
         inline = TRUE,
         prettyOptions = list(
@@ -212,19 +250,10 @@ server <- function(input, output, session) {
         )
       )
 
-      settings.store$reject.vec <- reject.vec
+      settings.store$reject.list <- reject.list
     }
   })
 
-
-
-
-
-  # counter total######
-  shiny::observe({
-    countertot$total <- nrow(original$new.data)
-  })
-
   # change the study with next and previous#######
   shiny::observeEvent(input$Next, {
     counter$countervalue <- counter$countervalue + 1
@@ -265,27 +294,27 @@ server <- function(input, output, session) {
       )
     ))
   })
-  
+
   # render title text highlighted based on search######
   output$title <- shiny::renderUI({
     shiny::HTML(paste(
       "<b>",
       highlight_text(as.character(StudyData()$Title),
-                     search = list(
-                       input$search1,
-                       input$search2,
-                       input$search3,
-                       input$search4,
-                       input$search5
-                     )
+        search = list(
+          input$search1,
+          input$search2,
+          input$search3,
+          input$search4,
+          input$search5
+        )
       ),
       "</b>"
     ))
   })
 
-  #error
+  # error
   output$hist.reason <- shiny::renderUI({
-    if(StudyData()$Screen == "Reject"){
+    if (StudyData()$Screen == "Reject") {
       shiny::HTML(paste(
         "<p>",
         "<b>Reject Reason:</b>",
@@ -305,21 +334,21 @@ server <- function(input, output, session) {
   })
 
   output$screen.comment <- shiny::renderUI({
-      shiny::HTML(paste(
-        "<p>",
-        "<b>Comment:</b>",
-        as.character(StudyData()$Comment),
-        "</p>"
-      ))
+    shiny::HTML(paste(
+      "<p>",
+      "<b>Comment:</b>",
+      as.character(StudyData()$Comment),
+      "</p>"
+    ))
   })
 
   output$name.screener <- shiny::renderUI({
-      shiny::HTML(paste(
-        "<p>",
-        "<b>Screener:</b>",
-        as.character(StudyData()$Screen.Name),
-        "</p>"
-      ))
+    shiny::HTML(paste(
+      "<p>",
+      "<b>Screener:</b>",
+      as.character(StudyData()$Screen.Name),
+      "</p>"
+    ))
   })
 
   output$author <- shiny::renderUI({
@@ -371,7 +400,7 @@ server <- function(input, output, session) {
       shinyalert::shinyalert(
         title = "Congratulations",
         text = "You've finished screening all papers!",
-        size = "s", 
+        size = "s",
         closeOnEsc = TRUE,
         closeOnClickOutside = TRUE,
         html = FALSE,
@@ -384,7 +413,7 @@ server <- function(input, output, session) {
         imageUrl = "",
         animation = TRUE
       )
-      cat(paste("\nCongratulations - you have finished screening",  countertot$total, "papers \n"))
+      cat(paste("\nCongratulations - you have finished screening", countertot$total, "papers \n"))
       counter$countervalue <- countertot$total
     }
     if (counter$countervalue == 0) {
@@ -401,7 +430,7 @@ server <- function(input, output, session) {
     shinyWidgets::updatePrettyRadioButtons(
       session = session,
       inputId = "reject.reason",
-      choices = reject.vec,
+      choices = reject.list,
       selected = character(0),
       inline = TRUE,
       prettyOptions = list(
@@ -433,7 +462,7 @@ server <- function(input, output, session) {
   shiny::observeEvent(input$Reject, {
     original$new.data[counter$countervalue, ]$Screen <- "Reject"
 
-    if (length(input$reject.reason > 0)) {
+    if (length(input$reject.reason > 0) & input$reject.reason != "") {
       original$new.data[counter$countervalue, ]$Reason <- input$reject.reason
     }
     if (input$comments != "") {
@@ -453,7 +482,7 @@ server <- function(input, output, session) {
       shinyalert::shinyalert(
         title = "Congratulations",
         text = "You've finished screening all papers!",
-        size = "s", 
+        size = "s",
         closeOnEsc = TRUE,
         closeOnClickOutside = TRUE,
         html = FALSE,
@@ -466,7 +495,7 @@ server <- function(input, output, session) {
         imageUrl = "",
         animation = TRUE
       )
-      cat(paste("\nCongratulations - you have finished screening",  countertot$total, "papers \n"))
+      cat(paste("\nCongratulations - you have finished screening", countertot$total, "papers \n"))
       counter$countervalue <- countertot$total
     }
     if (counter$countervalue == 0) {
@@ -478,7 +507,7 @@ server <- function(input, output, session) {
     shinyWidgets::updatePrettyRadioButtons(
       session = session,
       inputId = "reject.reason",
-      choices = reject.vec,
+      choices = reject.list,
       selected = character(0),
       inline = TRUE,
       prettyOptions = list(
@@ -530,7 +559,7 @@ server <- function(input, output, session) {
       shinyalert::shinyalert(
         title = "Congratulations",
         text = "You've finished screening all papers!",
-        size = "s", 
+        size = "s",
         closeOnEsc = TRUE,
         closeOnClickOutside = TRUE,
         html = FALSE,
@@ -543,7 +572,7 @@ server <- function(input, output, session) {
         imageUrl = "",
         animation = TRUE
       )
-      cat(paste("\nCongratulations - you have finished screening",  countertot$total, "papers \n"))
+      cat(paste("\nCongratulations - you have finished screening", countertot$total, "papers \n"))
       counter$countervalue <- countertot$total
     }
     if (counter$countervalue == 0) {
@@ -555,7 +584,7 @@ server <- function(input, output, session) {
     shinyWidgets::updatePrettyRadioButtons(
       session = session,
       inputId = "reject.reason",
-      choices = reject.vec,
+      choices = reject.list,
       selected = character(0),
       inline = TRUE,
       prettyOptions = list(

diff --git a/man/metRscreen.Rd b/man/metRscreen.Rd
diff --git a/metRscreen.Rproj b/metRscreen.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: bce1fe8b-f015-4032-af0d-02ecf1f3463c
 
 RestoreWorkspace: Default
 SaveWorkspace: Default