UI fixes, server code reorganization, CSV download fix #1

data/statistics.csv

@@ -0,0 +1,3 @@
+date,search,included,screened
+"April 7, 2020",1890,385,1217
+"April 11, 2020",3288,531,2289

markdown/About-Proj.md

@@ -1,8 +1,13 @@
 ## What is this?
-Recent literature on COVID-19 is highly variable in scope, quality, and applicability to the front-line physician. In a time where information and time are valuable resources, there must be a resource that provides curated primary and secondary literature so that clinical decisions can be made with more confidence. This project provides a way to browse current and relevant literature on COVID-19 that has been curated via a systematic review approach.
+Recent literature on COVID-19 is highly variable in scope, quality, and applicability to the front-line physician. In a time where information and time are valuable resources, there must be a resource that provides curated primary and secondary literature so that clinical decisions can be made with more confidence.
+
+This project aims to provide a way to explore higher-quality current literature on COVID-19 that has been curated via a systematic review approach.
 
 ## Contributors
-Citations and data were reviewed and curated by **Becky Jones**, **Daniel Levin**, **Hannah Kearney**, **Jasper Ho**, **Jillian Howden**, **John Kim**, **Maya Amar**, **Meghan Glibbery**, and **Sara Markovic**, all medical students at McMaster University.<br>This tool was coded and designed by **Jasper Ho** (<a href="https://www.twitter.com/jzpero">@jzpero</a>) in R using Shiny.  
+Citations are reviewed by **Becky Jones**, **Daniel Levin**, **Hannah Kearney**, **Jasper Ho**, **Jillian Howden**, **John Kim**, **Maya Amar**, **Meghan Glibbery**, and **Sara Markovic**, all medical students at McMaster University.
+
+This tool is created, maintained, and updated by **Jasper Ho** ([Twitter](https://www.twitter.com/jzpero), [GitHub](https://www.github.com/jzpero)).
+
 The project was conceptualized and is supervised by **Dr. Mark Crowther** MD, MSc, FRCPC.
 
 ## Contact Us

markdown/Methods.md

@@ -7,8 +7,8 @@ We searched for relevant articles on PubMed with the following search strategy:
 
 Our search is ongoing as new literature emerges. Our repository of unfiltered articles has been updated on the following dates:
 
-- March 28, 2020
-- April 8, 2020
+- March 28, 2020 (N=1890)
+- April 8, 2020 (N=3288)
 
 ## Inclusion Criteria
 No strict inclusion criteria were established; the purpose of this literature review is to provide high-yield pertinent research to the front-line clinician across a breadth of areas, specifically oriented towards the Ontario/Canada/North American context of COVID-19.
@@ -42,15 +42,15 @@ Few strict exclusion criteria were applied. As above, our assessment of referenc
  - Explanation of journal responses to COVID-19
  - Relevant only to overseas/international settings
 
-## Screening Methods
-References were independently screened via title/abstract review by two or more reviewers each.
-Disagreements were resolved by group consensus or a third reviewer when necessary.
-
-## Categorization
-Reference type, specialties of interest, and relevance to front-line clinicians were assessed and assigned.
+## Screening and Tagging Methods
+We review new references in a temporally sequential order, oldest to newest.
+References are independently screened via title/abstract review by two or more reviewers each.
+Disagreements are resolved by group consensus or a third reviewer when necessary.
+Reference type, specialties of interest, and relevance to front-line clinicians are assessed and assigned.
+We update this website with newly included references on a regular basis.
 
 ## Webtool Implementation
-This tool has been written in Shiny in R. Source code and data are available at https://github.com/jzpero/covid19lit. Interested in contributing? Contact: jasper.ho (at) medportal.ca.
+This fully open-source tool has been written in Shiny in R. Source code, data, and acknowledgements are available at https://github.com/jzpero/covid19lit. The backend is an Amazon EC2 instance running Shiny Server. Interested in contributing? Contact: jasper.ho (at) medportal.ca.
 
 ## Notes
 This tool is a work in progress. It was also developed by a non-professional. It relies on online data from PubMed parsed from official tools, with custom code or public libraries. As such, there may be occasional errors. Please do not rely on any specific data found on this online tool without appropriate confirmation from the source. Errors may include:

server.R

@@ -1,17 +1,24 @@
 library(dplyr)
 
-server <- function(input, output, session) {
+#Case formatting from https://stat.ethz.ch/R-manual/R-devel/library/base/html/chartr.html
+capwords <- function(s, strict = FALSE) {
+  cap <- function(s) paste(toupper(substring(s, 1, 1)),
+                           {s <- substring(s, 2); if(strict) tolower(s) else s},
+                           sep = "", collapse = " " )
+  sapply(strsplit(s, split = " "), cap, USE.NAMES = !is.null(names(s)))
+}
+
+#Create a PubMed link in HTML
+createLink <- function(PMID, text) {
+  sprintf('<a href="https://www.ncbi.nlm.nih.gov/pubmed/%s" target="_blank">%s</a>', PMID, text)
+}
+
+included.headers <- c("TitleLinks", "Author", "Journal","Date",  "PMID", "Type of Study", "Specialties")
+
+server <- function(input, output, session) { # Executes once per session (no need to restart service)
   #Update the data once
   link <- list.files("data/", pattern="(current)", full.names=TRUE)[1]
 
-  #Case formatting from https://stat.ethz.ch/R-manual/R-devel/library/base/html/chartr.html
-  capwords <- function(s, strict = FALSE) {
-    cap <- function(s) paste(toupper(substring(s, 1, 1)),
-                             {s <- substring(s, 2); if(strict) tolower(s) else s},
-                             sep = "", collapse = " " )
-    sapply(strsplit(s, split = " "), cap, USE.NAMES = !is.null(names(s)))
-  }
-
   #Data Processing (done once)
   rawtable <- read.csv(link, sep = ",", na.strings="", encoding = "UTF-8", check.names=FALSE, stringsAsFactors=FALSE)
   date_data <- read.csv("data/date_output.csv", header=T, colClasses = c("character", "character"))
@@ -29,36 +36,31 @@ server <- function(input, output, session) {
   }
   filtered.table$Date <- anytime::anydate(filtered.table$Date)
 
-  #Create dropdown choices
+  #Create filter choices
   unique.authors <- lapply(strsplit(paste(filtered.table$Author, collapse=','), ","), trimws)[[1]]
   unique.authors <<- sort(unique(unique.authors[lapply(unique.authors, nchar) > 0]))
   unique.journals <- sort(unique(filtered.table$Journal))
   unique.studytypes <<- sort(unique(filtered.table$'Type of Study'))
   unique.specialties <<- sort(c("Internal Medicine", "General", "Dermatology", "ICU", "Emergency Medicine", "Anesthesia", "Radiology", "OBGYN", "Public Health", "Cardiology", "Oncology", "Psych", "Family Medicine", "Gastroenterology", "Geriatrics", "Hematology", "Infectious Disease", "Immunology", "Medical Education", "Microbiology", "Nephrology", "Neurology", "Ophthalmology", "Palliative Care", "Pathology", "Pediatrics","Respirology", "Rheumatology", "Surgery", "Urology"))
 
+  # Special processing of specialty data
   spec.out <- vector("list", length=N)
   spec.cols <- grep("Spec", headers)
-  # View(colnames(filtered.table)[spec.cols])
   for (i in 1:N) {
     k <- unlist(filtered.table[i,spec.cols], use.names = F)
     k <- sort(k[!is.na(k)])
     spec.out[[i]] <- k
   }
   filtered.table$Areas <- spec.out
   filtered.table$Specialties <- sapply(filtered.table$Areas, function(x) paste(unlist(x), collapse=", "))
-
-  #Create a PubMed link in HTML
-  createLink <- function(PMID, text) {
-    sprintf('<a href="https://www.ncbi.nlm.nih.gov/pubmed/%s" target="_blank">%s</a>', PMID, text)
-  }
 
   #Populate the search filters
   updateSelectInput(session, "journal", choices = c("Select a journal" = "", unique.journals))
   updateSelectInput(session, "author", choices = c("Select authors" = "", unique.authors))
   updateSelectInput(session, "study", choices = c("Select a type" = "", unique.studytypes))
   updateSelectInput(session, "specialty", choices = c("Select an area of interest" = "", unique.specialties))
 
-  #Initiate table
+  #Initiate display table
   display.table <- filtered.table
 
   #clear all button actions
@@ -104,7 +106,7 @@ server <- function(input, output, session) {
     if (!is.null(input$specialty) & nrow(display.table)) {
       #Initialize FALSE Vector
       v <- vector("logical",nrow(display.table))
-      if (input$specSwitch){
+      if (input$specSwitch == "Any term"){
       #iterate over author rows and flag as TRUE if ANY of the selected authors present
         for (i in 1:nrow(display.table)) {
           for (query in input$specialty) {
@@ -124,30 +126,54 @@ server <- function(input, output, session) {
       if (!is.null(input$ex1_rows_selected)) {
         HTML(paste0(
           trimws(display.table[input$ex1_rows_selected,"Author"]), ". ",
-          "<b>",display.table[input$ex1_rows_selected,"Title"], "</b> ",
+          "<b>",display.table[input$ex1_rows_selected,"TitleLinks"], "</b> ",
           "<i>", trimws(display.table[input$ex1_rows_selected,"Journal"]), "</i>. <br><br>", if (is.na(display.table[input$ex1_rows_selected, "Abstract"])) "No abstract." else display.table[input$ex1_rows_selected, "Abstract"]
         ))} else HTML("<i>Select a reference...</i>")
     )
 
+    output$N <- renderText(nrow(display.table))
+
     #Create Links
-    display.table$Title <- createLink(display.table$PMID, display.table$Title)
+    display.table$TitleLinks <- createLink(display.table$PMID, display.table$Title)
+
+    #Export option
+    output$export <- downloadHandler(
+      filename = function() {
+        paste("references",Sys.Date(),".csv", sep = "")
+      },
+      content = function(file) {
+        write.csv(display.table[,gsub("TitleLinks", "Title", included.headers)], file, row.names = FALSE)
+      }
+    )
+
+    # PDF Rmd Report
+    # output$report <- downloadHandler(
+    #   filename = "report.pdf",
+    #   content = function(file) {
+    #     # Copy the report file to a temporary directory before processing it, in
+    #     # case we don't have write permissions to the current working dir (which
+    #     # can happen when deployed).
+    #     tempReport <- file.path(tempdir(), "report.Rmd")
+    #     file.copy("markdown/report.Rmd", tempReport, overwrite = TRUE)
+    #     
+    #     # Set up parameters to pass to Rmd document
+    #     params <- list(dtable=display.table[,included.headers])
+    #     
+    #     # Knit the document, passing in the `params` list, and eval it in a
+    #     # child of the global environment (this isolates the code in the document
+    #     # from the code in this app).
+    #     rmarkdown::render(tempReport, output_file = file,
+    #                       params = params,
+    #                       envir = new.env(parent = globalenv())
+    #     )
+    #   }
+    # )
 
     #Output
-    included.headers <- c("Title", "Author", "Journal","Date",  "PMID", "Type of Study", "Specialties")
     DT::datatable(
       display.table[,included.headers],
       extensions = "Responsive",
       options = list(pageLength = 10, order = list(list(3, "desc"), list(4, "desc"))),
       rownames= FALSE, escape=FALSE, selection = 'single')
-
-    # #Export option
-    # output$export <- downloadHandler(
-    #   filename = function() {
-    #     paste("references",Sys.Date(),".csv", sep = "")
-    #   },
-    #   content = function(file) {
-    #     write.csv(display.table[,included.headers], file, row.names = FALSE)
-    #   }
-    # )
   })
-}
+}

ui.R

@@ -1,54 +1,66 @@
+filterPanel <- wellPanel(
+  id = "searchpanel",
+  p(strong("Filter Options"), br(), "Any combination of filters accepted."),
+  selectInput(inputId = "journal", label="Journal", choices = NULL, multiple = TRUE, ),
+  div(style = "margin-top:-15px"),
+  selectInput(inputId = "study", "Type of Study", choices = NULL, multiple = TRUE),
+  div(style = "margin-top:-15px"),
+  selectInput(inputId = "author", "Author(s)",choices = NULL, multiple = TRUE),
+  div(style = "margin-top:-15px"),
+  selectInput(inputId = "specialty", "Specialty Bucket",choices = NULL, multiple = TRUE),
+  div(style = "margin-top:-15px"),
+  shinyWidgets::radioGroupButtons(inputId="specSwitch", size="sm", label="Specialty matches:", choices=c("Any term", "All terms"), selected="Any term", status="info"),
+  div(style = "margin-top:-10px"),
+  hr(),
+  div(style = "margin-top:-15px"),
+  p(textOutput("N", inline = TRUE), " result(s)."),
+  fluidRow(
+    column(6,dropdown(
+      downloadButton(outputId = "export", label = "CSV", class="btn-secondary btn-sm"),
+      # downloadButton(outputId = "report", label = "PDF", class="btn-secondary btn-sm"),
+      status="btn-primary btn-sm",
+      size="sm",
+      label="Download results"
+    )),
+    column(6, actionButton(inputId = "clearAll", "Clear filters", class="btn-primary btn-sm"))
+  )
+)
+
 ui <- navbarPage(
   title = 'COVID-19 Literature Review',
   position = c("fixed-top"),
   tabPanel(
-      'All',
+      'Included',
       id="tab-panel",
       shinyjs::useShinyjs(),
       fluidRow(
-        column(3,
-            fluidRow(
-              wellPanel(
-                id = "searchpanel",
-                p(strong("Filter Options")),
-                selectInput(inputId = "journal", label="Journal", choices = NULL, multiple = TRUE, ),
-                selectInput(inputId = "study", "Type of Study", choices = NULL, multiple = TRUE),
-                selectInput(inputId = "author", "Author(s)",choices = NULL, multiple = TRUE),
-                selectInput(inputId = "specialty", "Specialty Bucket",choices = NULL, multiple = TRUE),
-                shinyWidgets::switchInput(inputId="specSwitch", size="mini", label="Match", onLabel = "Any", offLabel = "All", value=TRUE, offStatus = "success"),
-                hr(),
-                actionButton(inputId = "clearAll", "Clear all", class="btn-primary btn-sm")
-                # downloadButton(outputId = "export", label = "Download all", class="btn-secondary btn-sm")
-                # downloadButton(outputId = "exportselected", label = "Download selected", class="btn-secondary btn-sm")
-              )
-            ),
-            fluidRow(
-              wellPanel(
-                htmlOutput("ref_caption")
-              )
-            )
-        ),
-        column(9,
-               DT::dataTableOutput('ex1')
-        )
+        column(3, filterPanel, wellPanel(htmlOutput("ref_caption"))),
+        column(9, DT::dataTableOutput('ex1'))
       )
   ),
-  # tabPanel("Critical Care"),
-  # tabPanel("Internal Medicine"),
-  # tabPanel("Emergency Medicine"),
-  # tabPanel("Pediatrics"),
-  # tabPanel("Radiology"),
-  # tabPanel("Epi and Public Health"),
-  # tabPanel("Basic Sciences"),
+  # tabPanel("Unreviewed",
+  #          fluidRow(
+  #            column(3,
+  #                   fluidRow(
+  #                     filterPanel
+  #                   ),
+  #                   fluidRow(
+  #                     wellPanel(
+  #                       htmlOutput("ref_caption")
+  #                     )
+  #                   )
+  #            ),
+  #            column(9)
+  #          )
+  # ),
   navbarMenu("About",
     tabPanel("The Project",
-           tags$style(type="text/css","body {padding-top: 70px;}"),
+           tags$style(type="text/css","body {padding-top:60px;}"),
            fluidRow(column(3),
              column(6,wellPanel(HTML(includeMarkdown("markdown/About-Proj.md")))),
              column(3))
     ),
     tabPanel('Methods',
-           tags$style(type="text/css","body {padding-top: 70px;}"),
            fluidRow(column(3),
                     column(6,wellPanel(HTML(includeMarkdown("markdown/Methods.md")))),
                     column(3))

www/yeti.css

@@ -3936,7 +3936,7 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
   }
 }
 .navbar-default {
-  background-color: #940049; /*originally 333333*/
+  background-color: #7a003c; /*originally 333333*/
   border-color: #222222;
 }
 .navbar-default .navbar-brand {