diff --git a/app.R b/app.R
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-# epsilon index R Shiny app
-# Corey Bradshaw
-# Flinders University
-
-## remove everything
-rm(list = ls())
-
-# load libraries
-library(shiny)
-library(scholar)
-
-# Google authentication
-library(googleID)
-library(shinyjs)
-library(googleAuthR)
-
-options(googleAuthR.scopes.selected = c("https://www.googleapis.com/auth/userinfo.email",
-                                        "https://www.googleapis.com/auth/userinfo.profile"
-                                        ))
-options("googleAuthR.webapp.client_id" = "500611116199-1let7ftg4hgni9ccv6b2297ovv1ij48i.apps.googleusercontent.com")
-options("googleAuthR.webapp.client_secret" = "h-U5SScXB1xKNJWOqMDaKMWL")
-
-#gar_set_client(scopes="https://www.googleapis.com/auth/analytics.readonly")
-
-library(googleAnalyticsR)
-
-## call functions
-source(file.path("./", "epsilonIndexFunc.R"), local=T)
-
-ui <- fluidPage(
-  
-  tags$head(
-    tags$meta(name="google-site-verification", content="bVQ54bgpekDeCqy30pOSnGOMgbNXXV1AdwIoMRXSAAI")
-  ),
-  
-  # title of app
-  titlePanel("calculate ε-index"),
-  
-  wellPanel(
-    tags$p(style="font-family:Avenir", "R Shiny App by", tags$a(href="https://globalecologyflinders.com/people/#CJAB", "Corey Bradshaw "),
-           tags$a(href = "mailto:corey.bradshaw@flinders.edu.au","(e-mail; "),
-           tags$a(href = "https://github.com/cjabradshaw", "Github)")),
-    tags$p(style="font-family:Avenir", "Existing citation-based indices used to rank research performance do not permit a fair comparison 
-           of researchers among career stages or disciplines, nor do they treat women and men equally. We designed 
-           the ε-index, which is simple to calculate, based on open-access data, corrects for disciplinary variation, 
-           can be adjusted for career breaks, and sets a sample-specific threshold above and below which a researcher 
-           is deemed to be performing above or below expectation. This R Shiny App estimates the ε-index and its variants 
-           using user-provided data files. All R code and example data necessary to reproduce these analyses is available ",
-           tags$a(href = "https://github.com/cjabradshaw/EpsilonIndex", "here"), ".")
-  ),
-  
-  tabsetPanel(id="tabs",
-              tabPanel(value="tab1", title="user-collated citation data",
-                       
-                       sidebarLayout(
-                         sidebarPanel(
-                           wellPanel(
-                             fileInput("file1", "choose delimited file with the necessary citation data (6 columns)",
-                                       multiple=F, buttonLabel="choose file",placeholder="no file selected"),
-                             radioButtons("sep","separator",choices=c(comma=',',space="",tab="\t")),
-                             checkboxInput("header1", "header?", TRUE),
-                             tags$hr(),
-                             selectInput("sortind", "choose index to sort by", 
-                                         c("ε-index"="e","gender-debiased ε-index"="d","ε′-index"="ep","gender-debiased ε′-index"="dp")),
-                             actionButton("calcButton", label="calculate ε-index"),
-                             br(),
-                             tags$small(style="font-family:Avenir", "(refresh page to clear data)"),
-                             br(),
-                             downloadButton('downloadData', 'download',icon = shiny::icon("download"))
-                           ),
-                         ),
-                         
-                         # open main panel
-                         mainPanel(
-                           
-                           fluidRow(
-                             tags$div(id = "firstOutput", 
-                                      h3("input data"),
-                                      dataTableOutput("table1")) 
-                           ),
-                           
-                           fluidRow(
-                             tags$div(id = "placeholder") # the dynamic UI will be inserted relative to this placeholder
-                           ),
-                           
-                         ) # close mainPanel
-                         
-                       ) # sidebarLayout
-              ), # end tab1
-              
-              tabPanel(value="tab2", title="retrieve Google Scholar citation data",
-                       useShinyjs(),
-                       sidebarLayout(
-                         sidebarPanel(
-                           #gar_auth_jsUI("auth"),
-                           
-                           p(style="font-family:Avenir","To use this function, you must log in to your Google account",
-                             googleAuthUI("gauth_login")),
-
-                           wellPanel(
-                             fileInput("file2", "choose delimited file with Google Scholar IDs & genders (2 columns)",
-                                       multiple=F, buttonLabel="choose file",placeholder="no file selected"),
-                             radioButtons("sep2","separator",choices=c(comma=',',space="",tab="\t")),
-                             checkboxInput("header2", "header?", TRUE),
-                             hr(),
-                             actionButton("genButton", label="retrieve GS data"),
-                             hr(),
-                             selectInput("sortind2", "choose index to sort by:", 
-                                         c("ε-index"="e","gender-debiased ε-index"="d","ε′-index"="ep","gender-debiased ε′-index"="dp")),
-                             actionButton("calcButton2", label="calculate ε-index"),
-                             br(),
-                             tags$small(style="font-family:Avenir", "(refresh page to clear data)"),
-                             br(),
-                             downloadButton('downloadData2', 'download',icon = shiny::icon("download"))
-                             
-                             
-                           ),
-                         ),
-                         
-                         # open main panel
-                         mainPanel(
-                           textOutput("display_username"),
-                           
-                           fluidRow(
-                             tags$div(id = "secondOutput", 
-                                      h3("input data"),
-                                      dataTableOutput("table2")) 
-                           ),
-                           
-                           fluidRow(
-                             tags$div(id = "placeholder2") # the dynamic UI will be inserted relative to this placeholder
-                           ),
-                           
-                           dataTableOutput("etable2")
-                           
-                         ) # close mainPanel
-                         
-                       ) # sidebarLayout
-                       
-              ), # end tab2
-              
-              tabPanel(value="tab3", title=tags$strong("notes (input/output column descriptions)"),
-                       tags$h2(style="font-family:Avenir", "Column descriptors"),
-                       tags$h3(style="font-family:Avenir", "User-collated citation data"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 1"),": ", tags$em("personID")," — any character identification of an individual researcher (can be a name)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 2"),": ", tags$em("gender")," — researcher's gender (F or M)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 3"),": ", tags$em("i10")," — researcher's i10 index (# papers with ≥ 10 citations); must be > 0"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 4"),": ", tags$em("h")," — researcher's h-index"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 5"),": ", tags$em("maxcit")," — number of citations of researcher's most cited peer-reviewed paper"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 6"),": ", tags$em("firstyrpub")," — the year of the researcher's first published peer-reviewed paper"),
-                       
-                       tags$h3(style="font-family:Avenir", "Google Scholar IDs & gender input"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 1"),": ", tags$em("GSID")," — Google Scholar researcher ID"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 2"),": ", tags$em("gender")," — researcher's gender (F or M)"),
-                       
-                       tags$h3(style="font-family:Avenir", "ε-index output"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 1"),": ", tags$em("ID")," — researcher ID"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 2"),": ", tags$em("gen")," — researcher's gender (F or M)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 3"),": ", tags$em("yrsP")," — number of years since first peer-reviewed paper"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 4"),": ", tags$em("genE")," — ε-index relative to others of the same gender in the sample"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 5"),": ", tags$em("exp")," — whether above or below expectation based on chosen index (default is 'e' = pooled index)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 6"),": ", tags$em("m")," — h-index ÷ yrsP"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 7"),": ", tags$em("h")," — h-index"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 8"),": ", tags$em("genRnk")," — rank from gender.eindex (1 = highest)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 9"),": ", tags$em("debRnk")," — gender-debiased rank (1 = highest)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 10"),": ", tags$em("poolE")," — ε-index generated from the entire sample (not gender-specific)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 11"),": ", tags$em("poolRnk")," — rank from poolE (1 = highest)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 12"),": ", tags$em("eP")," — scaled poolE (ε′-index)"),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 13"),": ", tags$em("debEP")," — scaled genE (gender ε′-index)"),
-                       tags$br(),
-                       tags$p(style="font-family:Avenir", tags$em("if sort index = 'ε′-index'")),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 14"),": ", tags$em("ePRnk")," — rank from ε′-index"),
-                       tags$br(),
-                       tags$p(style="font-family:Avenir", tags$em("if sort index = 'gender-debiased ε′-index'")),
-                       tags$p(style="font-family:Avenir", tags$strong("COLUMN 14"),": ", tags$em("ePddebRnk")," — rank from gender ε′-index"),
-                       tags$br()
-                       
-                       
-              ) # end tab3
-  ) # end tabsetPanel
-  
-) # close fluidPage
-
-
-server <- function(input, output, session) {
-  
-  observeEvent(input$tabs, {
-    
-    if(input$tabs == "tab1"){
-      
-      output$table1 <- renderDataTable({
-        file_to_read = input$file1
-        if(is.null(file_to_read)){
-          return()
-        }
-        read.table(file_to_read$datapath, sep=input$sep, header=input$header1)
-      }) # end output table1
-      
-      datin <- reactive({
-        fileinp <- input$file1
-        if(is.null(fileinp)){return()}
-        inpdat <- data.frame(read.csv(fileinp$datapath, header = input$header1))
-        return(inpdat)
-      }) # end datin
-      
-      # when action button pressed ...
-      observeEvent(input$calcButton, {
-        removeUI("div:has(>#firstOutput)")
-        insertUI(
-          selector = "#placeholder",
-          where = "afterEnd", # inserts UI after the end of the placeholder element
-          ui = fluidRow(
-            h3("output"),
-            output$etable <- renderDataTable({
-              if(is.null(datin())){return ()}
-              results <<- epsilonIndexFunc(datsamp=(datin()), sortindex=input$sortind)
-            })))
-      }) # end observeEvent
-      
-      output$downloadData <- downloadHandler(
-        filename = function() {
-          paste("epsilonIndexOut", "csv", sep = ".")
-        },
-        
-        content = function(file) {
-          sep <- ","
-          
-          write.table(results, file, sep=sep, row.names = F)
-        }
-      )
-    } # end if for tab1
-
-        
-    if(input$tabs == "tab2"){
-      #auth <- callModule(gar_auth_js, "auth")
-      
-      ## Global variables needed throughout the app
-      rv <- reactiveValues(
-        login = FALSE
-      )
-
-      ## Authentication
-      accessToken <- callModule(googleAuth, "gauth_login",
-                                login_class = "btn btn-primary",
-                                logout_class = "btn btn-primary")
-      userDetails <- reactive({
-        validate(
-          need(accessToken(), "not logged in")
-        )
-        rv$login <- TRUE
-        with_shiny(get_user_info, shiny_access_token = accessToken())
-      })
-
-      ## Display user's Google display name after successful login
-      output$display_username <- renderText({
-        validate(
-          need(userDetails(), "getting user details")
-        )
-        userDetails()$displayName
-      })
-
-      ## Workaround to avoid shinyaps.io URL problems
-      observe({
-        if (rv$login) {
-          shinyjs::onclick("gauth_login-googleAuthUi",
-                           shinyjs::runjs("window.location.href = 'https://cjabradshaw.shinyapps.io/epsilonIndex/';"))
-        }
-      })
-      
-      output$table2 <- renderDataTable({
-        file_to_read = input$file2
-        if(is.null(file_to_read)){
-          return()
-        }
-        read.table(file_to_read$datapath, sep=input$sep2, header=input$header2)
-      }) # end output table2
-      
-      datin2 <- reactive({
-        fileinp2 <- input$file2
-        if(is.null(fileinp2)){return()}
-        inpdat2 <- data.frame(read.csv(fileinp2$datapath, header = input$header2))
-        return(inpdat2)
-      }) # end datin2
-      
-      getProfileFunc <- function(gsdata) {
-        gsdatalen <- dim(gsdata)[1]
-        profileslist <- lapply(gsdata[,1], scholar::get_profile)
-        hs <- i10s <- maxcits <- Y1s <- rep(NA,gsdatalen)
-        for (r in 1:gsdatalen) {
-          hs[r] <- profileslist[[r]]$h_index
-          i10s[r] <- profileslist[[r]]$i10_index
-          maxcits[r] <- get_publications(as.character(profileslist[[r]]$id))$cites[1]
-          Y1s[r] <- get_oldest_article(profileslist[[r]]$id)
-        }
-        inputdata <- data.frame(gsdata[,1], gsdata[,2], i10s, hs, maxcits, Y1s)
-        colnames(inputdata) <- c("personID", "gender", "i10", "h", "maxcit","firstyrpub")
-        return(inputdata)
-      }
-      
-      # when action button pressed ...
-      observeEvent(input$genButton, {
-        removeUI("div:has(>#secondOutput)")
-        insertUI(
-          selector = "#placeholder2",
-          where = "afterEnd", # inserts UI after the end of the placeholder element
-          ui = fluidRow(
-            h3("GS data loading from server ..."),
-            output$gstable <- renderDataTable({
-              if(is.null(datin2())){return ()}
-              results2 <<- getProfileFunc(gsdata=(datin2()))
-            })))
-      }) # end observeEvent
-      
-      observeEvent(input$calcButton2,
-                   output$etable2 <- renderDataTable({
-                     results3 <<- epsilonIndexFunc(datsamp=(results2), sortindex=input$sortind2)
-                     results3
-                   })
-      ) # end observeEvent
-      
-      output$downloadData2 <- downloadHandler(
-        filename = function() {
-          paste("epsilonIndexOut", "csv", sep = ".")
-        },
-        
-        content = function(file2) {
-          sep <- ","
-          
-          write.table(results3, file2, sep=sep, row.names = F)
-        }
-      )
-      
-    } # end if for tab2
-    
-  }) # end tab Events
-  
-  session$onSessionEnded(stopApp)
-} # end server
-
-shinyApp(ui, server)
-