Starting Shiny app after password input

EDIT 2019: We can now use the package shinymanager to do this: the invactivity script is to timeout the login page after 2 mins of inactivity so you dont waste resources:

library(shiny)
library(shinymanager)

inactivity <- "function idleTimer() {
var t = setTimeout(logout, 120000);
window.onmousemove = resetTimer; // catches mouse movements
window.onmousedown = resetTimer; // catches mouse movements
window.onclick = resetTimer;     // catches mouse clicks
window.onscroll = resetTimer;    // catches scrolling
window.onkeypress = resetTimer;  //catches keyboard actions

function logout() {
window.close();  //close the window
}

function resetTimer() {
clearTimeout(t);
t = setTimeout(logout, 120000);  // time is in milliseconds (1000 is 1 second)
}
}
idleTimer();"


# data.frame with credentials info
credentials <- data.frame(
  user = c("1", "fanny", "victor", "benoit"),
  password = c("1", "azerty", "12345", "azerty"),
  # comment = c("alsace", "auvergne", "bretagne"), %>% 
  stringsAsFactors = FALSE
)

ui <- secure_app(head_auth = tags$script(inactivity),
                 fluidPage(
                   # classic app
                   headerPanel('Iris k-means clustering'),
                   sidebarPanel(
                     selectInput('xcol', 'X Variable', names(iris)),
                     selectInput('ycol', 'Y Variable', names(iris),
                                 selected=names(iris)[[2]]),
                     numericInput('clusters', 'Cluster count', 3,
                                  min = 1, max = 9)
                   ),
                   mainPanel(
                     plotOutput('plot1'),
                     verbatimTextOutput("res_auth")
                   )
                   
                 ))

server <- function(input, output, session) {
  
  result_auth <- secure_server(check_credentials = check_credentials(credentials))
  
  output$res_auth <- renderPrint({
    reactiveValuesToList(result_auth)
  })
  
  # classic app
  selectedData <- reactive({
    iris[, c(input$xcol, input$ycol)]
  })
  
  clusters <- reactive({
    kmeans(selectedData(), input$clusters)
  })
  
  output$plot1 <- renderPlot({
    palette(c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3",
              "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999"))
    
    par(mar = c(5.1, 4.1, 0, 1))
    plot(selectedData(),
         col = clusters()$cluster,
         pch = 20, cex = 3)
    points(clusters()$centers, pch = 4, cex = 4, lwd = 4)
  })
  
}


shinyApp(ui = ui, server = server)

Original Post:
I am going to answer #1 and for #2 you can simply expand on my example. Following this example Encrypt password with md5 for Shiny-app. you can do the following:

1. Create 2 pages and if the user inputs the correct username and password you can renderUI and use htmlOutput to output your page
2. You can style the position of the box with username and password with tagsas I did and color them if you want also using tags$style

You can then further look into the actual page and specify what should be created as a result of different users. You can also look into JavaScript Popup Boxes

EDIT 2018: Also have a look at the example here https://shiny.rstudio.com/gallery/authentication-and-database.html

rm(list = ls())
library(shiny)

Logged = FALSE;
my_username <- "test"
my_password <- "test"

ui1 <- function(){
  tagList(
    div(id = "login",
        wellPanel(textInput("userName", "Username"),
                  passwordInput("passwd", "Password"),
                  br(),actionButton("Login", "Log in"))),
    tags$style(type="text/css", "#login {font-size:10px;   text-align: left;position:absolute;top: 40%;left: 50%;margin-top: -100px;margin-left: -150px;}")
  )}

ui2 <- function(){tagList(tabPanel("Test"))}

ui = (htmlOutput("page"))
server = (function(input, output,session) {
  
  USER <- reactiveValues(Logged = Logged)
  
  observe({ 
    if (USER$Logged == FALSE) {
      if (!is.null(input$Login)) {
        if (input$Login > 0) {
          Username <- isolate(input$userName)
          Password <- isolate(input$passwd)
          Id.username <- which(my_username == Username)
          Id.password <- which(my_password == Password)
          if (length(Id.username) > 0 & length(Id.password) > 0) {
            if (Id.username == Id.password) {
              USER$Logged <- TRUE
            } 
          }
        } 
      }
    }    
  })
  observe({
    if (USER$Logged == FALSE) {
      
      output$page <- renderUI({
        div(class="outer",do.call(bootstrapPage,c("",ui1())))
      })
    }
    if (USER$Logged == TRUE) 
    {
      output$page <- renderUI({
        div(class="outer",do.call(navbarPage,c(inverse=TRUE,title = "Contratulations you got in!",ui2())))
      })
      print(ui)
    }
  })
})

runApp(list(ui = ui, server = server))