inst/shiny/ui.R

In ArchaeoPhases: Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'

library(shiny)
library(shinythemes)
library(ArchaeoPhases)
library(hdrcde)
library(coda)
#library(DT)


renderInputs0 <- function() {
    fluidRow(
      h4("Post-Processing of the Markov Chain Simulated by BCal, by ChronoModel or by Oxcal"),
      br(),
      h4("This is a Shiny application for BCal, ChronoModel or Oxcal users who want to use ArchaeoPhases package without having to know R software."),
      h4("The process is very simple !"),
      h4("First model your chronology with BCal, ChronoModel or Oxcal or any other software for constructing archaeological chronologies.  "),
      h4("Then extract the simulated Markov Chains and save it into a CSV file. "),
      h4("And finally, import the CSV file using this web application and analyse your chronological dates or groups of dates. "),
      br(),
      tags$div(class="header", checked=NA,
              tags$p("To visite BCal website"), tags$a(href="http://bcal.shef.ac.uk/.html", "Click Here!"),
              br(),
              tags$p("To visite ChronoModel website"), tags$a(href="http://www.chronomodel.fr/", "Click Here!"), 
              br(),
              tags$p("To visite Oxcal website"), tags$a(href="https://c14.arch.ox.ac.uk/oxcalhelp/hlp_contents.html", "Click Here!")
       ),
      br(),
      # adding the new div tag to the sidebar            
      tags$div(class="header", checked=NA,
               tags$p("Ready to take the ArchaeoPhases tutorial? If so"),
               tags$a(href="http://www.math.sciences.univ-nantes.fr/~philippe/Stat_&_Archaeology_files/ArchaeoPhasesTuto1.0.pdf", "Click Here!")
      ),       
      br(),
      # adding the new div tag to the sidebar            
      tags$div(class="header", checked=NA,
               tags$p("This application is developed by Anne Philippe and Marie-Anne Vibet members of the Laboratoire de mathématiques Jean Leray, Université de Nantes, France,"),
               tags$p("and by Thomas S. Dye from T. S. Dye & Colleagues, Archaeologists, Inc., Honolulu. "),
               tags$p("Maintainer : Anne Philippe <anne.philippe@univ-nantes.fr>"),
               tags$p("Last release : Septembre 2017")
      )
      
  )}

################################
### Onglet "Import CSV" ########

renderInputs11 <- function() {

  wellPanel(
    fluidRow(
      fileInput(inputId = "file11", label ="Choose file", multiple = FALSE),
      h5(helpText("Select separators below to read the CSV file")),
      column(6,radioButtons(inputId ='sep11', label="Cell separator", choices=c(Comma=',', Semicolon=';', Tab='\t', Space=''), selected=',')),
      column(6,radioButtons(inputId='dec11', label="Decimal separator", choices=c(Comma=',', Dot='.'), selected='.') ), 
      br(),
      br(),
      textInput(inputId='iterationColumn1', label="Number of the iteration column", "NULL" ),
      textInput(inputId='referenceYear1', label="Year of reference for non BC/AD format", "NULL" ),
      textInput(inputId='rowToWithdraw1', label="Row to be withdrawn", "NULL" )
    )
    
  )}

renderInputs12 <- function() {
  wellPanel(
    fluidRow(
      fileInput(inputId = "file12", label ="Choose file", multiple = FALSE),
      h5(helpText("Select separators below to read the CSV file")),
      column(6,radioButtons(inputId ='sep12', label="Cell separator", choices=c(Comma=',', Semicolon=';', Tab='\t', Space=''), selected=',')),
      column(6,radioButtons(inputId='dec12', label="Decimal separator", choices=c(Comma=',', Dot='.'), selected='.') ), 
      br(),
      textInput(inputId='iterationColumn2', label="Number of the iteration column", "NULL" ),
      textInput(inputId='referenceYear2', label="Year of reference for non BC/AD format", "NULL" ),
      textInput(inputId='rowToWithdraw2', label="Row to be withdrawn", "NULL" ),
      actionButton(inputId = "StockageFile2", label = "Use this file")
    )
    
  )}


renderInputs13 <- function() {
  wellPanel(
    fluidRow(
      h3("Create Group of dates"),
      h5(helpText("Dates selection")),
      actionButton(inputId = "selectAllG", 
                   label = "Select all"), 
      actionButton(inputId = "clearAllG", 
                   label = "Clear selection"), 
      uiOutput("ChainsSelectionG"),
      br(),
      textInput(inputId='name', label="Name of the group", "Group1" ),
      actionButton(inputId = "goButton", label = "Create group"),
      actionButton(inputId = "addButton", label = "Add group"),
      actionButton(inputId = "clearButton", label = "Clear groups"),
      downloadButton('downloadData', 'Download file'),
      actionButton(inputId = "StockageFile22", label = "Use this file")
    )
    
  )}

################################
### Onglet Convergence  ########

renderInputsCV <- function() {
  wellPanel(
    fluidRow(
      h3("Selection of groups in succession"),
      h5(helpText("Dates selection")),
      actionButton(inputId = "selectAllCV", 
                   label = "Select all"), 
      actionButton(inputId = "clearAllCV", 
                   label = "Clear selection"), 
      uiOutput("ChainsSelectionCV"),
      br(),
      h4(helpText("Number of chains")),
      numericInput(inputId ='NbChains', label="Number", value=2, min=1, max=100)
    )
    
  )}


################################
### Onglet Dates  ########

renderInputs2 <- function() {
  wellPanel(
    fluidRow(
      h3("Description of individual dates"),
      selectInput("variables", "Select chain names", character(0)),
      h5(helpText("Statistical options")),
      numericInput(inputId ='level', label="Confidence level", value=0.95,min=0, max=1),
      br(),
      h5(helpText("Graphic options")),
      textInput(inputId='titlePlot', label="Plot title", "Characteristics of a date" ),
      column(6,radioButtons(inputId='color', label="Colors", choices=c(Yes='TRUE', No='FALSE'), selected='TRUE') ),
      downloadButton('downloadPlotDates', 'Download Marginal plot')
      )
    
  )}


renderInputs22 <- function() {
  wellPanel(
    fluidRow(
      h3("Group of dates"),
      h5(helpText("Dates selection")),
      actionButton(inputId = "selectAll", 
                   label = "Select all"), 
      actionButton(inputId = "clearAll", 
                   label = "Clear selection"), 
      uiOutput("ChainsSelection"), 
      br(),
      h5(helpText("Statistical options")),
      numericInput(inputId ='level22', label="Confidence level", value=0.95,min=0, max=1),
      #br(),
      h5(helpText("Intervals plot options")),
      textInput(inputId='titleIntervalsplot', label="Intervals plot title", "Intervals plot" ),
      radioButtons(inputId='intervals', label="Intervals", choices=c("Credible Intervals"='CI', "Highest Posterior Density"='HPD'), selected='CI'),
      radioButtons(inputId='order', label="Order of y", choices=c("Default order"='default', "Increasing order"='increasing'), selected='default'),
      downloadButton('downloadIntervalPlot', 'Download Intervals plot'),
      br(),
      h5(helpText("Tempo plot options")),
      textInput(inputId='titleTempoplot', label="Tempo plot title", "Tempo plot" ),
      column(6,radioButtons(inputId='GaussCI', label="Gaussian approx", choices=c(Yes='TRUE', No='FALSE'), selected='FALSE')), 
      column(6,radioButtons(inputId='count', label="Counting process", choices=c(Number='TRUE', Probability='FALSE'), selected='TRUE')),
      textInput(inputId='xlabel', label="x-label", "Calendar year" ),
      uiOutput("ui"),
      column(6,radioButtons(inputId='colors', label="Use of colors", choices=c(Yes='TRUE', No='FALSE'), selected='TRUE')),
      downloadButton('downloadTempoPlot', 'Download Tempo plot'),
      downloadButton('downloadActivityPlot', 'Download Activity plot'),
      br(),
      h5(helpText("Occurrence plot options")),
      textInput(inputId='titleOccurrenceplot', label="Occurrence plot title", "Occurrence plot" ),
      #textInput(inputId='xlabelO', label="x-label", "Calendar year" ),
      #textInput(inputId='ylabelO', label="y-label", "Cumulative events" ),
      downloadButton('downloadOccurrencePlot', 'Download Occurrence plot')
    )
    
  )}




   ##################################
#######   Tests between dates   ##########


renderInputsTests <- function() {
  wellPanel(
    fluidRow(
      h3("Dates selection"),
      selectInput("variableTest1a", "Select chain names", choices = character(0), multiple = FALSE, selected = NULL),
      selectInput("variableTest1b", "Select chain names", choices = character(0), multiple = FALSE, selected = NULL),
      br(),
      h5(helpText("Statistical options")),
      numericInput(inputId ='levelTests', label="Confidence level", value=0.95,min=0, max=1)
    )
    
  )}


  ##################################
#######   Group of dates   ##########

renderInputs3 <- function() {
  wellPanel(
    fluidRow(
      h3("Selection of a group"),
      h5(helpText("Make sure that File2 is uploaded.")),
      selectInput("variablesMin", "Select chain names", choices = character(0), multiple = FALSE, selected = NULL),
      selectInput("variablesMax", "Select chain names", choices = character(0), multiple = FALSE, selected = NULL),
      br(),
      h5(helpText("Statistical options")),
      numericInput(inputId ='level2', label="Confidence level", value=0.95, min=0, max=1),
      br(),
      h5(helpText("Graphical options")),
      textInput(inputId='titlePlot2', label="Title", "Characterisation of a group" ),
      column(6,radioButtons(inputId='color2', label="Colors", choices=c(Yes='TRUE', No='FALSE'), selected='TRUE') ),
      downloadButton('downloadGroupPlot', 'Download plot')
    )
  )}

renderInputs32 <- function() {
  wellPanel(
    fluidRow(
      h3("Selection of groups (at least two)"),
      br(),
      h4(helpText("Warning : If groups are nested in each other, the CSV file should be reorganised. ")),
      br(),
      actionButton(inputId = "selectAll32", 
                   label = "Select all"),
      actionButton(inputId = "clearAll32", 
                   label = "Clear selection"), 
      uiOutput("PhasesSelection32"),
      br(),
      h5(helpText("Statistical options")),
      numericInput(inputId ='levelMultiPhases', label="Confidence level", value=0.95, min=0, max=1),
      br(),
      h5(helpText("Graphical options")),
      textInput(inputId='titleMultiPhases', label="Plot title", "Characterisation of several groups" ),
      downloadButton('downloadMultiPhasesPlot', 'Download Groups plot')
    )
  )}



    ##################################
#######   Succession of groups   ##########


renderInputs4 <- function() {
  wellPanel(
    fluidRow(
      h3("Selection of groups in succession"),
      br(),
      h4(helpText("Warning : temporal order constraints should have been introduced in the modelling. ")),
      br(),
      actionButton(inputId = "selectAll4", 
                   label = "Select all"),
      actionButton(inputId = "clearAll4", 
                   label = "Clear selection"), 
      uiOutput("PhasesSelection"),
      br(),
      h5(helpText("Statistical options")),
      numericInput(inputId ='levelSuccession', label="Confidence level", value=0.95, min=0, max=1),
      br(),
      h5(helpText("Graphical options")),
      textInput(inputId='titleSuccessionPlot', label="Plot title", "Characterisation of a succession of groups" ),
      downloadButton('downloadSuccessionPlot', 'Download Succession plot')
    )
    
  )}





shinyUI(fluidPage(
  headerPanel('ArchaeoPhases'),
  titlePanel('   Analysis of archaeological phases'),
  
  navbarPage(" ", theme = shinytheme("cerulean"),
             tabPanel("Home", 
                      renderInputs0()
             ),
             tabPanel("Import CSV", titlePanel("Import your CSV files"), 
                      fluidRow(
                        h2("File 1 : Dates"),
                        h4("First, import here the CSV file contaning the MCMC of all dates."),
                        h4("For modelling done with ChronoModel, this file is called 'events.csv'"),
                        h4("For any other software, import the CSV file extracted from it. ")
                      ),
                      fluidRow(
                        column(5, renderInputs11()),
                        column(6, uiOutput("AfficheTableLue11"))
                      )  ,
                      fluidRow(
                        h2("File 2 : Groups of dates"),
                        h4("Import here the CSV file contaning the MCMC of the minimum and maximum of all groups of dates if any."),
                        h4("For modelling done with ChronoModel, this file is called 'phases.csv'. "),
                        h4("For any other software, you may create it using Create CSV. "),
                        h4(helpText("Warning : please click on 'Use this file' at the bottom of either of these tab in order to go one. ")),
                        tabsetPanel(
                                    tabPanel("Import a CSV file", 
                                            # h4("Import here the CSV file contaning the MCMC of the minimum and maximum of all groups of dates."),
                                             fluidRow(
                                                  column(5, renderInputs12()),
                                                  column(6, uiOutput("AfficheTableLue12"))
                                                )  
                                             ),
                                    tabPanel("Create groups of dates", 
                                            # h4("Creating the file containing the minimim and maximum of all groups of dates."),
                                             fluidRow(
                                                  column(5, renderInputs13()),
                                                  column(6, uiOutput("result13"))
                                                
                                                )
                                             )
                        )
                      )
                      ),
             tabPanel("Convergence", titlePanel("Check the convergence of the Markov chains"),
                      fluidRow(
                        column(5, renderInputsCV()),
                        column(6, uiOutput("Diagnostics"))
                      )
             ),
             tabPanel("Dates", titlePanel("Description of individual dates"), 
                      fluidRow(
                        column(5, renderInputs2()),
                        column(6, uiOutput("result2"))
                      ),
                      fluidRow(
                        column(4, renderInputs22()),
                        column(7, uiOutput("result22"))
                      )
                      ),
             tabPanel("Tests between dates", titlePanel("Tests between dates"), 
                      h4("Two tests between dates are available : "),
                      h4("A posterior probability that a date is earlier than another one. "),
                      h4("A testing procedure to check the presence of a gap between two dates. A gap interval is estimated if we accept its existence."),
                      fluidRow(
                        column(5, renderInputsTests()),
                        column(6, uiOutput("resultTests"))
                      )
             ),
             tabPanel("Group of dates", titlePanel("Description of individual group of dates"),   
                      fluidRow(
                        column(4, renderInputs3()),
                        column(7, uiOutput("result3"))
                      ),
                      fluidRow(
                        column(4, renderInputs32()),
                        column(7, uiOutput("result32"))
                      )
                      ),
             tabPanel("Succession of groups", titlePanel("Description of a succession of groups"),    
                      fluidRow(
                        fluidRow( column(4, renderInputs4() ), column(8, uiOutput("Inputs4")) )
                      )
             )
  )
  
                  
  

  
))