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inst/shiny/server.R
In ArchaeoPhases: Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'
shinyServer(function(input, output, clientData, session) {
# By default, Shiny limits file uploads to 5MB per file. You can modify this limit by using the shiny.maxRequestSize option.
# For example, adding options(shiny.maxRequestSize=30*1024^2) to the top of server.R would increase the limit to 30MB.
options(shiny.maxRequestSize=30*1024^2)
#######################################
#### Onglet : Import CSV #####
dataInput <- reactive({
file1 <- input$file11
if(is.null(file1)){return()}
if(input$iterationColumn1=="NULL"){
itCol = NULL
}else{
itCol = as.numeric(input$iterationColumn1)
}
if(input$referenceYear1=="NULL"){
refY = NULL
}else{
refY = as.numeric(input$referenceYear1)
}
if(input$rowToWithdraw1=="NULL"){
rowW = NULL
}else{
rowW = as.numeric(input$rowToWithdraw1)
}
ImportCSV(file=file1$datapath, sep=input$sep11, dec=input$dec11, header=TRUE, comment.char="#", iterationColumn = itCol, referenceYear = refY, rowToWithdraw = rowW)
})
output$filedf11 <- renderTable({
if(is.null(dataInput())){return()}
input$file11
})
output$table11 <- DT::renderDataTable({
if(is.null(dataInput())){return()}
DT::datatable(dataInput(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
output$AfficheTableLue11 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("About file", tableOutput("filedf11")), tabPanel("Data", DT::dataTableOutput("table11")))
})
##################################################
#### MCMC des MinMax des groupes ###
namesG <- reactive({
names = colnames(dataInput())
return(names)
})
# Initialize reactive values
valuesG <- reactiveValues()
dataInput12 <- reactive({
file2 <- input$file12
if(is.null(file2)){return()}
if(input$iterationColumn2=="NULL"){
itCol = NULL
}else{
itCol = as.numeric(input$iterationColumn2)
}
if(input$referenceYear2=="NULL"){
refY = NULL
}else{
refY = as.numeric(input$referenceYear2)
}
if(input$rowToWithdraw2=="NULL"){
rowW = NULL
}else{
rowW = as.numeric(input$rowToWithdraw2)
}
ImportCSV(file=file2$datapath, sep=input$sep12, dec=input$dec12, header=TRUE, comment.char="#", iterationColumn = itCol, referenceYear = refY, rowToWithdraw = rowW)
})
output$filedf12 <- renderTable({
if(is.null(dataInput12())){return()}
input$file12
})
output$table12 <- DT::renderDataTable({
if(is.null(dataInput12())){return()}
DT::datatable(dataInput12(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
output$AfficheTableLue12 <- renderUI({
if(is.null(dataInput12()))
h5("No data imported")
else
tabsetPanel(tabPanel("About file", tableOutput("filedf12")), tabPanel("Data", DT::dataTableOutput("table12")))
})
observeEvent(input$StockageFile2, {
valuesG$file2 <- dataInput12()
})
##################################################
#### Creation des groupes de dates ####
#### pour calcul des MinMax ###
output$ChainsSelectionG <- renderUI({
themesG <- namesG()
valuesG$namesG <- themesG
checkboxGroupInput('ChainsSelectionG', 'Select a series of dates:', themesG)
})
# Add observer on select-all button
observeEvent(input$selectAllG, {
valuesG$namesG <- namesG()
updateCheckboxGroupInput(session, 'ChainsSelectionG', selected = valuesG$namesG)
})
# Add observer on clear-all button
observeEvent(input$clearAllG, {
valuesG$namesG <- c()
updateCheckboxGroupInput(session, 'ChainsSelectionG', selected = "none")
})
# data selectionnees
selectDataG <- reactive({
dataInput()[, input$ChainsSelectionG, drop = FALSE]
})
# affichage table de donnees
output$DatasetG <- DT::renderDataTable({
if(is.null(selectDataG())){return( )}
DT::datatable(selectDataG(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
## CreateMinMaxGroup
createGroup1 <- eventReactive(input$goButton, {
position = seq(1, length(input$ChainsSelectionG))
dataGroup = CreateMinMaxGroup(selectDataG(), position=position, name =input$name, add=NULL)
})
observeEvent(input$goButton, {
valuesG$dataGroup <- createGroup1()
})
observeEvent(input$addButton, {
valuesG$dataGroup <- addGroup()
})
addGroup <- eventReactive(input$addButton, {
position = seq(1, length(input$ChainsSelectionG))
addGroup = CreateMinMaxGroup(selectDataG(), position=position, name =input$name, add=valuesG$dataGroup)#, exportFile=export)
return(addGroup)
})
observeEvent(input$clearButton, {
valuesG$dataGroup <- NULL
})
output$tableGroup <- DT::renderDataTable({
if(is.null(valuesG$dataGroup)){return()}
DT::datatable(valuesG$dataGroup, options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
output$result13 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetG")), tabPanel("Groups", DT::dataTableOutput("tableGroup")) )
})
output$downloadData <- downloadHandler(
filename = function() { paste("MinMaxGroup", '.csv', sep='') },
content = function(file) {
write.csv(valuesG$dataGroup, file)
}
)
observeEvent(input$StockageFile22, {
valuesG$file2 <- valuesG$dataGroup
})
#######################################
#### Onglet : Convergence ###
## Checking the Markov chains ##
# Affichage des colonnes du dataframe
namesCV <- reactive({
names = colnames(dataInput())
return(names)
})
# Initialize reactive values
valuesCV <- reactiveValues()
output$ChainsSelectionCV <- renderUI({
themesCV <- namesCV()
valuesCV$namesCV <- themesCV
checkboxGroupInput('ChainsSelectionCV', 'Select a series of dates (at least two):', choices =themesCV, selected = valuesCV$namesCV[1:2])
})
# Add observer on select-all button
observeEvent(input$selectAllCV, {
valuesCV$namesCV <- namesCV()
updateCheckboxGroupInput(session, 'ChainsSelectionCV', selected = valuesCV$namesCV)
})
# Add observer on clear-all button
observeEvent(input$clearAllCV, {
valuesCV$namesCV <- c()
updateCheckboxGroupInput(session, 'ChainsSelectionCV', selected = "none")
})
# data selectionnees
selectDataCV <- reactive({
dataInput()[, input$ChainsSelectionCV, drop = FALSE]
})
mcmc_List <- reactive({
if(is.null(selectDataCV)){return()}
coda.mcmc(selectDataCV(), numberChains = input$NbChains)#, iterationColumn = itC)
})
output$MCMCplot <- renderPlot({
plot(mcmc_List())
})
GelmanDiag <- reactive({
gelman.diag(mcmc_List())
})
output$GelmanDiagTable <- renderTable({
if(is.null(GelmanDiag())) {return()}
else {
res = GelmanDiag()$psrf
dim = dim(res)
namesRes = rownames(res)
PointEst = NULL
UpperCI = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, namesRes[i])
PointEst= c(PointEst, res[i,1])
UpperCI = c(UpperCI, res[i,2])
}
data.frame("names"=names,"Point estimate"=PointEst, "Upper Credible Interval" = UpperCI)
}
})
output$Gelmanplot <- renderPlot({
gelman.plot(mcmc_List())
})
output$Diagnostics <- renderUI({
if(is.null(selectDataCV()))
h5("No data imported")
else
tabsetPanel(tabPanel("History Plots", plotOutput("MCMCplot")), tabPanel("Gelman Plots", plotOutput("Gelmanplot")), tabPanel("Gelman Diagnostic", tableOutput("GelmanDiagTable")) )
})
#######################################
#### Onglet : Dates ####
#### Selection d une chaine ##
names <- reactive({
names = colnames(dataInput())
return(names)
})
observe({
updateSelectInput(session, inputId='variables', 'Select a MCMC chain', choices = names() )
})
selectChain <- reactive({
dataInput()[[ input$variables ]]
})
output$MarginalPlot <- renderPlot({
MarginalPlot(selectChain(), level = input$level, title = input$titlePlot, newWindow=FALSE)
})
MarginalStatisticsText <- reactive({
MarginalStatistics(selectChain(), level = input$level)
})
output$MarginalStatisticsUI <- renderUI({
tags$div(
tags$p("Mean = ", MarginalStatisticsText()[1,1]),
tags$p("MAP = ", MarginalStatisticsText()[2,1]),
tags$p("sd = ", MarginalStatisticsText()[3,1]),
tags$p("Q1 = ", MarginalStatisticsText()[4,1]),
tags$p("Median = ", MarginalStatisticsText()[5,1]),
tags$p("Q2 = ", MarginalStatisticsText()[6,1]),
tags$p("For a level of confidence at ", MarginalStatisticsText()[7,1]*100, "%"),
tags$p("Credible Interval = [", MarginalStatisticsText()[8,1], "," , MarginalStatisticsText()[9,1], "]"),
tags$p("HPD region = [", MarginalStatisticsText()[10,1], "," , MarginalStatisticsText()[11,1], "]")
)
})
output$result2 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Marginal plot", plotOutput("MarginalPlot")), tabPanel("Marginal statistics", uiOutput("MarginalStatisticsUI")))
})
output$downloadPlotDates <- downloadHandler(
filename = function() { paste("MarginalPlot", '.png', sep='') },
content = function(file) {
png(file)
MarginalPlot(selectChain(), level = input$level, title = input$titlePlot, colors=input$color )
dev.off()
}
)
##### Onglet : Dates - Selection plusieurs chaines ####
# Initialize reactive values
values <- reactiveValues()
output$ChainsSelection <- renderUI({
themes <- names()
values$names <- themes
checkboxGroupInput('multiChainsCI', 'Select numbers:', themes)
})
# Add observer on select-all button
observeEvent(input$selectAll, {
values$names <- names()
updateCheckboxGroupInput(session, 'multiChainsCI', selected = values$names)
})
# Add observer on clear-all button
observeEvent(input$clearAll, {
values$names <- c()
updateCheckboxGroupInput(session, 'multiChainsCI', selected = "none")
})
# data selectionnees
selectData <- reactive({
dataInput()[, input$multiChainsCI, drop = FALSE]
})
# affichage table de donnees
output$DatasetCI <- DT::renderDataTable({
if(is.null(selectData())){return( )}
DT::datatable(selectData(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
# calcul des IC
MultiCredibleIntervalText <- reactive({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
MultiCredibleInterval(selectData(), position, level = input$level22)
})
# affichage des resultats des IC
output$resultTableMCI <- renderTable({
if(is.null(MultiCredibleIntervalText())) {return()}
else {
dim = dim(MultiCredibleIntervalText())
names_CI = rownames(MultiCredibleIntervalText())
CIInf = NULL
CISup = NULL
name = NULL
for (i in 1:dim[1]){
name = c(name, names_CI[i])
CIInf= c(CIInf, MultiCredibleIntervalText()[i,2])
CISup = c(CISup, MultiCredibleIntervalText()[i,3])
}
data.frame("names"=name, "Credible Interval Inf"=CIInf, "Credible Interval Sup" = CISup)
}
})
### calcul des HPD
MultiHPDText <- reactive({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
MultiHPD(selectData(), position, level = input$level22)
})
# affichage des resultats des IC
output$resultTableMHPD <- renderTable({
if(is.null(MultiHPDText())) {return()}
else {
dim = dim(MultiHPDText())
names_HPD = rownames(MultiHPDText())
HPDInf = NULL
HPDSup = NULL
name = NULL
for (i in 1:dim[1]){
name = c(name, names_HPD[i])
HPDInf= c(HPDInf, MultiHPDText()[i,2])
HPDSup = c(HPDSup, MultiHPDText()[i,3])
}
data.frame("names"=name, "HPD Inf"=HPDInf, "HPD Sup" = HPDSup)
}
})
output$MultiDatesPlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
#if(input$exportFile22IT == "TRUE") { outFile = "IntervalsPlot"} else{ outFile = NULL}
MultiDatesPlot(selectData(), position, intervals =input$intervals, order = input$order, level = input$level, title = input$titleIntervalsplot, newWindow=FALSE, print.data.result = FALSE)
})#, height = 600, width = 800)
output$downloadIntervalPlot <- downloadHandler(
filename = function() { paste("downloadIntervalPlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
MultiDatesPlot(selectData(), position, intervals =input$intervals, level = input$level, title = input$titleIntervalsplot, print.data.result = FALSE)
dev.off()
}
)
output$ui<- renderUI({
switch(input$count,
"TRUE" = textInput(inputId='ylabel', label="y-label", "Cumulative events" ),
"FALSE" = textInput(inputId='ylabel', label="y-label", "Probability" )
)
})
output$TempoPlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
#if(input$exportFile22 == "TRUE") { outFile = "TempoPlot.png"} else{ outFile = NULL}
TempoPlot(selectData(), position, level = input$level, title = input$titleTempoplot, Gauss=input$GaussCI, count=input$count, x.label=input$xlabel, y.label=input$ylabel, colors = input$colors, newWindow=FALSE, print.data.result = FALSE)
})#, height = 600, width = 800)
output$TempoPlotUI <- renderUI({
if(is.null( input$multiChainsCI )) {h5(" Nothing to display ")}
else{
plotOutput("TempoPlot", width="80%")
}
})
output$downloadTempoPlot <- downloadHandler(
filename = function() { paste("downloadTempoPlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
TempoPlot(selectData(), position, level = input$level, title = input$titleTempoplot, Gauss=input$GaussCI, count=input$count, x.label=input$xlabel, y.label=input$ylabel, colors = input$colors, print.data.result = FALSE)#, out.file=outFile)
dev.off()
}
)
output$TempoActivityPlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
TempoActivityPlot(selectData(), position, level = input$level, count=input$count, newWindow=FALSE, print.data.result = FALSE)
})#, height = 600, width = 800)
output$TempoActivityPlotUI <- renderUI({
if(is.null( input$multiChainsCI )) {h5(" Nothing to display ")}
else{
plotOutput("TempoActivityPlot", width="80%")
}
})
output$downloadActivityPlot <- downloadHandler(
filename = function() { paste("downloadActivityPlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
TempoActivityPlot(selectData(), position, level = input$level, count=input$count, print.data.result = FALSE)
dev.off()
}
)
output$OccurrencePlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
OccurrencePlot(selectData(), position, level = input$level, count=input$count, newWindow=FALSE, print.data.result = FALSE)
})
output$OccurrencePlotUI <- renderUI({
if(is.null( input$multiChainsCI )) {h5(" Nothing to display ")}
else{
plotOutput("OccurrencePlot", width="80%")
}
})
output$downloadOccurrencePlot <- downloadHandler(
filename = function() { paste("downloadOccurrencePlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
OccurrencePlot(selectData(), position, level = input$level, count=input$count, print.data.result = FALSE)
dev.off()
}
)
output$result22 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetCI")),
tabPanel("Credible intervals", uiOutput("resultTableMCI")),
tabPanel("HPD regions", uiOutput("resultTableMHPD")),
tabPanel("Intervals Plot", plotOutput("MultiDatesPlot")),
tabPanel("Tempo Plot", plotOutput("TempoPlot"), br(), plotOutput("TempoActivityPlot")),
tabPanel("Occurrence Plot", plotOutput("OccurrencePlot"))
)
})
#######################################
#### Onglet : Tests ###
## Selection plusieurs chaines ##
# Initialize reactive values
# valuesTests <- reactiveValues()
namesTests <- reactive({
names = colnames(dataInput())
return(names)
})
observe({
updateSelectInput(session, inputId='variableTest1a', 'Select date a', choices = namesTests())
updateSelectInput(session, inputId='variableTest1b', 'Select date b', choices = namesTests())
})
selectChainTests <- reactive({
dataInput()[,c(input$variableTest1a, input$variableTest1b), drop = FALSE]
})
output$DataSelectedTests <- DT::renderDataTable({
if(is.null(selectChainTests())) { return( h5("")) }
else
DT::datatable(selectChainTests(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
MarginalProbaText <- renderText({
MarginalProba(dataInput()[,input$variableTest1a, drop=TRUE], dataInput()[,input$variableTest1b, drop=TRUE])
})
output$MarginalProbaUI <- renderUI({
tags$div(
tags$p("The posterior probability that 'date a' is earlier than 'date b' is "),
tags$p(MarginalProbaText())
)
})
DatesHiatusText <- reactive({
DatesHiatus(dataInput()[,input$variableTest1a, drop=TRUE], dataInput()[,input$variableTest1b, drop=TRUE], level = input$levelTests)
})
output$DatesHiatusUI <- renderUI({
tags$div(
tags$p("The testing procedure to check the presence of a gap between 'date a' and 'date b'"),
tags$p("It returns the endpoints of the longest hiatus between two parameters. The result is given in calendar year (in format BC/AD)."),
br(),
tags$p("If 'NA', there is no hiatus at this level of confidence between 'date a' and 'date b'."),
br(),
tags$p("The inferior endpoint of the interval is ",DatesHiatusText()[2]),
tags$p("The superior endpoint of the interval is ",DatesHiatusText()[3])
)
})
output$resultTests <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data selected", DT::dataTableOutput("DataSelectedTests")), tabPanel("Anteriority / Posteriority test", uiOutput("MarginalProbaUI")), tabPanel("Hiatus between dates", uiOutput("DatesHiatusUI")))
})
##############################################
#### Onglet : Group of dates ####
#### Selection d un group ###
dataGroup2 <- reactive({
as.data.frame(valuesG$file2)
})
namesGroups <- reactive({
names12 = colnames(dataGroup2())
return(names12)
})
observe({
updateSelectInput(session, inputId='variablesMin', 'Select the minimum of the group', choices = namesGroups())
updateSelectInput(session, inputId='variablesMax', 'Select the maximum of the group', choices = namesGroups())
})
selectChain2 <- reactive({
dataGroup2()[,c(input$variablesMin, input$variablesMax), drop = FALSE]
})
TestPhaseSelected <- reactive({
if( sum(ifelse(dataGroup2()[,1] < dataGroup2()[,2], 1, 0)) == length(dataGroup2()[,1])) {return(1)}
})
output$selectedTable2 <- DT::renderDataTable({
if(is.null(selectChain2())) { return( h5("")) }
else
DT::datatable(selectChain2(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
PhaseStatisticsText <- reactive({
PhaseStatistics(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2)
})
output$PhaseStatisticsUI <- renderTable({
res = PhaseStatisticsText()
if(is.null(res)) {return()}
else {
dim = dim(res)
names_PS = rownames(res)
Minimum = NULL
Maximum = NULL
Duration = NULL
name = NULL
for (i in 1:dim[1]){
name = c(name, names_PS[i])
Minimum= c(Minimum, res[i,2])
Maximum = c(Maximum, res[i,3])
Duration = c(Duration, res[i,3])
}
data.frame("names"=name, "Minimum"=Minimum, "Maximum" = Maximum, "Duration" = Duration)
}
})
PhaseTimeRangeText <- reactive({
PhaseTimeRange(dataGroup2()[,input$variablesMin, drop=TRUE],dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2)
})
output$PhaseTimeRangeUI <- renderUI({
res = PhaseTimeRangeText()
tags$div(
tags$p("For a level of confidence at ", res[1]*100, "%"),
tags$p("Time Range = [", res[2], "," ,res[3], "]")
)
})
output$PhasePlotFunction <- renderPlot({
PhasePlot(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2, title = input$titlePlot2, colors=input$color2 )
})
output$downloadGroupPlot <- downloadHandler(
filename = function() { paste("downloadGroupPlot", '.png', sep='') },
content = function(file) {
png(file)
PhasePlot(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2, title = input$titlePlot2, colors=input$color2 )
dev.off()
}
)
output$PhaseDurationPlotFunction <- renderUI({
PhaseDurationPlot(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2, title = "Duration of the phase", colors=input$color2 )
})
output$PhasePlotUI <- renderUI({
if(is.null(dataGroup2()))
{h5(" Nothing to display ")}
else{
plotOutput("PhasePlotFunction")
}
})
output$PhaseDurationPlotUI <- renderUI({
if(is.null(dataGroup2()))
{h5(" Nothing to display ")}
else{
plotOutput("PhaseDurationPlotFunction")
}
})
output$result3 <- renderUI({
if(is.null(dataGroup2()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data selected", DT::dataTableOutput("selectedTable2")), tabPanel("Plot of the characteristics", fluidRow( uiOutput("PhasePlotUI")) ), tabPanel("Time range", uiOutput("PhaseTimeRangeUI")), tabPanel("Marginal Statistics", uiOutput("PhaseStatisticsUI")))
})
#####################################
#### Onglet : Several groups ####
# Initialize reactive values
phases <- reactiveValues()
output$PhasesSelection32 <- renderUI({
themes <- namesGroups()
succession$names <- themes
checkboxGroupInput('multiPhasesSelection32', 'Select the minimum and the maximum of each group:', themes)
})
# Add observer on select-all button
observeEvent(input$selectAll32, {
succession$names <- namesGroups()
updateCheckboxGroupInput(session, 'multiPhasesSelection32', selected = succession$names)
})
# Add observer on clear-all button
observeEvent(input$clearAll32, {
succession$names <- c()
updateCheckboxGroupInput(session, 'multiPhasesSelection32', selected = "none")
})
# data selectionnees
selectData32 <- reactive({
dataGroup2()[, input$multiPhasesSelection32, drop = FALSE]
})
# affichage table de donnees
output$DatasetPhases32 <- DT::renderDataTable({
if(is.null(selectData32())){return()}
DT::datatable(selectData32(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
Position_beginning32 <- reactive({
dim = dim(selectData32())[2]
pos = seq(1, dim, by = 2)
return(pos)
})
MultiPhaseTimeRangeFunction <- reactive({
MultiPhaseTimeRange(selectData32(), position_minimum = Position_beginning32(), level = input$levelMultiPhases)
})
output$MultiPhaseTimeRangeUI <- renderTable({
res = MultiPhaseTimeRangeFunction()
if(is.null(res)) {h5(" Nothing to display ")}
else {
dim = dim(res)
names_MTR = rownames(res)
PTInf = NULL
PTSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MTR[i])
PTInf= c(PTInf, res[i,2])
PTSup = c(PTSup, res[i,3])
}
data.frame("names"=names,"Time Range Inf"=PTInf, "Time Range Sup" = PTSup)
}
})
output$MultiPhasePlotFunction <- renderPlot({
MultiPhasePlot(selectData32(), position_minimum = Position_beginning32(), title = input$titleMultiPhases, level = input$levelMultiPhases)
})
output$MultiPhasePlotUI <- renderUI({
if(is.null(selectData32()))
{h5(" Nothing to display ")}
else
plotOutput("MultiPhasePlotFunction")
})
output$result32 <- renderUI({
if(is.null(dataGroup2()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetPhases32")), tabPanel("Time range", uiOutput("MultiPhaseTimeRangeUI")), tabPanel("Plot of the characteristics", "Marginal posterior densities of the minimum (oldest curve) and the maximum (youngest curve of the same color) of the selected groups and their time range interval (segment above the curves) at the desired level." ,uiOutput("MultiPhasePlotUI")))
})
output$downloadMultiPhasesPlot <- downloadHandler(
filename = function() { paste("downloadGroupsPlot", '.png', sep='') },
content = function(file) {
png(file)
MultiPhasePlot(selectData32(), position_minimum = Position_beginning32(), title = input$titleMultiPhases, level = input$levelMultiPhases)
dev.off()
}
)
##########################################
#### Onglet : Succession de phases ####
# Initialize reactive values
succession <- reactiveValues()
output$PhasesSelection <- renderUI({
themes <- namesGroups()
succession$names <- themes
checkboxGroupInput('multiPhasesSelection', 'Select the minimum and the maximum of each group:', themes)
})
# Add observer on select-all button
observeEvent(input$selectAll4, {
succession$names <- namesGroups()
updateCheckboxGroupInput(session, 'multiPhasesSelection', selected = succession$names)
})
# Add observer on clear-all button
observeEvent(input$clearAll4, {
succession$names <- c()
updateCheckboxGroupInput(session, 'multiPhasesSelection', selected = "none")
})
# data selectionnees
selectData4 <- reactive({
dataGroup2()[, input$multiPhasesSelection, drop = FALSE]
})
# affichage table de donnees
output$DatasetPhases <- DT::renderDataTable({
if(is.null(selectData4())){return()}
DT::datatable(selectData4(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
## Ordering
Position_beginning <- reactive({
ordre <- order(selectData4()[1,])
pos = seq(1,length(ordre), by = 2)
return(ordre[pos])
})
output$AffichagePositions <- renderUI({
tags$div(
tags$p("Positions of the beginnings 1", as.character(Position_beginning()[1]), ""),
tags$p("Positions of the beginnings 2", as.character(Position_beginning()[2])),
tags$p("Positions of the beginnings 3", as.character(Position_beginning()[3]), ""),
tags$p("Positions of the beginnings 4", as.character(Position_beginning()[4]))
)
})
## Succession plot
output$MultiSuccessionFunction <- renderPlot({
MultiSuccessionPlot(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession, title = input$titleSuccessionPlot)
}, height = 600, width = 800 )
output$MultiSuccessionUI <- renderUI({
if( length(Position_beginning() ) < 2)
h5(" Nothing to display ")
else
plotOutput("MultiSuccessionFunction", width="100%")
})
output$downloadSuccessionPlot <- downloadHandler(
filename = function() { paste("downloadSuccessionPlot", '.png', sep='') },
content = function(file) {
png(file)
MultiSuccessionPlot(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession, title = input$titleSuccessionPlot)
dev.off()
}
)
## Succession Transitions
MultiPhasesTransitionFunction <- reactive({
MultiPhasesTransition(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession)
})
output$MultiPhasesTransitionResults <- renderTable({
if( length(Position_beginning() ) < 2){ return()}
else {
res = MultiPhasesTransitionFunction()
dim = dim(res)
names_MTR = rownames(res)
TRInf = NULL
TRSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MTR[i])
TRInf= c(TRInf, res[i,2])
TRSup = c(TRSup, res[i,3])
}
data.frame("names"=names,"Transition range Inf"=TRInf, "Transition range Sup" = TRSup)
}
})
## Succession Gaps
MultiPhasesGapFunction <- reactive({
MultiPhasesGap(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession)
})
output$MultiPhasesGapResults <- renderTable({
if( length(Position_beginning() ) < 2) { return()}
else {
res = MultiPhasesGapFunction()
dim = dim(res)
names_MPG = rownames(res)
GapInf = NULL
GapSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MPG[i])
GapInf= c(GapInf, res[i,2])
GapSup = c(GapSup, res[i,3])
}
data.frame("names"=names,"Gap range Inf"= GapInf, "Gap range Sup" = GapSup)
}
})
## Succession Time range
MultiPhaseTimeRangeFunction4 <- reactive({
MultiPhaseTimeRange(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession)
})
output$MultiPhaseTimeRange4UI <- renderTable({
if( length(Position_beginning() ) < 2){ return()}
else {
res = MultiPhaseTimeRangeFunction4()
dim = dim(res)
names_MTR = rownames(res)
PTInf = NULL
PTSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MTR[i])
PTInf= c(PTInf, res[i,2])
PTSup = c(PTSup, res[i,3])
}
data.frame("names"=names,"Time Range Inf"=PTInf, "Time Range Sup" = PTSup)
}
})
## Output
output$Inputs4 <- renderUI({
if(is.null(dataGroup2()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetPhases")), tabPanel("Time ranges", uiOutput("MultiPhaseTimeRange4UI")), tabPanel("Transition ranges", uiOutput("MultiPhasesTransitionResults")), tabPanel("Gap ranges", uiOutput("MultiPhasesGapResults")), tabPanel("Succession plot", fluidRow("Curves represent the marginal posterior densities of the minimum and maximum of each group. Segments correspond to time range of the group of the same color, two-coloured segments correspond to transition interval or to the gap range. A cross instead of a two-coloured segment means that there is no gap range at the desired level of confidence."),fluidRow(uiOutput("MultiSuccessionUI")) ))
})
##########################################
})
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shinyServer(function(input, output, clientData, session) {
# By default, Shiny limits file uploads to 5MB per file. You can modify this limit by using the shiny.maxRequestSize option.
# For example, adding options(shiny.maxRequestSize=30*1024^2) to the top of server.R would increase the limit to 30MB.
options(shiny.maxRequestSize=30*1024^2)
#######################################
#### Onglet : Import CSV #####
dataInput <- reactive({
file1 <- input$file11
if(is.null(file1)){return()}
if(input$iterationColumn1=="NULL"){
itCol = NULL
}else{
itCol = as.numeric(input$iterationColumn1)
}
if(input$referenceYear1=="NULL"){
refY = NULL
}else{
refY = as.numeric(input$referenceYear1)
}
if(input$rowToWithdraw1=="NULL"){
rowW = NULL
}else{
rowW = as.numeric(input$rowToWithdraw1)
}
ImportCSV(file=file1$datapath, sep=input$sep11, dec=input$dec11, header=TRUE, comment.char="#", iterationColumn = itCol, referenceYear = refY, rowToWithdraw = rowW)
})
output$filedf11 <- renderTable({
if(is.null(dataInput())){return()}
input$file11
})
output$table11 <- DT::renderDataTable({
if(is.null(dataInput())){return()}
DT::datatable(dataInput(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
output$AfficheTableLue11 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("About file", tableOutput("filedf11")), tabPanel("Data", DT::dataTableOutput("table11")))
})
##################################################
#### MCMC des MinMax des groupes ###
namesG <- reactive({
names = colnames(dataInput())
return(names)
})
# Initialize reactive values
valuesG <- reactiveValues()
dataInput12 <- reactive({
file2 <- input$file12
if(is.null(file2)){return()}
if(input$iterationColumn2=="NULL"){
itCol = NULL
}else{
itCol = as.numeric(input$iterationColumn2)
}
if(input$referenceYear2=="NULL"){
refY = NULL
}else{
refY = as.numeric(input$referenceYear2)
}
if(input$rowToWithdraw2=="NULL"){
rowW = NULL
}else{
rowW = as.numeric(input$rowToWithdraw2)
}
ImportCSV(file=file2$datapath, sep=input$sep12, dec=input$dec12, header=TRUE, comment.char="#", iterationColumn = itCol, referenceYear = refY, rowToWithdraw = rowW)
})
output$filedf12 <- renderTable({
if(is.null(dataInput12())){return()}
input$file12
})
output$table12 <- DT::renderDataTable({
if(is.null(dataInput12())){return()}
DT::datatable(dataInput12(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
output$AfficheTableLue12 <- renderUI({
if(is.null(dataInput12()))
h5("No data imported")
else
tabsetPanel(tabPanel("About file", tableOutput("filedf12")), tabPanel("Data", DT::dataTableOutput("table12")))
})
observeEvent(input$StockageFile2, {
valuesG$file2 <- dataInput12()
})
##################################################
#### Creation des groupes de dates ####
#### pour calcul des MinMax ###
output$ChainsSelectionG <- renderUI({
themesG <- namesG()
valuesG$namesG <- themesG
checkboxGroupInput('ChainsSelectionG', 'Select a series of dates:', themesG)
})
# Add observer on select-all button
observeEvent(input$selectAllG, {
valuesG$namesG <- namesG()
updateCheckboxGroupInput(session, 'ChainsSelectionG', selected = valuesG$namesG)
})
# Add observer on clear-all button
observeEvent(input$clearAllG, {
valuesG$namesG <- c()
updateCheckboxGroupInput(session, 'ChainsSelectionG', selected = "none")
})
# data selectionnees
selectDataG <- reactive({
dataInput()[, input$ChainsSelectionG, drop = FALSE]
})
# affichage table de donnees
output$DatasetG <- DT::renderDataTable({
if(is.null(selectDataG())){return( )}
DT::datatable(selectDataG(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
## CreateMinMaxGroup
createGroup1 <- eventReactive(input$goButton, {
position = seq(1, length(input$ChainsSelectionG))
dataGroup = CreateMinMaxGroup(selectDataG(), position=position, name =input$name, add=NULL)
})
observeEvent(input$goButton, {
valuesG$dataGroup <- createGroup1()
})
observeEvent(input$addButton, {
valuesG$dataGroup <- addGroup()
})
addGroup <- eventReactive(input$addButton, {
position = seq(1, length(input$ChainsSelectionG))
addGroup = CreateMinMaxGroup(selectDataG(), position=position, name =input$name, add=valuesG$dataGroup)#, exportFile=export)
return(addGroup)
})
observeEvent(input$clearButton, {
valuesG$dataGroup <- NULL
})
output$tableGroup <- DT::renderDataTable({
if(is.null(valuesG$dataGroup)){return()}
DT::datatable(valuesG$dataGroup, options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
output$result13 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetG")), tabPanel("Groups", DT::dataTableOutput("tableGroup")) )
})
output$downloadData <- downloadHandler(
filename = function() { paste("MinMaxGroup", '.csv', sep='') },
content = function(file) {
write.csv(valuesG$dataGroup, file)
}
)
observeEvent(input$StockageFile22, {
valuesG$file2 <- valuesG$dataGroup
})
#######################################
#### Onglet : Convergence ###
## Checking the Markov chains ##
# Affichage des colonnes du dataframe
namesCV <- reactive({
names = colnames(dataInput())
return(names)
})
# Initialize reactive values
valuesCV <- reactiveValues()
output$ChainsSelectionCV <- renderUI({
themesCV <- namesCV()
valuesCV$namesCV <- themesCV
checkboxGroupInput('ChainsSelectionCV', 'Select a series of dates (at least two):', choices =themesCV, selected = valuesCV$namesCV[1:2])
})
# Add observer on select-all button
observeEvent(input$selectAllCV, {
valuesCV$namesCV <- namesCV()
updateCheckboxGroupInput(session, 'ChainsSelectionCV', selected = valuesCV$namesCV)
})
# Add observer on clear-all button
observeEvent(input$clearAllCV, {
valuesCV$namesCV <- c()
updateCheckboxGroupInput(session, 'ChainsSelectionCV', selected = "none")
})
# data selectionnees
selectDataCV <- reactive({
dataInput()[, input$ChainsSelectionCV, drop = FALSE]
})
mcmc_List <- reactive({
if(is.null(selectDataCV)){return()}
coda.mcmc(selectDataCV(), numberChains = input$NbChains)#, iterationColumn = itC)
})
output$MCMCplot <- renderPlot({
plot(mcmc_List())
})
GelmanDiag <- reactive({
gelman.diag(mcmc_List())
})
output$GelmanDiagTable <- renderTable({
if(is.null(GelmanDiag())) {return()}
else {
res = GelmanDiag()$psrf
dim = dim(res)
namesRes = rownames(res)
PointEst = NULL
UpperCI = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, namesRes[i])
PointEst= c(PointEst, res[i,1])
UpperCI = c(UpperCI, res[i,2])
}
data.frame("names"=names,"Point estimate"=PointEst, "Upper Credible Interval" = UpperCI)
}
})
output$Gelmanplot <- renderPlot({
gelman.plot(mcmc_List())
})
output$Diagnostics <- renderUI({
if(is.null(selectDataCV()))
h5("No data imported")
else
tabsetPanel(tabPanel("History Plots", plotOutput("MCMCplot")), tabPanel("Gelman Plots", plotOutput("Gelmanplot")), tabPanel("Gelman Diagnostic", tableOutput("GelmanDiagTable")) )
})
#######################################
#### Onglet : Dates ####
#### Selection d une chaine ##
names <- reactive({
names = colnames(dataInput())
return(names)
})
observe({
updateSelectInput(session, inputId='variables', 'Select a MCMC chain', choices = names() )
})
selectChain <- reactive({
dataInput()[[ input$variables ]]
})
output$MarginalPlot <- renderPlot({
MarginalPlot(selectChain(), level = input$level, title = input$titlePlot, newWindow=FALSE)
})
MarginalStatisticsText <- reactive({
MarginalStatistics(selectChain(), level = input$level)
})
output$MarginalStatisticsUI <- renderUI({
tags$div(
tags$p("Mean = ", MarginalStatisticsText()[1,1]),
tags$p("MAP = ", MarginalStatisticsText()[2,1]),
tags$p("sd = ", MarginalStatisticsText()[3,1]),
tags$p("Q1 = ", MarginalStatisticsText()[4,1]),
tags$p("Median = ", MarginalStatisticsText()[5,1]),
tags$p("Q2 = ", MarginalStatisticsText()[6,1]),
tags$p("For a level of confidence at ", MarginalStatisticsText()[7,1]*100, "%"),
tags$p("Credible Interval = [", MarginalStatisticsText()[8,1], "," , MarginalStatisticsText()[9,1], "]"),
tags$p("HPD region = [", MarginalStatisticsText()[10,1], "," , MarginalStatisticsText()[11,1], "]")
)
})
output$result2 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Marginal plot", plotOutput("MarginalPlot")), tabPanel("Marginal statistics", uiOutput("MarginalStatisticsUI")))
})
output$downloadPlotDates <- downloadHandler(
filename = function() { paste("MarginalPlot", '.png', sep='') },
content = function(file) {
png(file)
MarginalPlot(selectChain(), level = input$level, title = input$titlePlot, colors=input$color )
dev.off()
}
)
##### Onglet : Dates - Selection plusieurs chaines ####
# Initialize reactive values
values <- reactiveValues()
output$ChainsSelection <- renderUI({
themes <- names()
values$names <- themes
checkboxGroupInput('multiChainsCI', 'Select numbers:', themes)
})
# Add observer on select-all button
observeEvent(input$selectAll, {
values$names <- names()
updateCheckboxGroupInput(session, 'multiChainsCI', selected = values$names)
})
# Add observer on clear-all button
observeEvent(input$clearAll, {
values$names <- c()
updateCheckboxGroupInput(session, 'multiChainsCI', selected = "none")
})
# data selectionnees
selectData <- reactive({
dataInput()[, input$multiChainsCI, drop = FALSE]
})
# affichage table de donnees
output$DatasetCI <- DT::renderDataTable({
if(is.null(selectData())){return( )}
DT::datatable(selectData(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
# calcul des IC
MultiCredibleIntervalText <- reactive({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
MultiCredibleInterval(selectData(), position, level = input$level22)
})
# affichage des resultats des IC
output$resultTableMCI <- renderTable({
if(is.null(MultiCredibleIntervalText())) {return()}
else {
dim = dim(MultiCredibleIntervalText())
names_CI = rownames(MultiCredibleIntervalText())
CIInf = NULL
CISup = NULL
name = NULL
for (i in 1:dim[1]){
name = c(name, names_CI[i])
CIInf= c(CIInf, MultiCredibleIntervalText()[i,2])
CISup = c(CISup, MultiCredibleIntervalText()[i,3])
}
data.frame("names"=name, "Credible Interval Inf"=CIInf, "Credible Interval Sup" = CISup)
}
})
### calcul des HPD
MultiHPDText <- reactive({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
MultiHPD(selectData(), position, level = input$level22)
})
# affichage des resultats des IC
output$resultTableMHPD <- renderTable({
if(is.null(MultiHPDText())) {return()}
else {
dim = dim(MultiHPDText())
names_HPD = rownames(MultiHPDText())
HPDInf = NULL
HPDSup = NULL
name = NULL
for (i in 1:dim[1]){
name = c(name, names_HPD[i])
HPDInf= c(HPDInf, MultiHPDText()[i,2])
HPDSup = c(HPDSup, MultiHPDText()[i,3])
}
data.frame("names"=name, "HPD Inf"=HPDInf, "HPD Sup" = HPDSup)
}
})
output$MultiDatesPlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
#if(input$exportFile22IT == "TRUE") { outFile = "IntervalsPlot"} else{ outFile = NULL}
MultiDatesPlot(selectData(), position, intervals =input$intervals, order = input$order, level = input$level, title = input$titleIntervalsplot, newWindow=FALSE, print.data.result = FALSE)
})#, height = 600, width = 800)
output$downloadIntervalPlot <- downloadHandler(
filename = function() { paste("downloadIntervalPlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
MultiDatesPlot(selectData(), position, intervals =input$intervals, level = input$level, title = input$titleIntervalsplot, print.data.result = FALSE)
dev.off()
}
)
output$ui<- renderUI({
switch(input$count,
"TRUE" = textInput(inputId='ylabel', label="y-label", "Cumulative events" ),
"FALSE" = textInput(inputId='ylabel', label="y-label", "Probability" )
)
})
output$TempoPlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
#if(input$exportFile22 == "TRUE") { outFile = "TempoPlot.png"} else{ outFile = NULL}
TempoPlot(selectData(), position, level = input$level, title = input$titleTempoplot, Gauss=input$GaussCI, count=input$count, x.label=input$xlabel, y.label=input$ylabel, colors = input$colors, newWindow=FALSE, print.data.result = FALSE)
})#, height = 600, width = 800)
output$TempoPlotUI <- renderUI({
if(is.null( input$multiChainsCI )) {h5(" Nothing to display ")}
else{
plotOutput("TempoPlot", width="80%")
}
})
output$downloadTempoPlot <- downloadHandler(
filename = function() { paste("downloadTempoPlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
TempoPlot(selectData(), position, level = input$level, title = input$titleTempoplot, Gauss=input$GaussCI, count=input$count, x.label=input$xlabel, y.label=input$ylabel, colors = input$colors, print.data.result = FALSE)#, out.file=outFile)
dev.off()
}
)
output$TempoActivityPlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
TempoActivityPlot(selectData(), position, level = input$level, count=input$count, newWindow=FALSE, print.data.result = FALSE)
})#, height = 600, width = 800)
output$TempoActivityPlotUI <- renderUI({
if(is.null( input$multiChainsCI )) {h5(" Nothing to display ")}
else{
plotOutput("TempoActivityPlot", width="80%")
}
})
output$downloadActivityPlot <- downloadHandler(
filename = function() { paste("downloadActivityPlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
TempoActivityPlot(selectData(), position, level = input$level, count=input$count, print.data.result = FALSE)
dev.off()
}
)
output$OccurrencePlot <- renderPlot({
if(is.null( input$multiChainsCI )) { return()}
position = seq(1, length(input$multiChainsCI))
OccurrencePlot(selectData(), position, level = input$level, count=input$count, newWindow=FALSE, print.data.result = FALSE)
})
output$OccurrencePlotUI <- renderUI({
if(is.null( input$multiChainsCI )) {h5(" Nothing to display ")}
else{
plotOutput("OccurrencePlot", width="80%")
}
})
output$downloadOccurrencePlot <- downloadHandler(
filename = function() { paste("downloadOccurrencePlot", '.png', sep='') },
content = function(file) {
position = seq(1, length(input$multiChainsCI))
png(file)
OccurrencePlot(selectData(), position, level = input$level, count=input$count, print.data.result = FALSE)
dev.off()
}
)
output$result22 <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetCI")),
tabPanel("Credible intervals", uiOutput("resultTableMCI")),
tabPanel("HPD regions", uiOutput("resultTableMHPD")),
tabPanel("Intervals Plot", plotOutput("MultiDatesPlot")),
tabPanel("Tempo Plot", plotOutput("TempoPlot"), br(), plotOutput("TempoActivityPlot")),
tabPanel("Occurrence Plot", plotOutput("OccurrencePlot"))
)
})
#######################################
#### Onglet : Tests ###
## Selection plusieurs chaines ##
# Initialize reactive values
# valuesTests <- reactiveValues()
namesTests <- reactive({
names = colnames(dataInput())
return(names)
})
observe({
updateSelectInput(session, inputId='variableTest1a', 'Select date a', choices = namesTests())
updateSelectInput(session, inputId='variableTest1b', 'Select date b', choices = namesTests())
})
selectChainTests <- reactive({
dataInput()[,c(input$variableTest1a, input$variableTest1b), drop = FALSE]
})
output$DataSelectedTests <- DT::renderDataTable({
if(is.null(selectChainTests())) { return( h5("")) }
else
DT::datatable(selectChainTests(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
MarginalProbaText <- renderText({
MarginalProba(dataInput()[,input$variableTest1a, drop=TRUE], dataInput()[,input$variableTest1b, drop=TRUE])
})
output$MarginalProbaUI <- renderUI({
tags$div(
tags$p("The posterior probability that 'date a' is earlier than 'date b' is "),
tags$p(MarginalProbaText())
)
})
DatesHiatusText <- reactive({
DatesHiatus(dataInput()[,input$variableTest1a, drop=TRUE], dataInput()[,input$variableTest1b, drop=TRUE], level = input$levelTests)
})
output$DatesHiatusUI <- renderUI({
tags$div(
tags$p("The testing procedure to check the presence of a gap between 'date a' and 'date b'"),
tags$p("It returns the endpoints of the longest hiatus between two parameters. The result is given in calendar year (in format BC/AD)."),
br(),
tags$p("If 'NA', there is no hiatus at this level of confidence between 'date a' and 'date b'."),
br(),
tags$p("The inferior endpoint of the interval is ",DatesHiatusText()[2]),
tags$p("The superior endpoint of the interval is ",DatesHiatusText()[3])
)
})
output$resultTests <- renderUI({
if(is.null(dataInput()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data selected", DT::dataTableOutput("DataSelectedTests")), tabPanel("Anteriority / Posteriority test", uiOutput("MarginalProbaUI")), tabPanel("Hiatus between dates", uiOutput("DatesHiatusUI")))
})
##############################################
#### Onglet : Group of dates ####
#### Selection d un group ###
dataGroup2 <- reactive({
as.data.frame(valuesG$file2)
})
namesGroups <- reactive({
names12 = colnames(dataGroup2())
return(names12)
})
observe({
updateSelectInput(session, inputId='variablesMin', 'Select the minimum of the group', choices = namesGroups())
updateSelectInput(session, inputId='variablesMax', 'Select the maximum of the group', choices = namesGroups())
})
selectChain2 <- reactive({
dataGroup2()[,c(input$variablesMin, input$variablesMax), drop = FALSE]
})
TestPhaseSelected <- reactive({
if( sum(ifelse(dataGroup2()[,1] < dataGroup2()[,2], 1, 0)) == length(dataGroup2()[,1])) {return(1)}
})
output$selectedTable2 <- DT::renderDataTable({
if(is.null(selectChain2())) { return( h5("")) }
else
DT::datatable(selectChain2(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
PhaseStatisticsText <- reactive({
PhaseStatistics(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2)
})
output$PhaseStatisticsUI <- renderTable({
res = PhaseStatisticsText()
if(is.null(res)) {return()}
else {
dim = dim(res)
names_PS = rownames(res)
Minimum = NULL
Maximum = NULL
Duration = NULL
name = NULL
for (i in 1:dim[1]){
name = c(name, names_PS[i])
Minimum= c(Minimum, res[i,2])
Maximum = c(Maximum, res[i,3])
Duration = c(Duration, res[i,3])
}
data.frame("names"=name, "Minimum"=Minimum, "Maximum" = Maximum, "Duration" = Duration)
}
})
PhaseTimeRangeText <- reactive({
PhaseTimeRange(dataGroup2()[,input$variablesMin, drop=TRUE],dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2)
})
output$PhaseTimeRangeUI <- renderUI({
res = PhaseTimeRangeText()
tags$div(
tags$p("For a level of confidence at ", res[1]*100, "%"),
tags$p("Time Range = [", res[2], "," ,res[3], "]")
)
})
output$PhasePlotFunction <- renderPlot({
PhasePlot(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2, title = input$titlePlot2, colors=input$color2 )
})
output$downloadGroupPlot <- downloadHandler(
filename = function() { paste("downloadGroupPlot", '.png', sep='') },
content = function(file) {
png(file)
PhasePlot(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2, title = input$titlePlot2, colors=input$color2 )
dev.off()
}
)
output$PhaseDurationPlotFunction <- renderUI({
PhaseDurationPlot(dataGroup2()[,input$variablesMin, drop=TRUE], dataGroup2()[,input$variablesMax, drop=TRUE], level = input$level2, title = "Duration of the phase", colors=input$color2 )
})
output$PhasePlotUI <- renderUI({
if(is.null(dataGroup2()))
{h5(" Nothing to display ")}
else{
plotOutput("PhasePlotFunction")
}
})
output$PhaseDurationPlotUI <- renderUI({
if(is.null(dataGroup2()))
{h5(" Nothing to display ")}
else{
plotOutput("PhaseDurationPlotFunction")
}
})
output$result3 <- renderUI({
if(is.null(dataGroup2()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data selected", DT::dataTableOutput("selectedTable2")), tabPanel("Plot of the characteristics", fluidRow( uiOutput("PhasePlotUI")) ), tabPanel("Time range", uiOutput("PhaseTimeRangeUI")), tabPanel("Marginal Statistics", uiOutput("PhaseStatisticsUI")))
})
#####################################
#### Onglet : Several groups ####
# Initialize reactive values
phases <- reactiveValues()
output$PhasesSelection32 <- renderUI({
themes <- namesGroups()
succession$names <- themes
checkboxGroupInput('multiPhasesSelection32', 'Select the minimum and the maximum of each group:', themes)
})
# Add observer on select-all button
observeEvent(input$selectAll32, {
succession$names <- namesGroups()
updateCheckboxGroupInput(session, 'multiPhasesSelection32', selected = succession$names)
})
# Add observer on clear-all button
observeEvent(input$clearAll32, {
succession$names <- c()
updateCheckboxGroupInput(session, 'multiPhasesSelection32', selected = "none")
})
# data selectionnees
selectData32 <- reactive({
dataGroup2()[, input$multiPhasesSelection32, drop = FALSE]
})
# affichage table de donnees
output$DatasetPhases32 <- DT::renderDataTable({
if(is.null(selectData32())){return()}
DT::datatable(selectData32(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
Position_beginning32 <- reactive({
dim = dim(selectData32())[2]
pos = seq(1, dim, by = 2)
return(pos)
})
MultiPhaseTimeRangeFunction <- reactive({
MultiPhaseTimeRange(selectData32(), position_minimum = Position_beginning32(), level = input$levelMultiPhases)
})
output$MultiPhaseTimeRangeUI <- renderTable({
res = MultiPhaseTimeRangeFunction()
if(is.null(res)) {h5(" Nothing to display ")}
else {
dim = dim(res)
names_MTR = rownames(res)
PTInf = NULL
PTSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MTR[i])
PTInf= c(PTInf, res[i,2])
PTSup = c(PTSup, res[i,3])
}
data.frame("names"=names,"Time Range Inf"=PTInf, "Time Range Sup" = PTSup)
}
})
output$MultiPhasePlotFunction <- renderPlot({
MultiPhasePlot(selectData32(), position_minimum = Position_beginning32(), title = input$titleMultiPhases, level = input$levelMultiPhases)
})
output$MultiPhasePlotUI <- renderUI({
if(is.null(selectData32()))
{h5(" Nothing to display ")}
else
plotOutput("MultiPhasePlotFunction")
})
output$result32 <- renderUI({
if(is.null(dataGroup2()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetPhases32")), tabPanel("Time range", uiOutput("MultiPhaseTimeRangeUI")), tabPanel("Plot of the characteristics", "Marginal posterior densities of the minimum (oldest curve) and the maximum (youngest curve of the same color) of the selected groups and their time range interval (segment above the curves) at the desired level." ,uiOutput("MultiPhasePlotUI")))
})
output$downloadMultiPhasesPlot <- downloadHandler(
filename = function() { paste("downloadGroupsPlot", '.png', sep='') },
content = function(file) {
png(file)
MultiPhasePlot(selectData32(), position_minimum = Position_beginning32(), title = input$titleMultiPhases, level = input$levelMultiPhases)
dev.off()
}
)
##########################################
#### Onglet : Succession de phases ####
# Initialize reactive values
succession <- reactiveValues()
output$PhasesSelection <- renderUI({
themes <- namesGroups()
succession$names <- themes
checkboxGroupInput('multiPhasesSelection', 'Select the minimum and the maximum of each group:', themes)
})
# Add observer on select-all button
observeEvent(input$selectAll4, {
succession$names <- namesGroups()
updateCheckboxGroupInput(session, 'multiPhasesSelection', selected = succession$names)
})
# Add observer on clear-all button
observeEvent(input$clearAll4, {
succession$names <- c()
updateCheckboxGroupInput(session, 'multiPhasesSelection', selected = "none")
})
# data selectionnees
selectData4 <- reactive({
dataGroup2()[, input$multiPhasesSelection, drop = FALSE]
})
# affichage table de donnees
output$DatasetPhases <- DT::renderDataTable({
if(is.null(selectData4())){return()}
DT::datatable(selectData4(), options = list(pageLength = 5, dom = 'tip'), rownames=FALSE)
})
## Ordering
Position_beginning <- reactive({
ordre <- order(selectData4()[1,])
pos = seq(1,length(ordre), by = 2)
return(ordre[pos])
})
output$AffichagePositions <- renderUI({
tags$div(
tags$p("Positions of the beginnings 1", as.character(Position_beginning()[1]), ""),
tags$p("Positions of the beginnings 2", as.character(Position_beginning()[2])),
tags$p("Positions of the beginnings 3", as.character(Position_beginning()[3]), ""),
tags$p("Positions of the beginnings 4", as.character(Position_beginning()[4]))
)
})
## Succession plot
output$MultiSuccessionFunction <- renderPlot({
MultiSuccessionPlot(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession, title = input$titleSuccessionPlot)
}, height = 600, width = 800 )
output$MultiSuccessionUI <- renderUI({
if( length(Position_beginning() ) < 2)
h5(" Nothing to display ")
else
plotOutput("MultiSuccessionFunction", width="100%")
})
output$downloadSuccessionPlot <- downloadHandler(
filename = function() { paste("downloadSuccessionPlot", '.png', sep='') },
content = function(file) {
png(file)
MultiSuccessionPlot(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession, title = input$titleSuccessionPlot)
dev.off()
}
)
## Succession Transitions
MultiPhasesTransitionFunction <- reactive({
MultiPhasesTransition(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession)
})
output$MultiPhasesTransitionResults <- renderTable({
if( length(Position_beginning() ) < 2){ return()}
else {
res = MultiPhasesTransitionFunction()
dim = dim(res)
names_MTR = rownames(res)
TRInf = NULL
TRSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MTR[i])
TRInf= c(TRInf, res[i,2])
TRSup = c(TRSup, res[i,3])
}
data.frame("names"=names,"Transition range Inf"=TRInf, "Transition range Sup" = TRSup)
}
})
## Succession Gaps
MultiPhasesGapFunction <- reactive({
MultiPhasesGap(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession)
})
output$MultiPhasesGapResults <- renderTable({
if( length(Position_beginning() ) < 2) { return()}
else {
res = MultiPhasesGapFunction()
dim = dim(res)
names_MPG = rownames(res)
GapInf = NULL
GapSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MPG[i])
GapInf= c(GapInf, res[i,2])
GapSup = c(GapSup, res[i,3])
}
data.frame("names"=names,"Gap range Inf"= GapInf, "Gap range Sup" = GapSup)
}
})
## Succession Time range
MultiPhaseTimeRangeFunction4 <- reactive({
MultiPhaseTimeRange(selectData4(), position_minimum = Position_beginning(), level = input$levelSuccession)
})
output$MultiPhaseTimeRange4UI <- renderTable({
if( length(Position_beginning() ) < 2){ return()}
else {
res = MultiPhaseTimeRangeFunction4()
dim = dim(res)
names_MTR = rownames(res)
PTInf = NULL
PTSup = NULL
names = NULL
for (i in 1:dim[1]){
names = c(names, names_MTR[i])
PTInf= c(PTInf, res[i,2])
PTSup = c(PTSup, res[i,3])
}
data.frame("names"=names,"Time Range Inf"=PTInf, "Time Range Sup" = PTSup)
}
})
## Output
output$Inputs4 <- renderUI({
if(is.null(dataGroup2()))
h5("No data imported")
else
tabsetPanel(tabPanel("Data", DT::dataTableOutput("DatasetPhases")), tabPanel("Time ranges", uiOutput("MultiPhaseTimeRange4UI")), tabPanel("Transition ranges", uiOutput("MultiPhasesTransitionResults")), tabPanel("Gap ranges", uiOutput("MultiPhasesGapResults")), tabPanel("Succession plot", fluidRow("Curves represent the marginal posterior densities of the minimum and maximum of each group. Segments correspond to time range of the group of the same color, two-coloured segments correspond to transition interval or to the gap range. A cross instead of a two-coloured segment means that there is no gap range at the desired level of confidence."),fluidRow(uiOutput("MultiSuccessionUI")) ))
})
##########################################
})
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