R/app.r
In danielpereztr/DCEtool: Efficient and Accessible Discrete Choice Experiments
Defines functions
DCEtool
Documented in
DCEtool
#' @export
DCEtool <- function(){
requireNamespace('shiny')
requireNamespace('rlist')
requireNamespace('shinythemes')
requireNamespace('shinyWidgets')
requireNamespace('mvtnorm')
requireNamespace('DT')
requireNamespace('shinycssloaders')
requireNamespace('writexl')
requireNamespace('readxl')
requireNamespace('rlist')
requireNamespace('idefix')
requireNamespace('shinyBS')
requireNamespace('survival')
requireNamespace('tidyr')
requireNamespace('mlogit')
requireNamespace('ggplot2')
requireNamespace('bslib')
requireNamespace('dfidx')
#' @importFrom shinyBS bsModal
#' @importFrom graphics barplot
#' @importFron usethis use_pipe
#' @importFrom magrittr %>%
#' @importFrom survival strata
#' @importFrom survival coxph
#' @importFrom survival clogit
#' @importFrom ggplot2 aes
#' @importFrom ggplot2 geom_bar
#' @importFrom ggplot2 geom_errorbar
#' @importFrom ggplot2 scale_x_discrete
#' @importFrom ggplot2 xlab
#' @importFrom ggplot2 ylab
#' @importFrom shiny actionButton
#' @importFrom shiny checkboxGroupInput
#' @importFrom shiny shinyApp
#' @importFrom rlist list.match
#external variables
savechoices <- c()
resultados <- c()
num <- c()
y <- c()
se <- c()
ui <- shiny::navbarPage(
"DCEtool", id = 'inTabset',
shiny::tabPanel("Home", value = "start",
shiny::fluidRow(
shiny::column(12,
align = "center",
htmltools::img(src = "assets/granada.png", width = "50%"), # prefix + filename
htmltools::p("Welcome to DCEtool. ",style="text-align:justify;color:black;background-color:LightGrey;padding:15px;border-radius:10px"),
shiny::HTML("<p>Find more <a href = 'https://danielpereztr.github.io/DCEtool/'>here</a>.</p>"),
shiny::HTML("<p>Please cite as Pérez-Troncoso (2022). Efficient and Accessible Discrete Choice Experiments: DCEtool (Version 1.0.0). danielpereztr.github.io/DCEtool</p>")
)
)
), #Home tab
shiny::tabPanel("Design settings", value = "params", #Design settings tab
shiny::sidebarLayout(
shiny::sidebarPanel( #Inputs sidebar panel
shiny::numericInput('ats', "Number of attributes", 0),
shiny::uiOutput('dynamic'),
shiny::actionButton('loadats','Save attributes'),
htmltools::hr(),
shiny::uiOutput('altbut'),
shiny::uiOutput('csetbut'),
shiny::uiOutput('optcheck'),
shiny::uiOutput('bayescheck'),
shiny::uiOutput('savebut'),
htmltools::hr(),
shiny::uiOutput('priorsbut'),
shiny::uiOutput('seedbut'),
shiny::uiOutput('saveopt')
),
shiny::mainPanel(
shiny::verbatimTextOutput('levelsnumber'),
shiny::verbatimTextOutput('errorscheck'),
shiny::uiOutput('gobut')
)
)
),
shiny::tabPanel(title = "Design matrix", value = "desmattab", #Design matrix tab
shiny::sidebarLayout(
shiny::sidebarPanel( # Design matrix left tab
shiny::actionButton("gendesign", "Generate design"),
htmltools::br(),
htmltools::br(),
shiny::downloadButton("downloaddesing","Save design", icon = shiny::icon("download")), #save design
shiny::fileInput(inputId = "loaddesign",label = "", multiple = FALSE), #load design
shiny::actionButton("showdesdetails", "Show design details", icon = shiny::icon("eye")),
htmltools::br(),
htmltools::br(),
shiny::actionButton("writeatnames", "Name the attributes", icon = shiny::icon("braille")),
htmltools::br(),
htmltools::br(),
shiny::uiOutput("atnames"),
htmltools::br(),
shiny::uiOutput('levdropdown'),
shiny::uiOutput('levtext')
),
shiny::mainPanel( # Design matrix main panel
shiny::uiOutput("spinner"),
shiny::verbatimTextOutput("desdetails"),
shiny::verbatimTextOutput("printlevnames"),
shiny::uiOutput('modmatrix')
)
)
),
shiny::tabPanel(title = "Create a survey", value = "createsurv", # Crear la encuesta
shiny::sidebarLayout(
shiny::sidebarPanel( # Sidebar Panel for survey creator
htmltools::p("Intro and end text: "),
shiny::textAreaInput("intro", "Introductory text in Markdown", rows = 3),
shiny::textAreaInput("outro", "End text in Markdown", rows = 3),
htmltools::hr(),
htmltools::p("Label each alternative: "),
shiny::uiOutput("labels"),
htmltools::hr()
),
shiny::mainPanel(
htmltools::p("Survey preview"),
htmltools::hr(),
shiny::uiOutput("dispintrotext"),
htmltools::br(),
htmltools::hr(),
shiny::uiOutput('cstext'),
shiny::tableOutput("designcoded"),
shiny::uiOutput('radiodummy', width = '100%'),
htmltools::br(),
htmltools::hr(),
shiny::uiOutput("dispoutrotext"),
)
)
),
shiny::tabPanel(title = "Survey",
shiny::fluidRow(
shiny::column(12,
align = "center",
shiny::uiOutput("serialui")
)
),
shiny::fluidRow(
shiny::column(12,
align = "center",
shiny::actionButton(inputId = "popbut", "Launch survey"),
htmltools::br(),
htmltools::br(),
shiny::uiOutput("resultsbut")
)
),
shinyBS::bsModal("modalExample", "", "popbut", size = "large",
shiny::fluidRow(
shiny::column(12,
align = "left",
shiny::uiOutput("texts"),
),
shiny::column(12,
align = "center",
shiny::tableOutput("css"),
shiny::uiOutput("cssbut")
),
shiny::column(12,
align = "right",
shiny::uiOutput('contsurv1')
)
)
)
),
shiny::tabPanel(title = "Results", value = "results",
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::tabsetPanel(id = "restabs",
shiny::tabPanel("Data",
htmltools::br(),
shiny::downloadButton("downloadresults","Save results", icon = shiny::icon("download")),
shiny::fileInput(inputId = "loadresults",label = "", multiple = FALSE), #load results
shiny::selectInput(
inputId = "pricevarcoding",
label = "Price variable coding",
choices = c("Dummy coding" = "dumcod",
#"There is already a continuous price variable" = "already",
"Code price as continuous variable" = "cont")
),
shiny::uiOutput("atpriceselect"),
shiny::uiOutput("savethem"),
shiny::uiOutput("pricelevbr")
),
shiny::tabPanel("Estimation",
htmltools::br(),
shiny::selectInput("modelname", "Choose estimate",
choices = c("Select a model" == "nullselect",
"Conditional logit" = "clogit",
"Mixed logit" = "mixlogit",
"Willingness to pay" = "wtp",
"Figures" = "figures")
),
shiny::uiOutput("modopt"),
htmltools::hr(),
shiny::uiOutput("modopt2")
)
)
),
shiny::mainPanel(
DT::DTOutput("restable"),
shiny::verbatimTextOutput("clog"),
shiny::plotOutput("figure")
)
)
),
shiny::tabPanel(title = "About",
shiny::fluidRow(
shiny::column(12,
align = "Left",
htmltools::h3("About"),
shiny::HTML("<p>This app was created by Daniel Pérez-Troncoso in 2021. Version 1.0.0 was released in April 2022.</p>"),
shiny::HTML("<p>Please, if you use this app in your research, reference it as 'Pérez-Troncoso, D. (2022). DCEtool (1.0.0) [Software]. https://cran.r-project.org/package=DCEtool ' </p>"),
shiny::HTML("<p>Find a guide in <a href = 'https://danielpereztr.github.io/posts/DCEtool/'>this link</a></p>"),
htmltools::h3("Downloads"),
shiny::plotOutput("downloads")
)
)
)
)
server <- function(input, output, session){
# Check if there is a newer version in CRAN
shiny::observeEvent(input$inTabset == "start", {
db <- utils::available.packages(filters = "duplicates")
cranvers <- db[db[,1] == "DCEtool"][2]
thisvers <- utils::packageVersion("DCEtool")
if (cranvers == thisvers){
} else if (cranvers != thisvers) {
shiny::showNotification("There is a newer version of DCEtool on CRAN. Run install.packages('DCEtool') to update DCEtool.")
}
})
#Close shiny
session$onSessionEnded(function() {
shiny::stopApp()
})
#change tab
shiny::observeEvent(input$create_DCE, {
shiny::updateTabsetPanel(session, 'inTabset', selected = "params")
})
# Values across functions
values <- shiny::reactiveValues()
# Download flag for later
values$downloadflag <- 0
# Choices storage for the survey
values$choices <- as.data.frame(matrix(ncol = 2, nrow = 0))
# Designstorage
values$designstor <- data.frame()
# Create as many inputs as attributes are
output$dynamic <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in seq_len(input$ats)) {
tags[[i]] <- shiny::numericInput(paste0('at', i),
paste0('Levels in attribute ', i),
0)
}
tags
})
# Create the vector 'levels' with the attributes' levels
shiny::observeEvent(input$loadats, {
nats <- input$ats
levels <- c()
for (i in seq_len(nats)){
levels <- append(levels, eval(parse(text = paste0("input$at",i))))
}
values$levels <- levels
values$nats <- nats
# Print the number of attributes and levels
output$levelsnumber <- shiny::renderPrint({
cat("Design settings \nNumber of attributes: ", values$nats, "\nLevels per attribute: ", values$levels)
})
#Ask the alternatives and csets after sending attributes
output$altbut <- shiny::renderUI({
shiny::numericInput("nalt", "Alternatives per choice set", value = 2, max = 5, min = 2)
})
#Ask the number of choice sets
output$csetbut <- shiny::renderUI({
shiny::numericInput("nset", "Number of choice sets", value = 12, min = 4)
})
#Checkbox if opt-out alternative
output$optcheck <- shiny::renderUI({
shinyWidgets::materialSwitch(inputId = "optout", label = "Opt-out alternative", value = FALSE, status = "danger")
})
# Checkboxes to select the optimization procedure
output$bayescheck <- shiny::renderUI({
shinyWidgets::materialSwitch(inputId = "bayesian", label = "Bayesian design", status = "danger", value = FALSE)
})
#Print the button to save the settings
output$savebut <- shiny::renderUI({
shiny::actionButton("saveset", "Save settings")
})
})
# Save and print settings
shiny::observeEvent(input$saveset,{
values$alts <- input$nalt
values$sets <- input$nset
values$optout <- input$optout
values$bayesian <- input$bayesian
output$levelsnumber <- shiny::renderPrint({
cat("Design settings \nNumber of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian)
})
# Show button for priors
output$priorsbut <- shiny::renderUI({
optout <- values$optout
levels <- values$levels
nats <- values$nats
null <- ifelse(optout == TRUE, 1, 0)
npar <- sum(levels)-nats+null
priors <- c()
for (x in seq_len(npar)){
priors <- append(priors, 0)
}
values$npar <- npar
shiny::textInput("priorsinput", "Prior coefficients", value = paste(shQuote(priors, type="cmd2"), collapse=", "))
})
# show button for random seed
output$seedbut <- shiny::renderUI({
shiny::numericInput("randomseed", "Random seed", value = 9999)
})
# save options button
output$saveopt <- shiny::renderUI({
shiny::actionButton("finalsave", "Save options")
})
})
# Print the final saved options
shiny::observeEvent(input$finalsave,{
values$priors <- as.numeric(strsplit(as.character(input$priorsinput), ",")[[1]])
values$seed <- input$randomseed
output$levelsnumber <- shiny::renderPrint({
cat("Design settings \nNumber of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian, "\nPriors: ", values$priors, "\nSeed: ", values$seed)
})
#Check errors
output$errorscheck <- shiny::renderPrint({
cat("Error checker results: \n")
if (length(values$levels) != values$nats){
cat("Some error occurred. Please restart DCEtool.\n")
} else if (values$sets < (sum(values$levels)-1)){
cat("The number of sets is not enough. Try with ", sum(values$levels)-1, " sets or more.\n")
} else if (length(values$priors) != values$npar){
cat("The number of priors does not correspond with the number of parameters. Try using ", values$npar, " prior parameters.")
} else {
cat("No errors found.")
}
})
# Button to create the design matrix
output$gobut <- shiny::renderUI({
shiny::actionButton("go", "Happy with the settings? Go to next step")
})
})
# Move to the next tab
shiny::observeEvent(input$go,{
#Move to the Design matrix tab
shiny::updateTabsetPanel(session, 'inTabset', selected = "desmattab")
})
shiny::observeEvent(input$gendesign,{
# Loader
output$spinner <- shiny::renderUI({
shinycssloaders::withSpinner(DT::dataTableOutput("design"))
})
# Render the design table
output$design <- DT::renderDT({
# Decide if bayesian
if (values$bayesian == TRUE){
alg = "cea"
} else {
alg = "fedorov"
}
values$alg <- alg
# Priors
if (values$bayesian == TRUE){
values$bpriors <- mvtnorm::rmvnorm(100, values$priors, diag(length(values$priors)))
} else {
values$bpriors <- values$priors
}
# Generate
design <- dce_toolbox(attributes = values$levels, csets = values$sets,
alts = values$alts, nochoice = values$optout,
priors = values$bpriors, alg = alg)
values$design <- design$design
values$`D-error` <- design$`D-error`
values$details <- design$details
as.data.frame(design$design)
})
})
# Download button
output$downloaddesing <- shiny::downloadHandler(
filename = function() {"design.xlsx"},
content = function(file) {values$downloadflag <- values$downloadflag+1
writexl::write_xlsx(values$deslist, file)}
)
# Load saved design
shiny::observeEvent(input$loaddesign, {
#Spinner loader
output$spinner <- shiny::renderUI({
shinycssloaders::withSpinner(DT::dataTableOutput("design"))
})
# Design loader
output$design <- DT::renderDT({
if (!is.null(input$loaddesign)){
values$`D-error` <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "Derror"))) #Update
values$details <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "details"))) #Update
values$nats <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "nats"))) #Update
values$levels <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "levels"))) #Update
values$sets <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "sets"))) #Update
values$optout <- as.logical(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "optout"))) #Update
values$priors <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "priors"))) #Update
values$alts <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "alts"))) #Update
values$bayesian <- as.logical(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "bayesian")))
values$atnames <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "atnames")))
values$levnames <- as.list(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "levnames")))
values$design <- readxl::read_excel(input$loaddesign$datapath) # Print this one
}
})
})
#Show design details
shiny::observeEvent(input$showdesdetails, {
output$desdetails <- shiny::renderPrint(
cat("Number of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian, "\nPriors: ", values$priors, "\nAttribute names: ", values$atnames,
"\nLevel names: ", unlist(values$levnames), "\nDetails:", values$details)
)
})
# Create inputs for attribute names
shiny::observeEvent(input$writeatnames, {
output$atnames <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in seq_len(values$nats)) {
tags[[i]] <- shiny::textInput(paste0('atn', i),
paste0('Name of attribute ', i),
value = paste0("atrib",i))
}
tags[[i+1]] <- shiny::actionButton("saveatnames", "Save names")
tags
})
})
# Save the attribute names
shiny::observeEvent(input$saveatnames, {
atnames <- c()
for (i in seq_len(values$nats)){
atnames <- append(atnames, eval(parse(text = paste0("input$atn",i))))
}
values$atnames <- atnames
output$desdetails <- shiny::renderPrint(
cat("Number of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian, "\nPriors: ", values$priors, "\nAttribute names: ", values$atnames,
"\nLevel names: ", unlist(values$levnames), "\nDetails:", values$details)
)
# Create buttons with the attribute names
shiny::observeEvent(input$saveatnames, {
output$levdropdown <- shiny::renderUI({
shiny::selectInput("levdrop", "Change level names", as.list(atnames))
})
values$levnames <- list()
})
# Level names
shiny::observeEvent(input$levdrop,{
pos <- match(input$levdrop, values$atnames)
output$levtext <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in seq_len(values$levels[pos])){
tags[[i]] <- shiny::textInput(paste0("at",pos,"lev",i), paste0("Name level",i),
value = paste0("at",pos,"lev",i))
tags[[i+1]] <- shiny::actionButton(paste0("savelevs",pos), paste0("Save level ",pos))
}
tags
})
#save level names
levnames <- list()
shiny::observeEvent(eval(parse(text = paste0("input$savelevs",pos))),{
acum <- c()
for (i in seq_len(values$levels[pos])){
acum <- append(acum, eval(parse(text = paste0("input$at",pos,"lev",i))))
}
values$levnames[[paste0(values$atnames[pos])]] <- acum
output$printlevnames <- shiny::renderPrint({
values$levnames
})
# If all levels have a name, option to paste in the design matrix
if (length(values$levnames) == length(values$levels)){
output$modmatrix <- shiny::renderUI({
shiny::actionButton("modmatbut", "Change names in design matrix")
})
}
})
})
})
#Put names in the design matrix
shiny::observeEvent(input$modmatbut, {
levvector <- c()
for (i in 1:length(values$levnames)){
levvector <- append(levvector, rlist::list.match(values$levnames, values$atnames[i]))
}
if (values$optout == FALSE){
namvect <- append(c("task","alt"), unlist(lapply(levvector, function(x) x[-1])))
} else {
namvect <- append(c("task","alt", "optout"), unlist(lapply(levvector, function(x) x[-1])))
}
print(namvect)
colnames(values$design) <- namvect
#Print the table
output$design <- DT::renderDT({
values$design <- as.data.frame(values$design)
})
})
# Save design and other design info (if design changes)
shiny::observeEvent(values$design, {
deslist <- list("design" = as.data.frame(values$design), # Save in a list to download in the excel
"priors" = as.data.frame(values$priors),
"alts" = as.data.frame(values$alts),
"optout" = as.data.frame(values$optout),
"Derror" = as.data.frame(values$`D-error`),
"nats" = as.data.frame(values$nats),
"sets" = as.data.frame(values$sets),
"details" = as.data.frame(values$details),
"levels" = as.data.frame(values$levels),
"bayesian" = as.data.frame(values$bayesian),
"atnames" = as.data.frame(values$atnames),
"levnames" = as.data.frame(unlist(values$levnames)))
values$deslist <- deslist
atnames <- values$atnames
levnames <- values$levnames
#list the levnames correctly
if (length(values$levnames)>0 && length(levnames) > length(atnames)){
levnames2 <- list()
levnames <- as.vector(unlist(values$levnames))
for (i in 1:length(values$atnames)){
levnames2[[i]] <- levnames[1:values$levels[[i]]]
levnames <- levnames[-c(1:values$levels[i])]
}
values$levnames2 <- levnames2
} else {
values$levnames2 <- levnames
}
# Generate another variable with +1 if null
if (values$optout == TRUE){
values$ncalts <- values$alts + 1
} else {
values$ncalts <- values$alts
}
#Generate the vector indicating the null alternative
if (values$optout == TRUE){
values$nullvect <- c()
for (i in seq_len(values$alts)){
values$nullvect <- c(values$nullvect, 0)
}
values$nullvect <- c(values$nullvect, 1)
}
#Generate a no.choice integer to indicate the position
if (values$optout == TRUE){
values$no.choice <- values$ncalts
} else {
values$no.choice <- NULL
}
})
# survey creator
output$labels <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in 1:values$ncalts) {
tags[[i]] <- shiny::textInput(paste0('alt_label_', i),
paste0('Alternative ', i),
paste0('Alternative ',i))
}
tags[[i+1]] <- shiny::actionButton("savelabelsbut", "Save labels")
tags
})
#Observe labels and save them
shiny::observeEvent(input$savelabelsbut, {
labels <- c()
a <- 0
for (i in seq_len(values$ncalts)){
a <- eval(parse(text = paste0("input$alt_label_",i)))
labels <- append(labels, a)
}
values$labels <- labels
})
# Observe and print intro text
shiny::observeEvent(input$intro, {
output$dispintrotext <- shiny::renderUI({
shiny::markdown(input$intro, .noWS = TRUE)
})
values$intro <- input$intro
})
#Observe and print end text
shiny::observeEvent(input$outro, {
output$dispoutrotext <- shiny::renderUI({
shiny::markdown(input$outro, .noWS = TRUE)
})
values$outro <- input$outro
})
#Render the choice sets
shiny::observeEvent(input$savelabelsbut,{
output$designcoded <- shiny::renderTable({
#Create the coding vector
coding <- c()
for (i in seq_len(values$nats)){
coding <- append(coding, "D")
}
levnames2 <- values$levnames2
values$coding <- coding
print(coding)
decodes <- idefix::Decode(as.matrix(values$design[,3:ncol(values$design)]), values$ncalts, values$levnames2,
coding = coding, no.choice = values$no.choice, alt.cte = values$nullvect)
decodes <- decodes$design
decodes <- cbind("set" = rep(1:values$sets, each = values$ncalts), decodes)
decodes <- decodes[decodes$set == 1,]
decodes <- decodes[,2:ncol(decodes)]
decodes <- t(decodes)
colnames(decodes) <- values$labels
decodes <- cbind("Attributes" = values$atnames,decodes)
decodes
})
#show serial mode
if (length(values$choices) == 2){
output$serialui <- shiny::renderUI({
shiny::radioButtons("serialmode", label = "Serial mode" ,choices = c("No" = "no",
"Bliemer & Rose (each respondent)" = "pure",
"Each 5 respondents" = "five"),
inline = TRUE)
})
}
})
# Radio dummies
shiny::observeEvent(input$savelabelsbut, {
output$radiodummy <- shiny::renderUI(
shiny::radioButtons("nullinp", label = "", choices = values$labels, inline = TRUE)
)
})
#Show cs text
shiny::observeEvent(input$savelabelsbut, {
output$cstext <- shiny::renderUI({
htmltools::h5("First choice set")
})
})
# Decide when showing the Next > button
output$contsurv1 <- shiny::renderUI({
if (values$survclick != values$sets+1){
shiny::actionButton("contsurv", "Next >")
} else if (values$survclick == values$sets+1){
shiny::actionButton("nextresp", "Next respondent >")
}
})
# Survey in popup
shiny::observeEvent(input$popbut, once = TRUE, {
values$survclick <- 0
shiny::observeEvent(input$contsurv, {
values$survclick <- values$survclick + 1
})
shiny::observeEvent(values$survclick,{
if (values$survclick == 0){
output$css <- NULL
output$cssbut <- NULL
output$texts <- shiny::renderUI({
shiny::markdown(values$intro, .noWS = TRUE)
})
} else if (values$survclick > 0 && values$survclick <= values$sets){
output$texts <- NULL
output$css <- shiny::renderTable({
### Load the table
decodes <- idefix::Decode(as.matrix(values$design[,3:ncol(values$design)]), values$ncalts, values$levnames2,
coding = values$coding, no.choice = values$no.choice, alt.cte = values$nullvect)
decodes <- decodes$design
decodes <- cbind("set" = rep(1:values$sets, each = values$ncalts), decodes)
decodes <- decodes[decodes$set == values$survclick,]
decodes <- decodes[,2:ncol(decodes)]
decodes <- t(decodes)
colnames(decodes) <- values$labels
decodes <- cbind("Attributes" = values$atnames,decodes)
decodes
})
output$cssbut <- shiny::renderUI({
shiny::radioButtons("choices", label = "", choices = values$labels, inline = TRUE,
selected = "0")
})
} else if (values$survclick == values$sets+1){
output$css <- NULL
output$cssbut <- NULL
output$texts <- shiny::renderUI({
shiny::markdown(values$outro, .noWS = TRUE)
})
}
# Save responses to the survey
shiny::observeEvent(values$survclick, once = TRUE,{
if (values$survclick > 1 && (values$survclick < values$sets+2)){
current <- c("cs" = values$survclick-1, "choice" = input$choices)
values$choices <- rbind(values$choices, current)
current <- NULL
}
names(values$choices) <- c("task", "choice")
savechoices <<- values$choices
})
if (length(values$choices > 0)){
output$resultsbut <- shiny::renderUI({
shiny::actionButton("resultsgo", "Analyze the results")
})
}
}) # End of the function to show the choice sets
# Count the number of respondents
shiny::observeEvent(input$contsurv, {
values$respondents <- floor(nrow(values$choices) / values$sets)
# Add the design to the accumulated frame
if (values$respondents == 0){
values$designstor <- values$design
}
})
#Load old or new design depending on the mode
shiny::observeEvent(input$nextresp, {
if (input$serialmode == "no"){
values$survclick <- 0
} else if (input$serialmode == "pure"){
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray %>% tidyr::drop_na(num)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
#extract the regressors' name to input it in the model
regressors <- names(cdesmat[,4:(ncol(cdesmat)-1)])
regressors <- paste0('`',regressors, '`')
clog <- survival::clogit(stats::as.formula(paste0("choice ~ ",do.call(paste, c(as.list(regressors), sep = " + ")), " + strata(task)")),
data = as.data.frame(cdesmat))
clog <- summary(clog)
clog$coefficients <- as.data.frame(clog$coefficients)
clog <- cbind(clog$coefficients[,1],clog$coefficients[,5])
clog <- cbind(clog,ifelse(clog[,2] <= 0.05, clog[,1], 0))
if(sum(clog[,3]) != 0){
for (i in 1:length(clog[,3])){
if (clog[,3][i] != 0){
values$priors[i] <- clog[,3][i]
}
}
# Decide if bayesian
if (values$bayesian == TRUE){
alg = "cea"
} else {
alg = "fedorov"
}
values$alg <- alg
# Priors
if (values$bayesian == TRUE){
values$bpriors <- mvtnorm::rmvnorm(100, values$priors, diag(length(values$priors)))
} else {
values$bpriors <- values$priors
}
# Generate
design <- dce_toolbox(attributes = values$levels, csets = values$sets,
alts = values$alts, nochoice = values$optout,
priors = values$bpriors, alg = alg)
design <- design$design
#Replace the global design
tempnam <- colnames(values$design)
colnames(design) <- tempnam
values$design <- design
}
} else if (input$serialmode == "five"){
if ((values$respondents+1) %% 5 == 0){
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray %>% tidyr::drop_na(num)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
#extract the regressors' name to input it in the model
regressors <- names(cdesmat[,4:(ncol(cdesmat)-1)])
regressors <- paste0('`',regressors, '`')
clog <- survival::clogit(stats::as.formula(paste0("choice ~ ",do.call(paste, c(as.list(regressors), sep = " + ")), " + strata(task)")),
data = as.data.frame(cdesmat))
clog <- summary(clog)
clog$coefficients <- as.data.frame(clog$coefficients)
clog <- cbind(clog$coefficients[,1],clog$coefficients[,5])
clog <- cbind(clog,ifelse(clog[,2] <= 0.05, clog[,1], 0))
if(sum(clog[,3]) != 0){
for (i in 1:length(clog[,3])){
if (clog[,3][i] != 0){
values$priors[i] <- clog[,3][i]
}
}
# Decide if bayesian
if (values$bayesian == TRUE){
alg = "cea"
} else {
alg = "fedorov"
}
values$alg <- alg
# Priors
if (values$bayesian == TRUE){
values$bpriors <- mvtnorm::rmvnorm(100, values$priors, diag(length(values$priors)))
} else {
values$bpriors <- values$priors
}
# Generate
design <- dce_toolbox(attributes = values$levels, csets = values$sets,
alts = values$alts, nochoice = values$optout,
priors = values$bpriors, alg = alg)
design <- design$design
#Replace the global design
tempnam <- colnames(values$design)
colnames(design) <- tempnam
values$design <- design
}
} else {
values$survclick <- 0
}
}
#Reload the choice sets
values$designstor <- rbind(values$designstor, values$design)
designstor <- values$designstor
values$survclick <- 0
})
}) # End of the popup
# Move to results when click on analyze the survey
shiny::observeEvent(input$resultsgo, {
shiny::updateTabsetPanel(session, 'inTabset', selected = "results")
#detect if the number of responses correspond to the designs stored
storedchoices <- nrow(savechoices)*values$ncalts
#if they are the same then reshape the dataset
if (storedchoices == nrow(values$designstor)){
#Reshape and present
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
resultados <<- cdesmat
cdesmat$gid <- rep(1:(nrow(cdesmat)/values$ncalts), each = values$ncalts)
values$cdesmat <- cdesmat
# Render the table with the results
output$restable <- DT::renderDT({
cdesmat
})
} else if (storedchoices != nrow(values$designstor)){
#Cut the design storage if it's bigger than the response
values$designstor <- values$designstor[1:storedchoices,]
#Now reshape the database
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
resultados <<- cdesmat
cdesmat$gid <- rep(1:(nrow(cdesmat)/values$ncalts), each = values$ncalts)
values$cdesmat <- cdesmat
# Render the table with the results
output$restable <- DT::renderDT({
cdesmat
})
}
})
# Download the coded design
output$downloadresults <- shiny::downloadHandler(
filename = function() {"results.xlsx"},
content = function(file) {
writexl::write_xlsx(values$cdesmat, file)}
)
#Load a results
shiny::observeEvent(input$loadresults, {
# Design loader
output$restable <- DT::renderDT({
values$cdesmat <- readxl::read_excel(input$loadresults$datapath) #Update
})
})
# Estimate a conditional logit
shiny::observeEvent(input$modelname, {
cdesmat <- values$cdesmat
output$modopt <- NULL
if (input$modelname == "clogit"){
output$modopt <- shiny::renderUI({
options <- htmltools::tagList(
shinyWidgets::pickerInput("dep", "Dependent variable", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("ind", "Independent variables", choices = colnames(cdesmat), multiple = TRUE),
shinyWidgets::pickerInput("gid", "Group variable", choices = colnames(cdesmat), multiple = FALSE),
shiny::actionButton("goest", "Estimate")
)
options
})
} else if (input$modelname == "nullselect"){
output$modopt <- NULL
} else if (input$modelname == "mixlogit"){
output$modopt <- shiny::renderUI({
options <- htmltools::tagList(
shinyWidgets::pickerInput("dep", "Dependent variable", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("ind", "Independent variables", choices = colnames(cdesmat), multiple = TRUE),
shinyWidgets::pickerInput("gid", "Group variable", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("pid", "Individual identificator", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("alt", "Alternative identificator", choices = colnames(cdesmat), multiple = FALSE),
shiny::actionButton("goest", "Estimate")
)
options
})
} else if (input$modelname == "wtp"){
output$modopt <- shiny::renderUI({
options <- htmltools::tagList(
shinyWidgets::pickerInput("pr", "Continuous 'price' variable", choices = rownames(values$clog$coefficients), multiple = FALSE),
shinyWidgets::pickerInput("rl", "Rest of levels", choices = rownames(values$clog$coefficients), multiple = TRUE),
shiny::actionButton("goest", "Estimate")
)
options
})
} else if (input$modelname == "figures"){
ui <- htmltools::tagList(
shinyWidgets::pickerInput("coefs", "Select levels to plot", choices = rownames(values$clog$coefficients), multiple = TRUE),
shiny::actionButton("plotit", "Create figure")
#numericInput("ngrup", "Number of groups (attributes)", value = 0)
)
output$modopt <- shiny::renderUI({
ui
})
}
})
# Future implementation
# observeEvent(input$ngrup,{
# output$modopt2 <- renderUI({
# if (input$ngrup > 0) {
# tags <- tagList()
# for (i in seq_len(input$ngrup)) {
# tags[[i]] <- textInput(paste0('gr', i),
# paste0('Name group ', i))
# }
# tags[[i+1]] <- actionButton("plotit", "Create figure")
# tags
# } else {
# actionButton("plotit", "Create figure")
# }
# })
# })
# Estimations
shiny::observeEvent(input$goest, {
cdesmat <- values$cdesmat
if (input$modelname == "clogit"){
ind <- input$ind
ind <- paste0("`",ind, "`")
dep <- input$dep
dep <- paste0("`",dep, "`")
clog <- survival::clogit(stats::as.formula(paste0(paste0(dep," ~"),do.call(paste, c(as.list(ind), sep = " + ")), " + strata(",paste0(input$gid) ,")")),
data = as.data.frame(cdesmat))
clog <- summary(clog)
#Render the results
output$clog <- shiny::renderPrint({
clog
})
clog <<- clog
values$clog <- clog
### Mixlogit
} else if (input$modelname == "mixlogit"){
dep <- input$dep
dep <- paste0("`",dep, "`")
gid <- input$gid
alt <- input$alt
pid <- input$pid
ind <- input$ind
ind <- paste0("`",ind, "`")
rpar <- c()
for (i in 1:length(ind)){
rpar <- append(rpar, "n")
}
names(rpar) <- ind
ind <- input$ind
ind <- paste0("`",ind, "`")
cdesmat$choice <- as.logical(cdesmat$choice)
disMIX <- dfidx::dfidx(cdesmat, choice="choice", idx = list(c(paste0(gid), paste0(pid)), paste0(alt)), idnames= c("cs", "alt"))
modeloMIX <- try(mlogit::mlogit(stats::as.formula(paste0(paste0(dep," ~"),do.call(paste, c(as.list(ind), sep = " + ")), " | 0")), disMIX,
rpar = rpar, R = 100, halton = NA))
clog <- summary(modeloMIX)
if (typeof(clog) == "character"){
ind <- input$ind
rpar <- c()
for (i in 1:length(ind)){
rpar <- append(rpar, "n")
}
names(rpar) <- ind
ind <- input$ind
ind <- paste0("`",ind, "`")
cdesmat$choice <- as.logical(cdesmat$choice)
disMIX <- dfidx::dfidx(cdesmat, choice="choice", idx = list(c(paste0(gid), paste0(pid)), paste0(alt)), idnames= c("cs", "alt"))
modeloMIX <- try(mlogit::mlogit(stats::as.formula(paste0(paste0(dep," ~"),do.call(paste, c(as.list(ind), sep = " + ")), " | 0")), disMIX,
rpar = rpar, R = 100, halton = NA))
clog <- summary(modeloMIX)
if (typeof(clog) == "character"){
clog <- "There is a problem related with the variable names. More likely, you combined level names with and without numbers and blank spaces. Save the design and modify the excel file by deleting all numbers and blanks from the variable names."
}
}
#Render the results
output$clog <- shiny::renderPrint({
clog
})
} else if (input$modelname == "wtp") {
if (is.null(values$clog)){
output$clog <- shiny::renderPrint({
"First estimate the conditional logit"
})
} else {
reswtp <- as.data.frame(values$clog$coefficients)
results <- -reswtp[input$rl,]/as.numeric(reswtp[input$pr,][1])
output$clog <- shiny::renderPrint({
results
})
}
}
})
# If click on figures, render the graph based on the coefficients of the clogit and the user selection
shiny::observeEvent(input$modelname,{
if (input$modelname == "figures"){
shiny::observeEvent(input$plotit, {
if (!is.null(values$clog)){
df <- data.frame(names = input$coefs, y = values$clog$coefficients[,1][input$coefs], se = values$clog$coefficients[,3][input$coefs])
values$df <- df
output$clog <- NULL
output$figure <- shiny::renderPlot(
ggplot2::ggplot(df, aes(x=names, y=y)) + geom_bar(stat = "identity", fill="skyblue", alpha=0.7) +
geom_errorbar( ggplot2::aes(x=names, ymin=y-se, ymax=y+se), width=0.4, colour="orange", alpha=0.9, size=1.3)
)
} else {
output$clog <- shiny::renderPrint(
"First, estimate a conditional logit model."
)
}
})
}
})
# Change level names and axis names in the graph
shiny::observeEvent(input$plotit, {
tl <- htmltools::tagList()
for (i in 1:length(input$coefs)){
tl[[i]] <- shiny::textInput(inputId = paste0("coefplot", i), label = paste0(input$coefs[i]), value = paste0(input$coefs[i]))
}
tl[[i+1]] <- shiny::textInput(inputId = "xlabnew", "X axis")
tl[[i+2]] <- shiny::textInput(inputId = "ylabnew", "Y axis")
tl[[i+3]] <- actionButton(inputId = "changenames", label = "Change names")
output$modopt2 <- shiny::renderUI({
tl
})
})
shiny::observeEvent(input$changenames, {
newnames <- c()
for (i in 1:length(input$coefs)){
newnames <- append(newnames, eval(parse(text = paste0("input$coefplot", i))))
}
output$figure <- shiny::renderPlot(
ggplot2::ggplot(values$df, aes(x=names, y=y)) + geom_bar(stat = "identity", fill="skyblue", alpha=0.7) +
geom_errorbar( aes(x=names, ymin=y-se, ymax=y+se), width=0.4, colour="orange", alpha=0.9, size=2) +
scale_x_discrete(labels = newnames) + xlab(input$xlabnew) + ylab(input$ylabnew)
)
})
shiny::observeEvent(input$pricevarcoding, {
if (input$pricevarcoding == "cont"){
cdesmat <- values$cdesmat
regressors <- names(cdesmat[,4:(ncol(cdesmat)-1)])
output$atpriceselect <- shiny::renderUI({
checkboxGroupInput(
inputId = "pricelevs",
label = "Select price levels",
choices = names(cdesmat)
)
})
output$savethem <- shiny::renderUI({
actionButton("savepricelevs", "Save price levels")
})
} else if (input$pricevarcoding == "already"){
cdesmat <- values$cdesmat
output$atpriceselect <- shiny::renderUI({
checkboxGroupInput(
inputId = "selectedcontvar",
label = "Select the continuous price variable",
choices = names(cdesmat)
)
})
}
})
shiny::observeEvent(input$pricevarcoding, {
if (!is.null(input$selectedcontvar)){
cdesmat <- values$cdesmat
cdesmat$price <- eval(parse(text = paste0("cdesmat$selectedcontvar")))
}
})
shiny::observeEvent(input$savepricelevs, {
pricevect <- input$pricelevs
output$pricelevbr <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in 1:length(input$pricelevs)) {
tags[[i]] <- shiny::numericInput(paste0('pricelev', i),
paste0(input$pricelevs[i]),
0)
}
omittedlev <- shiny::numericInput("omlev", "Omitted level (In monetary units)", value = 0)
tags <- htmltools::tagList(omittedlev, tags, actionButton("sprc", "Add variable to the data frame"))
tags
})
})
shiny::observeEvent(input$sprc, {
cdesmat <- values$cdesmat
if (!is.null(cdesmat$cont_price)){
cdesmat$cont_price <- NULL
} else if (is.null(cdesmat$cont_price)){
pricelevs <- input$pricelevs
cdesmat$cont_price <- ifelse(rowSums(cdesmat[colnames(cdesmat) == pricelevs]) == 0, input$omlev, NA)
for (i in 1:length(pricelevs)){
inppric <- pricelevs[i]
cdesmat$cont_price <- ifelse(eval(parse(text = paste0("cdesmat$`", inppric,"`")))== 1, eval(parse(text = paste0("input$pricelev", i))) , cdesmat$cont_price)
}
cdesmat <- cbind(cdesmat[,1:(ncol(cdesmat)-2)], "cont_price" = cdesmat[,ncol(cdesmat):ncol(cdesmat)], "gid" = cdesmat[,(ncol(cdesmat)-1):(ncol(cdesmat)-1)])
values$cdesmat <- cdesmat
}
output$restable <- DT::renderDT({
values$cdesmat
})
output$pricelevbr <- NULL
})
shiny::observe({
if (shiny::req(input$inTabset == "About")){
x <- adjustedcranlogs::adj_cran_downloads("DCEtool",when="last-month")[,c(1,3)]
}
output$downloads <- shiny::renderPlot({
if (!is.null(x)) {
barplot(count ~ date, data = x)
}
})
})
}
shinyApp(ui, server)
}
danielpereztr/DCEtool documentation built on April 16, 2024, 6:36 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions DCEtool
Documented in DCEtool
#' @export
DCEtool <- function(){
requireNamespace('shiny')
requireNamespace('rlist')
requireNamespace('shinythemes')
requireNamespace('shinyWidgets')
requireNamespace('mvtnorm')
requireNamespace('DT')
requireNamespace('shinycssloaders')
requireNamespace('writexl')
requireNamespace('readxl')
requireNamespace('rlist')
requireNamespace('idefix')
requireNamespace('shinyBS')
requireNamespace('survival')
requireNamespace('tidyr')
requireNamespace('mlogit')
requireNamespace('ggplot2')
requireNamespace('bslib')
requireNamespace('dfidx')
#' @importFrom shinyBS bsModal
#' @importFrom graphics barplot
#' @importFron usethis use_pipe
#' @importFrom magrittr %>%
#' @importFrom survival strata
#' @importFrom survival coxph
#' @importFrom survival clogit
#' @importFrom ggplot2 aes
#' @importFrom ggplot2 geom_bar
#' @importFrom ggplot2 geom_errorbar
#' @importFrom ggplot2 scale_x_discrete
#' @importFrom ggplot2 xlab
#' @importFrom ggplot2 ylab
#' @importFrom shiny actionButton
#' @importFrom shiny checkboxGroupInput
#' @importFrom shiny shinyApp
#' @importFrom rlist list.match
#external variables
savechoices <- c()
resultados <- c()
num <- c()
y <- c()
se <- c()
ui <- shiny::navbarPage(
"DCEtool", id = 'inTabset',
shiny::tabPanel("Home", value = "start",
shiny::fluidRow(
shiny::column(12,
align = "center",
htmltools::img(src = "assets/granada.png", width = "50%"), # prefix + filename
htmltools::p("Welcome to DCEtool. ",style="text-align:justify;color:black;background-color:LightGrey;padding:15px;border-radius:10px"),
shiny::HTML("<p>Find more <a href = 'https://danielpereztr.github.io/DCEtool/'>here</a>.</p>"),
shiny::HTML("<p>Please cite as Pérez-Troncoso (2022). Efficient and Accessible Discrete Choice Experiments: DCEtool (Version 1.0.0). danielpereztr.github.io/DCEtool</p>")
)
)
), #Home tab
shiny::tabPanel("Design settings", value = "params", #Design settings tab
shiny::sidebarLayout(
shiny::sidebarPanel( #Inputs sidebar panel
shiny::numericInput('ats', "Number of attributes", 0),
shiny::uiOutput('dynamic'),
shiny::actionButton('loadats','Save attributes'),
htmltools::hr(),
shiny::uiOutput('altbut'),
shiny::uiOutput('csetbut'),
shiny::uiOutput('optcheck'),
shiny::uiOutput('bayescheck'),
shiny::uiOutput('savebut'),
htmltools::hr(),
shiny::uiOutput('priorsbut'),
shiny::uiOutput('seedbut'),
shiny::uiOutput('saveopt')
),
shiny::mainPanel(
shiny::verbatimTextOutput('levelsnumber'),
shiny::verbatimTextOutput('errorscheck'),
shiny::uiOutput('gobut')
)
)
),
shiny::tabPanel(title = "Design matrix", value = "desmattab", #Design matrix tab
shiny::sidebarLayout(
shiny::sidebarPanel( # Design matrix left tab
shiny::actionButton("gendesign", "Generate design"),
htmltools::br(),
htmltools::br(),
shiny::downloadButton("downloaddesing","Save design", icon = shiny::icon("download")), #save design
shiny::fileInput(inputId = "loaddesign",label = "", multiple = FALSE), #load design
shiny::actionButton("showdesdetails", "Show design details", icon = shiny::icon("eye")),
htmltools::br(),
htmltools::br(),
shiny::actionButton("writeatnames", "Name the attributes", icon = shiny::icon("braille")),
htmltools::br(),
htmltools::br(),
shiny::uiOutput("atnames"),
htmltools::br(),
shiny::uiOutput('levdropdown'),
shiny::uiOutput('levtext')
),
shiny::mainPanel( # Design matrix main panel
shiny::uiOutput("spinner"),
shiny::verbatimTextOutput("desdetails"),
shiny::verbatimTextOutput("printlevnames"),
shiny::uiOutput('modmatrix')
)
)
),
shiny::tabPanel(title = "Create a survey", value = "createsurv", # Crear la encuesta
shiny::sidebarLayout(
shiny::sidebarPanel( # Sidebar Panel for survey creator
htmltools::p("Intro and end text: "),
shiny::textAreaInput("intro", "Introductory text in Markdown", rows = 3),
shiny::textAreaInput("outro", "End text in Markdown", rows = 3),
htmltools::hr(),
htmltools::p("Label each alternative: "),
shiny::uiOutput("labels"),
htmltools::hr()
),
shiny::mainPanel(
htmltools::p("Survey preview"),
htmltools::hr(),
shiny::uiOutput("dispintrotext"),
htmltools::br(),
htmltools::hr(),
shiny::uiOutput('cstext'),
shiny::tableOutput("designcoded"),
shiny::uiOutput('radiodummy', width = '100%'),
htmltools::br(),
htmltools::hr(),
shiny::uiOutput("dispoutrotext"),
)
)
),
shiny::tabPanel(title = "Survey",
shiny::fluidRow(
shiny::column(12,
align = "center",
shiny::uiOutput("serialui")
)
),
shiny::fluidRow(
shiny::column(12,
align = "center",
shiny::actionButton(inputId = "popbut", "Launch survey"),
htmltools::br(),
htmltools::br(),
shiny::uiOutput("resultsbut")
)
),
shinyBS::bsModal("modalExample", "", "popbut", size = "large",
shiny::fluidRow(
shiny::column(12,
align = "left",
shiny::uiOutput("texts"),
),
shiny::column(12,
align = "center",
shiny::tableOutput("css"),
shiny::uiOutput("cssbut")
),
shiny::column(12,
align = "right",
shiny::uiOutput('contsurv1')
)
)
)
),
shiny::tabPanel(title = "Results", value = "results",
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::tabsetPanel(id = "restabs",
shiny::tabPanel("Data",
htmltools::br(),
shiny::downloadButton("downloadresults","Save results", icon = shiny::icon("download")),
shiny::fileInput(inputId = "loadresults",label = "", multiple = FALSE), #load results
shiny::selectInput(
inputId = "pricevarcoding",
label = "Price variable coding",
choices = c("Dummy coding" = "dumcod",
#"There is already a continuous price variable" = "already",
"Code price as continuous variable" = "cont")
),
shiny::uiOutput("atpriceselect"),
shiny::uiOutput("savethem"),
shiny::uiOutput("pricelevbr")
),
shiny::tabPanel("Estimation",
htmltools::br(),
shiny::selectInput("modelname", "Choose estimate",
choices = c("Select a model" == "nullselect",
"Conditional logit" = "clogit",
"Mixed logit" = "mixlogit",
"Willingness to pay" = "wtp",
"Figures" = "figures")
),
shiny::uiOutput("modopt"),
htmltools::hr(),
shiny::uiOutput("modopt2")
)
)
),
shiny::mainPanel(
DT::DTOutput("restable"),
shiny::verbatimTextOutput("clog"),
shiny::plotOutput("figure")
)
)
),
shiny::tabPanel(title = "About",
shiny::fluidRow(
shiny::column(12,
align = "Left",
htmltools::h3("About"),
shiny::HTML("<p>This app was created by Daniel Pérez-Troncoso in 2021. Version 1.0.0 was released in April 2022.</p>"),
shiny::HTML("<p>Please, if you use this app in your research, reference it as 'Pérez-Troncoso, D. (2022). DCEtool (1.0.0) [Software]. https://cran.r-project.org/package=DCEtool ' </p>"),
shiny::HTML("<p>Find a guide in <a href = 'https://danielpereztr.github.io/posts/DCEtool/'>this link</a></p>"),
htmltools::h3("Downloads"),
shiny::plotOutput("downloads")
)
)
)
)
server <- function(input, output, session){
# Check if there is a newer version in CRAN
shiny::observeEvent(input$inTabset == "start", {
db <- utils::available.packages(filters = "duplicates")
cranvers <- db[db[,1] == "DCEtool"][2]
thisvers <- utils::packageVersion("DCEtool")
if (cranvers == thisvers){
} else if (cranvers != thisvers) {
shiny::showNotification("There is a newer version of DCEtool on CRAN. Run install.packages('DCEtool') to update DCEtool.")
}
})
#Close shiny
session$onSessionEnded(function() {
shiny::stopApp()
})
#change tab
shiny::observeEvent(input$create_DCE, {
shiny::updateTabsetPanel(session, 'inTabset', selected = "params")
})
# Values across functions
values <- shiny::reactiveValues()
# Download flag for later
values$downloadflag <- 0
# Choices storage for the survey
values$choices <- as.data.frame(matrix(ncol = 2, nrow = 0))
# Designstorage
values$designstor <- data.frame()
# Create as many inputs as attributes are
output$dynamic <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in seq_len(input$ats)) {
tags[[i]] <- shiny::numericInput(paste0('at', i),
paste0('Levels in attribute ', i),
0)
}
tags
})
# Create the vector 'levels' with the attributes' levels
shiny::observeEvent(input$loadats, {
nats <- input$ats
levels <- c()
for (i in seq_len(nats)){
levels <- append(levels, eval(parse(text = paste0("input$at",i))))
}
values$levels <- levels
values$nats <- nats
# Print the number of attributes and levels
output$levelsnumber <- shiny::renderPrint({
cat("Design settings \nNumber of attributes: ", values$nats, "\nLevels per attribute: ", values$levels)
})
#Ask the alternatives and csets after sending attributes
output$altbut <- shiny::renderUI({
shiny::numericInput("nalt", "Alternatives per choice set", value = 2, max = 5, min = 2)
})
#Ask the number of choice sets
output$csetbut <- shiny::renderUI({
shiny::numericInput("nset", "Number of choice sets", value = 12, min = 4)
})
#Checkbox if opt-out alternative
output$optcheck <- shiny::renderUI({
shinyWidgets::materialSwitch(inputId = "optout", label = "Opt-out alternative", value = FALSE, status = "danger")
})
# Checkboxes to select the optimization procedure
output$bayescheck <- shiny::renderUI({
shinyWidgets::materialSwitch(inputId = "bayesian", label = "Bayesian design", status = "danger", value = FALSE)
})
#Print the button to save the settings
output$savebut <- shiny::renderUI({
shiny::actionButton("saveset", "Save settings")
})
})
# Save and print settings
shiny::observeEvent(input$saveset,{
values$alts <- input$nalt
values$sets <- input$nset
values$optout <- input$optout
values$bayesian <- input$bayesian
output$levelsnumber <- shiny::renderPrint({
cat("Design settings \nNumber of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian)
})
# Show button for priors
output$priorsbut <- shiny::renderUI({
optout <- values$optout
levels <- values$levels
nats <- values$nats
null <- ifelse(optout == TRUE, 1, 0)
npar <- sum(levels)-nats+null
priors <- c()
for (x in seq_len(npar)){
priors <- append(priors, 0)
}
values$npar <- npar
shiny::textInput("priorsinput", "Prior coefficients", value = paste(shQuote(priors, type="cmd2"), collapse=", "))
})
# show button for random seed
output$seedbut <- shiny::renderUI({
shiny::numericInput("randomseed", "Random seed", value = 9999)
})
# save options button
output$saveopt <- shiny::renderUI({
shiny::actionButton("finalsave", "Save options")
})
})
# Print the final saved options
shiny::observeEvent(input$finalsave,{
values$priors <- as.numeric(strsplit(as.character(input$priorsinput), ",")[[1]])
values$seed <- input$randomseed
output$levelsnumber <- shiny::renderPrint({
cat("Design settings \nNumber of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian, "\nPriors: ", values$priors, "\nSeed: ", values$seed)
})
#Check errors
output$errorscheck <- shiny::renderPrint({
cat("Error checker results: \n")
if (length(values$levels) != values$nats){
cat("Some error occurred. Please restart DCEtool.\n")
} else if (values$sets < (sum(values$levels)-1)){
cat("The number of sets is not enough. Try with ", sum(values$levels)-1, " sets or more.\n")
} else if (length(values$priors) != values$npar){
cat("The number of priors does not correspond with the number of parameters. Try using ", values$npar, " prior parameters.")
} else {
cat("No errors found.")
}
})
# Button to create the design matrix
output$gobut <- shiny::renderUI({
shiny::actionButton("go", "Happy with the settings? Go to next step")
})
})
# Move to the next tab
shiny::observeEvent(input$go,{
#Move to the Design matrix tab
shiny::updateTabsetPanel(session, 'inTabset', selected = "desmattab")
})
shiny::observeEvent(input$gendesign,{
# Loader
output$spinner <- shiny::renderUI({
shinycssloaders::withSpinner(DT::dataTableOutput("design"))
})
# Render the design table
output$design <- DT::renderDT({
# Decide if bayesian
if (values$bayesian == TRUE){
alg = "cea"
} else {
alg = "fedorov"
}
values$alg <- alg
# Priors
if (values$bayesian == TRUE){
values$bpriors <- mvtnorm::rmvnorm(100, values$priors, diag(length(values$priors)))
} else {
values$bpriors <- values$priors
}
# Generate
design <- dce_toolbox(attributes = values$levels, csets = values$sets,
alts = values$alts, nochoice = values$optout,
priors = values$bpriors, alg = alg)
values$design <- design$design
values$`D-error` <- design$`D-error`
values$details <- design$details
as.data.frame(design$design)
})
})
# Download button
output$downloaddesing <- shiny::downloadHandler(
filename = function() {"design.xlsx"},
content = function(file) {values$downloadflag <- values$downloadflag+1
writexl::write_xlsx(values$deslist, file)}
)
# Load saved design
shiny::observeEvent(input$loaddesign, {
#Spinner loader
output$spinner <- shiny::renderUI({
shinycssloaders::withSpinner(DT::dataTableOutput("design"))
})
# Design loader
output$design <- DT::renderDT({
if (!is.null(input$loaddesign)){
values$`D-error` <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "Derror"))) #Update
values$details <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "details"))) #Update
values$nats <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "nats"))) #Update
values$levels <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "levels"))) #Update
values$sets <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "sets"))) #Update
values$optout <- as.logical(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "optout"))) #Update
values$priors <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "priors"))) #Update
values$alts <- as.numeric(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "alts"))) #Update
values$bayesian <- as.logical(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "bayesian")))
values$atnames <- as.vector(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "atnames")))
values$levnames <- as.list(unlist(readxl::read_excel(input$loaddesign$datapath, sheet = "levnames")))
values$design <- readxl::read_excel(input$loaddesign$datapath) # Print this one
}
})
})
#Show design details
shiny::observeEvent(input$showdesdetails, {
output$desdetails <- shiny::renderPrint(
cat("Number of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian, "\nPriors: ", values$priors, "\nAttribute names: ", values$atnames,
"\nLevel names: ", unlist(values$levnames), "\nDetails:", values$details)
)
})
# Create inputs for attribute names
shiny::observeEvent(input$writeatnames, {
output$atnames <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in seq_len(values$nats)) {
tags[[i]] <- shiny::textInput(paste0('atn', i),
paste0('Name of attribute ', i),
value = paste0("atrib",i))
}
tags[[i+1]] <- shiny::actionButton("saveatnames", "Save names")
tags
})
})
# Save the attribute names
shiny::observeEvent(input$saveatnames, {
atnames <- c()
for (i in seq_len(values$nats)){
atnames <- append(atnames, eval(parse(text = paste0("input$atn",i))))
}
values$atnames <- atnames
output$desdetails <- shiny::renderPrint(
cat("Number of attributes: ", values$nats, "\nLevels per attribute: ",
values$levels, "\nAlternatives per choice set: ", values$alts,
"\nNumber of sets: ", values$sets,
"\nNull alternative: ", values$optout, "\nBayesian priors: ",
values$bayesian, "\nPriors: ", values$priors, "\nAttribute names: ", values$atnames,
"\nLevel names: ", unlist(values$levnames), "\nDetails:", values$details)
)
# Create buttons with the attribute names
shiny::observeEvent(input$saveatnames, {
output$levdropdown <- shiny::renderUI({
shiny::selectInput("levdrop", "Change level names", as.list(atnames))
})
values$levnames <- list()
})
# Level names
shiny::observeEvent(input$levdrop,{
pos <- match(input$levdrop, values$atnames)
output$levtext <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in seq_len(values$levels[pos])){
tags[[i]] <- shiny::textInput(paste0("at",pos,"lev",i), paste0("Name level",i),
value = paste0("at",pos,"lev",i))
tags[[i+1]] <- shiny::actionButton(paste0("savelevs",pos), paste0("Save level ",pos))
}
tags
})
#save level names
levnames <- list()
shiny::observeEvent(eval(parse(text = paste0("input$savelevs",pos))),{
acum <- c()
for (i in seq_len(values$levels[pos])){
acum <- append(acum, eval(parse(text = paste0("input$at",pos,"lev",i))))
}
values$levnames[[paste0(values$atnames[pos])]] <- acum
output$printlevnames <- shiny::renderPrint({
values$levnames
})
# If all levels have a name, option to paste in the design matrix
if (length(values$levnames) == length(values$levels)){
output$modmatrix <- shiny::renderUI({
shiny::actionButton("modmatbut", "Change names in design matrix")
})
}
})
})
})
#Put names in the design matrix
shiny::observeEvent(input$modmatbut, {
levvector <- c()
for (i in 1:length(values$levnames)){
levvector <- append(levvector, rlist::list.match(values$levnames, values$atnames[i]))
}
if (values$optout == FALSE){
namvect <- append(c("task","alt"), unlist(lapply(levvector, function(x) x[-1])))
} else {
namvect <- append(c("task","alt", "optout"), unlist(lapply(levvector, function(x) x[-1])))
}
print(namvect)
colnames(values$design) <- namvect
#Print the table
output$design <- DT::renderDT({
values$design <- as.data.frame(values$design)
})
})
# Save design and other design info (if design changes)
shiny::observeEvent(values$design, {
deslist <- list("design" = as.data.frame(values$design), # Save in a list to download in the excel
"priors" = as.data.frame(values$priors),
"alts" = as.data.frame(values$alts),
"optout" = as.data.frame(values$optout),
"Derror" = as.data.frame(values$`D-error`),
"nats" = as.data.frame(values$nats),
"sets" = as.data.frame(values$sets),
"details" = as.data.frame(values$details),
"levels" = as.data.frame(values$levels),
"bayesian" = as.data.frame(values$bayesian),
"atnames" = as.data.frame(values$atnames),
"levnames" = as.data.frame(unlist(values$levnames)))
values$deslist <- deslist
atnames <- values$atnames
levnames <- values$levnames
#list the levnames correctly
if (length(values$levnames)>0 && length(levnames) > length(atnames)){
levnames2 <- list()
levnames <- as.vector(unlist(values$levnames))
for (i in 1:length(values$atnames)){
levnames2[[i]] <- levnames[1:values$levels[[i]]]
levnames <- levnames[-c(1:values$levels[i])]
}
values$levnames2 <- levnames2
} else {
values$levnames2 <- levnames
}
# Generate another variable with +1 if null
if (values$optout == TRUE){
values$ncalts <- values$alts + 1
} else {
values$ncalts <- values$alts
}
#Generate the vector indicating the null alternative
if (values$optout == TRUE){
values$nullvect <- c()
for (i in seq_len(values$alts)){
values$nullvect <- c(values$nullvect, 0)
}
values$nullvect <- c(values$nullvect, 1)
}
#Generate a no.choice integer to indicate the position
if (values$optout == TRUE){
values$no.choice <- values$ncalts
} else {
values$no.choice <- NULL
}
})
# survey creator
output$labels <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in 1:values$ncalts) {
tags[[i]] <- shiny::textInput(paste0('alt_label_', i),
paste0('Alternative ', i),
paste0('Alternative ',i))
}
tags[[i+1]] <- shiny::actionButton("savelabelsbut", "Save labels")
tags
})
#Observe labels and save them
shiny::observeEvent(input$savelabelsbut, {
labels <- c()
a <- 0
for (i in seq_len(values$ncalts)){
a <- eval(parse(text = paste0("input$alt_label_",i)))
labels <- append(labels, a)
}
values$labels <- labels
})
# Observe and print intro text
shiny::observeEvent(input$intro, {
output$dispintrotext <- shiny::renderUI({
shiny::markdown(input$intro, .noWS = TRUE)
})
values$intro <- input$intro
})
#Observe and print end text
shiny::observeEvent(input$outro, {
output$dispoutrotext <- shiny::renderUI({
shiny::markdown(input$outro, .noWS = TRUE)
})
values$outro <- input$outro
})
#Render the choice sets
shiny::observeEvent(input$savelabelsbut,{
output$designcoded <- shiny::renderTable({
#Create the coding vector
coding <- c()
for (i in seq_len(values$nats)){
coding <- append(coding, "D")
}
levnames2 <- values$levnames2
values$coding <- coding
print(coding)
decodes <- idefix::Decode(as.matrix(values$design[,3:ncol(values$design)]), values$ncalts, values$levnames2,
coding = coding, no.choice = values$no.choice, alt.cte = values$nullvect)
decodes <- decodes$design
decodes <- cbind("set" = rep(1:values$sets, each = values$ncalts), decodes)
decodes <- decodes[decodes$set == 1,]
decodes <- decodes[,2:ncol(decodes)]
decodes <- t(decodes)
colnames(decodes) <- values$labels
decodes <- cbind("Attributes" = values$atnames,decodes)
decodes
})
#show serial mode
if (length(values$choices) == 2){
output$serialui <- shiny::renderUI({
shiny::radioButtons("serialmode", label = "Serial mode" ,choices = c("No" = "no",
"Bliemer & Rose (each respondent)" = "pure",
"Each 5 respondents" = "five"),
inline = TRUE)
})
}
})
# Radio dummies
shiny::observeEvent(input$savelabelsbut, {
output$radiodummy <- shiny::renderUI(
shiny::radioButtons("nullinp", label = "", choices = values$labels, inline = TRUE)
)
})
#Show cs text
shiny::observeEvent(input$savelabelsbut, {
output$cstext <- shiny::renderUI({
htmltools::h5("First choice set")
})
})
# Decide when showing the Next > button
output$contsurv1 <- shiny::renderUI({
if (values$survclick != values$sets+1){
shiny::actionButton("contsurv", "Next >")
} else if (values$survclick == values$sets+1){
shiny::actionButton("nextresp", "Next respondent >")
}
})
# Survey in popup
shiny::observeEvent(input$popbut, once = TRUE, {
values$survclick <- 0
shiny::observeEvent(input$contsurv, {
values$survclick <- values$survclick + 1
})
shiny::observeEvent(values$survclick,{
if (values$survclick == 0){
output$css <- NULL
output$cssbut <- NULL
output$texts <- shiny::renderUI({
shiny::markdown(values$intro, .noWS = TRUE)
})
} else if (values$survclick > 0 && values$survclick <= values$sets){
output$texts <- NULL
output$css <- shiny::renderTable({
### Load the table
decodes <- idefix::Decode(as.matrix(values$design[,3:ncol(values$design)]), values$ncalts, values$levnames2,
coding = values$coding, no.choice = values$no.choice, alt.cte = values$nullvect)
decodes <- decodes$design
decodes <- cbind("set" = rep(1:values$sets, each = values$ncalts), decodes)
decodes <- decodes[decodes$set == values$survclick,]
decodes <- decodes[,2:ncol(decodes)]
decodes <- t(decodes)
colnames(decodes) <- values$labels
decodes <- cbind("Attributes" = values$atnames,decodes)
decodes
})
output$cssbut <- shiny::renderUI({
shiny::radioButtons("choices", label = "", choices = values$labels, inline = TRUE,
selected = "0")
})
} else if (values$survclick == values$sets+1){
output$css <- NULL
output$cssbut <- NULL
output$texts <- shiny::renderUI({
shiny::markdown(values$outro, .noWS = TRUE)
})
}
# Save responses to the survey
shiny::observeEvent(values$survclick, once = TRUE,{
if (values$survclick > 1 && (values$survclick < values$sets+2)){
current <- c("cs" = values$survclick-1, "choice" = input$choices)
values$choices <- rbind(values$choices, current)
current <- NULL
}
names(values$choices) <- c("task", "choice")
savechoices <<- values$choices
})
if (length(values$choices > 0)){
output$resultsbut <- shiny::renderUI({
shiny::actionButton("resultsgo", "Analyze the results")
})
}
}) # End of the function to show the choice sets
# Count the number of respondents
shiny::observeEvent(input$contsurv, {
values$respondents <- floor(nrow(values$choices) / values$sets)
# Add the design to the accumulated frame
if (values$respondents == 0){
values$designstor <- values$design
}
})
#Load old or new design depending on the mode
shiny::observeEvent(input$nextresp, {
if (input$serialmode == "no"){
values$survclick <- 0
} else if (input$serialmode == "pure"){
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray %>% tidyr::drop_na(num)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
#extract the regressors' name to input it in the model
regressors <- names(cdesmat[,4:(ncol(cdesmat)-1)])
regressors <- paste0('`',regressors, '`')
clog <- survival::clogit(stats::as.formula(paste0("choice ~ ",do.call(paste, c(as.list(regressors), sep = " + ")), " + strata(task)")),
data = as.data.frame(cdesmat))
clog <- summary(clog)
clog$coefficients <- as.data.frame(clog$coefficients)
clog <- cbind(clog$coefficients[,1],clog$coefficients[,5])
clog <- cbind(clog,ifelse(clog[,2] <= 0.05, clog[,1], 0))
if(sum(clog[,3]) != 0){
for (i in 1:length(clog[,3])){
if (clog[,3][i] != 0){
values$priors[i] <- clog[,3][i]
}
}
# Decide if bayesian
if (values$bayesian == TRUE){
alg = "cea"
} else {
alg = "fedorov"
}
values$alg <- alg
# Priors
if (values$bayesian == TRUE){
values$bpriors <- mvtnorm::rmvnorm(100, values$priors, diag(length(values$priors)))
} else {
values$bpriors <- values$priors
}
# Generate
design <- dce_toolbox(attributes = values$levels, csets = values$sets,
alts = values$alts, nochoice = values$optout,
priors = values$bpriors, alg = alg)
design <- design$design
#Replace the global design
tempnam <- colnames(values$design)
colnames(design) <- tempnam
values$design <- design
}
} else if (input$serialmode == "five"){
if ((values$respondents+1) %% 5 == 0){
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray %>% tidyr::drop_na(num)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
#extract the regressors' name to input it in the model
regressors <- names(cdesmat[,4:(ncol(cdesmat)-1)])
regressors <- paste0('`',regressors, '`')
clog <- survival::clogit(stats::as.formula(paste0("choice ~ ",do.call(paste, c(as.list(regressors), sep = " + ")), " + strata(task)")),
data = as.data.frame(cdesmat))
clog <- summary(clog)
clog$coefficients <- as.data.frame(clog$coefficients)
clog <- cbind(clog$coefficients[,1],clog$coefficients[,5])
clog <- cbind(clog,ifelse(clog[,2] <= 0.05, clog[,1], 0))
if(sum(clog[,3]) != 0){
for (i in 1:length(clog[,3])){
if (clog[,3][i] != 0){
values$priors[i] <- clog[,3][i]
}
}
# Decide if bayesian
if (values$bayesian == TRUE){
alg = "cea"
} else {
alg = "fedorov"
}
values$alg <- alg
# Priors
if (values$bayesian == TRUE){
values$bpriors <- mvtnorm::rmvnorm(100, values$priors, diag(length(values$priors)))
} else {
values$bpriors <- values$priors
}
# Generate
design <- dce_toolbox(attributes = values$levels, csets = values$sets,
alts = values$alts, nochoice = values$optout,
priors = values$bpriors, alg = alg)
design <- design$design
#Replace the global design
tempnam <- colnames(values$design)
colnames(design) <- tempnam
values$design <- design
}
} else {
values$survclick <- 0
}
}
#Reload the choice sets
values$designstor <- rbind(values$designstor, values$design)
designstor <- values$designstor
values$survclick <- 0
})
}) # End of the popup
# Move to results when click on analyze the survey
shiny::observeEvent(input$resultsgo, {
shiny::updateTabsetPanel(session, 'inTabset', selected = "results")
#detect if the number of responses correspond to the designs stored
storedchoices <- nrow(savechoices)*values$ncalts
#if they are the same then reshape the dataset
if (storedchoices == nrow(values$designstor)){
#Reshape and present
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
resultados <<- cdesmat
cdesmat$gid <- rep(1:(nrow(cdesmat)/values$ncalts), each = values$ncalts)
values$cdesmat <- cdesmat
# Render the table with the results
output$restable <- DT::renderDT({
cdesmat
})
} else if (storedchoices != nrow(values$designstor)){
#Cut the design storage if it's bigger than the response
values$designstor <- values$designstor[1:storedchoices,]
#Now reshape the database
larray <- merge(cbind("num" = seq(len = nrow(savechoices)),savechoices), cbind("choice" = values$labels, "userselect" = seq(len = length(values$labels))), by = c("choice"), all = TRUE)
larray <- larray[order(larray$num),]
larray$pid <- rep(1:(nrow(larray)/values$sets), len = nrow(savechoices), each = values$sets)
designstor <- values$designstor
designstor$pid <- rep(1:(nrow(designstor)/(values$ncalts*values$sets)), each = (values$sets*values$ncalts))
larray <- merge(designstor, larray, by = c("pid","task"), order = TRUE)
larray <- larray[order(larray$pid,larray$num),]
larray$choice <- NULL
larray$num <- NULL
larray$choice <- ifelse(larray$userselect == larray$alt, 1, 0)
larray$userselect <- NULL
cdesmat <- larray
resultados <<- cdesmat
cdesmat$gid <- rep(1:(nrow(cdesmat)/values$ncalts), each = values$ncalts)
values$cdesmat <- cdesmat
# Render the table with the results
output$restable <- DT::renderDT({
cdesmat
})
}
})
# Download the coded design
output$downloadresults <- shiny::downloadHandler(
filename = function() {"results.xlsx"},
content = function(file) {
writexl::write_xlsx(values$cdesmat, file)}
)
#Load a results
shiny::observeEvent(input$loadresults, {
# Design loader
output$restable <- DT::renderDT({
values$cdesmat <- readxl::read_excel(input$loadresults$datapath) #Update
})
})
# Estimate a conditional logit
shiny::observeEvent(input$modelname, {
cdesmat <- values$cdesmat
output$modopt <- NULL
if (input$modelname == "clogit"){
output$modopt <- shiny::renderUI({
options <- htmltools::tagList(
shinyWidgets::pickerInput("dep", "Dependent variable", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("ind", "Independent variables", choices = colnames(cdesmat), multiple = TRUE),
shinyWidgets::pickerInput("gid", "Group variable", choices = colnames(cdesmat), multiple = FALSE),
shiny::actionButton("goest", "Estimate")
)
options
})
} else if (input$modelname == "nullselect"){
output$modopt <- NULL
} else if (input$modelname == "mixlogit"){
output$modopt <- shiny::renderUI({
options <- htmltools::tagList(
shinyWidgets::pickerInput("dep", "Dependent variable", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("ind", "Independent variables", choices = colnames(cdesmat), multiple = TRUE),
shinyWidgets::pickerInput("gid", "Group variable", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("pid", "Individual identificator", choices = colnames(cdesmat), multiple = FALSE),
shinyWidgets::pickerInput("alt", "Alternative identificator", choices = colnames(cdesmat), multiple = FALSE),
shiny::actionButton("goest", "Estimate")
)
options
})
} else if (input$modelname == "wtp"){
output$modopt <- shiny::renderUI({
options <- htmltools::tagList(
shinyWidgets::pickerInput("pr", "Continuous 'price' variable", choices = rownames(values$clog$coefficients), multiple = FALSE),
shinyWidgets::pickerInput("rl", "Rest of levels", choices = rownames(values$clog$coefficients), multiple = TRUE),
shiny::actionButton("goest", "Estimate")
)
options
})
} else if (input$modelname == "figures"){
ui <- htmltools::tagList(
shinyWidgets::pickerInput("coefs", "Select levels to plot", choices = rownames(values$clog$coefficients), multiple = TRUE),
shiny::actionButton("plotit", "Create figure")
#numericInput("ngrup", "Number of groups (attributes)", value = 0)
)
output$modopt <- shiny::renderUI({
ui
})
}
})
# Future implementation
# observeEvent(input$ngrup,{
# output$modopt2 <- renderUI({
# if (input$ngrup > 0) {
# tags <- tagList()
# for (i in seq_len(input$ngrup)) {
# tags[[i]] <- textInput(paste0('gr', i),
# paste0('Name group ', i))
# }
# tags[[i+1]] <- actionButton("plotit", "Create figure")
# tags
# } else {
# actionButton("plotit", "Create figure")
# }
# })
# })
# Estimations
shiny::observeEvent(input$goest, {
cdesmat <- values$cdesmat
if (input$modelname == "clogit"){
ind <- input$ind
ind <- paste0("`",ind, "`")
dep <- input$dep
dep <- paste0("`",dep, "`")
clog <- survival::clogit(stats::as.formula(paste0(paste0(dep," ~"),do.call(paste, c(as.list(ind), sep = " + ")), " + strata(",paste0(input$gid) ,")")),
data = as.data.frame(cdesmat))
clog <- summary(clog)
#Render the results
output$clog <- shiny::renderPrint({
clog
})
clog <<- clog
values$clog <- clog
### Mixlogit
} else if (input$modelname == "mixlogit"){
dep <- input$dep
dep <- paste0("`",dep, "`")
gid <- input$gid
alt <- input$alt
pid <- input$pid
ind <- input$ind
ind <- paste0("`",ind, "`")
rpar <- c()
for (i in 1:length(ind)){
rpar <- append(rpar, "n")
}
names(rpar) <- ind
ind <- input$ind
ind <- paste0("`",ind, "`")
cdesmat$choice <- as.logical(cdesmat$choice)
disMIX <- dfidx::dfidx(cdesmat, choice="choice", idx = list(c(paste0(gid), paste0(pid)), paste0(alt)), idnames= c("cs", "alt"))
modeloMIX <- try(mlogit::mlogit(stats::as.formula(paste0(paste0(dep," ~"),do.call(paste, c(as.list(ind), sep = " + ")), " | 0")), disMIX,
rpar = rpar, R = 100, halton = NA))
clog <- summary(modeloMIX)
if (typeof(clog) == "character"){
ind <- input$ind
rpar <- c()
for (i in 1:length(ind)){
rpar <- append(rpar, "n")
}
names(rpar) <- ind
ind <- input$ind
ind <- paste0("`",ind, "`")
cdesmat$choice <- as.logical(cdesmat$choice)
disMIX <- dfidx::dfidx(cdesmat, choice="choice", idx = list(c(paste0(gid), paste0(pid)), paste0(alt)), idnames= c("cs", "alt"))
modeloMIX <- try(mlogit::mlogit(stats::as.formula(paste0(paste0(dep," ~"),do.call(paste, c(as.list(ind), sep = " + ")), " | 0")), disMIX,
rpar = rpar, R = 100, halton = NA))
clog <- summary(modeloMIX)
if (typeof(clog) == "character"){
clog <- "There is a problem related with the variable names. More likely, you combined level names with and without numbers and blank spaces. Save the design and modify the excel file by deleting all numbers and blanks from the variable names."
}
}
#Render the results
output$clog <- shiny::renderPrint({
clog
})
} else if (input$modelname == "wtp") {
if (is.null(values$clog)){
output$clog <- shiny::renderPrint({
"First estimate the conditional logit"
})
} else {
reswtp <- as.data.frame(values$clog$coefficients)
results <- -reswtp[input$rl,]/as.numeric(reswtp[input$pr,][1])
output$clog <- shiny::renderPrint({
results
})
}
}
})
# If click on figures, render the graph based on the coefficients of the clogit and the user selection
shiny::observeEvent(input$modelname,{
if (input$modelname == "figures"){
shiny::observeEvent(input$plotit, {
if (!is.null(values$clog)){
df <- data.frame(names = input$coefs, y = values$clog$coefficients[,1][input$coefs], se = values$clog$coefficients[,3][input$coefs])
values$df <- df
output$clog <- NULL
output$figure <- shiny::renderPlot(
ggplot2::ggplot(df, aes(x=names, y=y)) + geom_bar(stat = "identity", fill="skyblue", alpha=0.7) +
geom_errorbar( ggplot2::aes(x=names, ymin=y-se, ymax=y+se), width=0.4, colour="orange", alpha=0.9, size=1.3)
)
} else {
output$clog <- shiny::renderPrint(
"First, estimate a conditional logit model."
)
}
})
}
})
# Change level names and axis names in the graph
shiny::observeEvent(input$plotit, {
tl <- htmltools::tagList()
for (i in 1:length(input$coefs)){
tl[[i]] <- shiny::textInput(inputId = paste0("coefplot", i), label = paste0(input$coefs[i]), value = paste0(input$coefs[i]))
}
tl[[i+1]] <- shiny::textInput(inputId = "xlabnew", "X axis")
tl[[i+2]] <- shiny::textInput(inputId = "ylabnew", "Y axis")
tl[[i+3]] <- actionButton(inputId = "changenames", label = "Change names")
output$modopt2 <- shiny::renderUI({
tl
})
})
shiny::observeEvent(input$changenames, {
newnames <- c()
for (i in 1:length(input$coefs)){
newnames <- append(newnames, eval(parse(text = paste0("input$coefplot", i))))
}
output$figure <- shiny::renderPlot(
ggplot2::ggplot(values$df, aes(x=names, y=y)) + geom_bar(stat = "identity", fill="skyblue", alpha=0.7) +
geom_errorbar( aes(x=names, ymin=y-se, ymax=y+se), width=0.4, colour="orange", alpha=0.9, size=2) +
scale_x_discrete(labels = newnames) + xlab(input$xlabnew) + ylab(input$ylabnew)
)
})
shiny::observeEvent(input$pricevarcoding, {
if (input$pricevarcoding == "cont"){
cdesmat <- values$cdesmat
regressors <- names(cdesmat[,4:(ncol(cdesmat)-1)])
output$atpriceselect <- shiny::renderUI({
checkboxGroupInput(
inputId = "pricelevs",
label = "Select price levels",
choices = names(cdesmat)
)
})
output$savethem <- shiny::renderUI({
actionButton("savepricelevs", "Save price levels")
})
} else if (input$pricevarcoding == "already"){
cdesmat <- values$cdesmat
output$atpriceselect <- shiny::renderUI({
checkboxGroupInput(
inputId = "selectedcontvar",
label = "Select the continuous price variable",
choices = names(cdesmat)
)
})
}
})
shiny::observeEvent(input$pricevarcoding, {
if (!is.null(input$selectedcontvar)){
cdesmat <- values$cdesmat
cdesmat$price <- eval(parse(text = paste0("cdesmat$selectedcontvar")))
}
})
shiny::observeEvent(input$savepricelevs, {
pricevect <- input$pricelevs
output$pricelevbr <- shiny::renderUI({
tags <- htmltools::tagList()
for (i in 1:length(input$pricelevs)) {
tags[[i]] <- shiny::numericInput(paste0('pricelev', i),
paste0(input$pricelevs[i]),
0)
}
omittedlev <- shiny::numericInput("omlev", "Omitted level (In monetary units)", value = 0)
tags <- htmltools::tagList(omittedlev, tags, actionButton("sprc", "Add variable to the data frame"))
tags
})
})
shiny::observeEvent(input$sprc, {
cdesmat <- values$cdesmat
if (!is.null(cdesmat$cont_price)){
cdesmat$cont_price <- NULL
} else if (is.null(cdesmat$cont_price)){
pricelevs <- input$pricelevs
cdesmat$cont_price <- ifelse(rowSums(cdesmat[colnames(cdesmat) == pricelevs]) == 0, input$omlev, NA)
for (i in 1:length(pricelevs)){
inppric <- pricelevs[i]
cdesmat$cont_price <- ifelse(eval(parse(text = paste0("cdesmat$`", inppric,"`")))== 1, eval(parse(text = paste0("input$pricelev", i))) , cdesmat$cont_price)
}
cdesmat <- cbind(cdesmat[,1:(ncol(cdesmat)-2)], "cont_price" = cdesmat[,ncol(cdesmat):ncol(cdesmat)], "gid" = cdesmat[,(ncol(cdesmat)-1):(ncol(cdesmat)-1)])
values$cdesmat <- cdesmat
}
output$restable <- DT::renderDT({
values$cdesmat
})
output$pricelevbr <- NULL
})
shiny::observe({
if (shiny::req(input$inTabset == "About")){
x <- adjustedcranlogs::adj_cran_downloads("DCEtool",when="last-month")[,c(1,3)]
}
output$downloads <- shiny::renderPlot({
if (!is.null(x)) {
barplot(count ~ date, data = x)
}
})
})
}
shinyApp(ui, server)
}
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