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#' @title jsSurveyGadget: Shiny Gadget of survey data analysis.
#' @description Shiny Gadget including Data, Label info, Table 1, svyglm, Basic plot
#' @param data data
#' @param nfactor.limit nlevels limit for categorical variables
#' @return Shiny Gadget including Data, Label info, Table 1, svyglm, Basic plot
#' @details Shiny Gadget including Data, Label info, Table 1, svyglm, Basic plot
#' @examples
#' if (interactive()) {
#' jsSurveyGadget(mtcars)
#' }
#' @rdname jsSurveyGadget
#' @export
#' @importFrom GGally ggpairs
#' @importFrom stats as.formula binomial
#' @importFrom data.table data.table := .SD
#' @importFrom DT datatable %>% formatStyle styleEqual renderDT DTOutput
#' @importFrom shinycustomloader withLoader
#' @importFrom jstable opt.data opt.tb1 opt.tbreg
#' @importFrom survey svyglm
#' @import ggplot2
#' @import shiny
jsSurveyGadget <- function(data, nfactor.limit = 20) {
requireNamespace("survival")
# requireNamespace("survC1")
options(survey.lonely.psu = "certainty")
## To remove NOTE.
val_label <- BinaryGroupRandom <- variable <- NULL
out <- data.table(data, check.names = F)
name.old <- names(out)
out <- data.table(data, check.names = T)
name.new <- names(out)
# ref <- data.table(name.old = name.old, name.new = name.new);setkey(ref, name.new)
ref <- list(name.old = name.old, name.new = name.new)
## factor variable
factor_vars <- names(out)[out[, lapply(.SD, class) %in% c("factor", "character")]]
out[, (factor_vars) := lapply(.SD, as.factor), .SDcols = factor_vars]
conti_vars <- setdiff(names(out), factor_vars)
nclass <- unlist(out[, lapply(.SD, function(x) {
length(unique(x))
}), .SDcols = conti_vars])
# except_vars <- names(nclass)[ nclass== 1 | nclass >= 10]
add_vars <- names(nclass)[nclass >= 1 & nclass <= 5]
data.list <- list(data = out, factor_original = factor_vars, conti_original = conti_vars, factor_adds_list = names(nclass)[nclass <= nfactor.limit], factor_adds = add_vars)
ui <- navbarPage(
"Survey data analysis",
tabPanel("Data",
icon = icon("table"),
sidebarLayout(
sidebarPanel(
uiOutput("factor"),
uiOutput("survey"),
uiOutput("binary_check"),
uiOutput("binary_var"),
uiOutput("binary_val"),
uiOutput("ref_check"),
uiOutput("ref_var"),
uiOutput("ref_val"),
uiOutput("subset_check"),
uiOutput("subset_var"),
uiOutput("subset_val")
),
mainPanel(
tabsetPanel(
type = "pills",
tabPanel("Data", withLoader(DTOutput("data"), type = "html", loader = "loader6")),
tabPanel("Label", withLoader(DTOutput("data_label", width = "100%"), type = "html", loader = "loader6"))
)
)
)
),
tabPanel("Table 1",
icon = icon("percentage"),
sidebarLayout(
sidebarPanel(
tb1moduleUI("tb1")
),
mainPanel(
tabsetPanel(
type = "pills",
tabPanel(
"Unweighted",
withLoader(DTOutput("untable1"), type = "html", loader = "loader6"),
wellPanel(
h5("Normal continuous variables are summarized with Mean (SD) and t-test(2 groups) or ANOVA(> 2 groups)"),
h5("Non-normal continuous variables are summarized with median [IQR or min,max] and kruskal-wallis test"),
h5("Categorical variables are summarized with table")
)
),
tabPanel(
"Weighted",
withLoader(DTOutput("table1"), type = "html", loader = "loader6"),
wellPanel(
h5("Normal continuous variables are summarized with Mean (SD) and complex survey regression"),
h5("Non-normal continuous variables are summarized with median [IQR or min,max] and complex sampling rank test"),
h5("Categorical variables are summarized with table and svychisq test")
)
)
)
)
)
),
navbarMenu("Survey regression",
icon = icon("list-alt"),
tabPanel(
"Linear",
sidebarLayout(
sidebarPanel(
regressModuleUI("linear")
),
mainPanel(
withLoader(DTOutput("lineartable"), type = "html", loader = "loader6")
)
)
),
tabPanel(
"Binomial",
sidebarLayout(
sidebarPanel(
regressModuleUI("logistic")
),
mainPanel(
withLoader(DTOutput("logistictable"), type = "html", loader = "loader6")
)
)
),
tabPanel(
"Cox model",
sidebarLayout(
sidebarPanel(
coxUI("cox")
),
mainPanel(
withLoader(DTOutput("coxtable"), type = "html", loader = "loader6")
)
)
)
),
navbarMenu("Plot",
icon = icon("bar-chart-o"),
tabPanel(
"Scatter plot",
sidebarLayout(
sidebarPanel(
ggpairsModuleUI1("ggpairs")
),
mainPanel(
withLoader(plotOutput("ggpairs_plot"), type = "html", loader = "loader6"),
ggpairsModuleUI2("ggpairs")
)
)
),
tabPanel(
"Kaplan-meier plot",
sidebarLayout(
sidebarPanel(
kaplanUI("kaplan")
),
mainPanel(
optionUI("kaplan"),
withLoader(plotOutput("kaplan_plot"), type = "html", loader = "loader6"),
ggplotdownUI("kaplan")
)
)
)
),
navbarMenu("ROC analysis",
icon = icon("check"),
tabPanel(
"ROC",
sidebarLayout(
sidebarPanel(
rocUI("roc")
),
mainPanel(
withLoader(plotOutput("plot_roc"), type = "html", loader = "loader6"),
ggplotdownUI("roc"),
withLoader(DTOutput("table_roc"), type = "html", loader = "loader6")
)
)
),
tabPanel(
"Time-dependent ROC",
sidebarLayout(
sidebarPanel(
timerocUI("timeroc")
),
mainPanel(
withLoader(plotOutput("plot_timeroc"), type = "html", loader = "loader6"),
ggplotdownUI("timeroc"),
withLoader(DTOutput("table_timeroc"), type = "html", loader = "loader6")
)
)
)
)
)
server <- function(input, output, session) {
output$factor <- renderUI({
selectInput("factor_vname",
label = "Additional categorical variables",
choices = data.list$factor_adds_list, multiple = T,
selected = data.list$factor_adds
)
})
observeEvent(input$factor_vname, {
output$survey <- renderUI({
conti_new <- setdiff(data.list$conti_original, input$factor_vname)
# validate(
# need(length(conti_new) > 0, "No candidate variables to be weight.")
# )
candidate.weight <- c("wt", "weight", "Weight", "WEIGHT", "WEIGHTS", "Weights", "weights")
selected.weight <- unlist(purrr::map(candidate.weight, ~ grep(.x, conti_new)))
selected.weight.final <- ifelse(length(selected.weight) > 0, conti_new[selected.weight[1]], "None")
candidate.cluster <- c("psu", "id")
selected.cluster <- unlist(purrr::map(candidate.cluster, ~ grep(.x, names(data.list$data))))
selected.cluster.final <- ifelse(length(selected.cluster) > 0, conti_new[selected.cluster[1]], "None")
candidate.strata <- c("strata")
selected.strata <- unlist(purrr::map(candidate.strata, ~ grep(.x, names(data.list$data))))
selected.strata.final <- ifelse(length(selected.strata) > 0, conti_new[selected.strata[1]], "None")
tagList(
h4(tags$strong("Survey design")),
selectInput(session$ns("cluster_vname"),
label = "Cluster ID",
choices = c("None", names(data.list$data)), multiple = F,
selected = selected.cluster.final
),
selectInput(session$ns("strata_vname"),
label = "Strata",
choices = c("None", names(data.list$data)), multiple = F,
selected = selected.strata.final
),
selectInput(session$ns("weights_vname"),
label = "Weights",
choices = c("None", conti_new), multiple = F,
selected = selected.weight.final
)
)
})
})
observeEvent(c(data.list$factor_original, input$factor_vname, input$repeated_vname, input$cluster_vname, input$strata_vname, input$weights_vname), {
output$binary_check <- renderUI({
checkboxInput("check_binary", "Make binary variables")
})
output$ref_check <- renderUI({
checkboxInput("check_ref", "Change reference of categorical variables")
})
output$subset_check <- renderUI({
checkboxInput("check_subset", "Subset data")
})
var.conti <- setdiff(names(data.list$data), c(data.list$factor_original, input$factor_vname, input$repeated_vname, input$cluster_vname, input$strata_vname, input$weights_vname))
output$binary_var <- renderUI({
req(input$check_binary == T)
selectInput("var_binary", "Variables to dichotomize",
choices = var.conti, multiple = T,
selected = var.conti[1]
)
})
output$binary_val <- renderUI({
req(input$check_binary == T)
req(length(input$var_binary) > 0)
outUI <- tagList()
for (v in seq_along(input$var_binary)) {
med <- stats::quantile(data.list$data[[input$var_binary[[v]]]], c(0.05, 0.5, 0.95), na.rm = T)
outUI[[v]] <- splitLayout(
cellWidths = c("25%", "75%"),
selectInput(paste0("con_binary", v), paste0("Define reference:"),
choices = c("\u2264", "\u2265", "\u003c", "\u003e"), selected = "\u2264"
),
numericInput(paste0("cut_binary", v), input$var_binary[[v]],
value = med[2], min = med[1], max = med[3]
)
)
}
outUI
})
var.factor <- setdiff(c(data.list$factor_original, input$factor_vname), c(input$repeated_vname, input$cluster_vname, input$strata_vname, input$weights_vname))
output$ref_var <- renderUI({
req(input$check_ref == T)
selectInput("var_ref", "Variables to change reference",
choices = var.factor, multiple = T,
selected = var.factor[1]
)
})
output$ref_val <- renderUI({
req(input$check_ref == T)
req(length(input$var_ref) > 0)
outUI <- tagList()
for (v in seq_along(input$var_ref)) {
outUI[[v]] <- selectInput(paste0("con_ref", v), paste0("Reference: ", input$var_ref[[v]]),
choices = levels(factor(data.list$data[[input$var_ref[[v]]]])), selected = levels(factor(data.list$data[[input$var_ref[[v]]]]))[2]
)
}
outUI
})
})
observeEvent(input$check_subset, {
output$subset_var <- renderUI({
req(input$check_subset == T)
# factor_subset <- setdiff(c(data.list$factor_original, input$factor_vname), c(input$repeated_vname, input$strata_vname, input$weights_vname))
# validate(
# need(length(factor_subset) > 0 , "No factor variable for subsetting")
# )
tagList(
selectInput("var_subset", "Subset variables",
choices = names(data.list$data), multiple = T,
selected = names(data.list$data)[1]
)
)
})
output$subset_val <- renderUI({
req(input$check_subset == T)
req(input$var_subset)
var.factor <- c(data.list$factor_original, input$factor_vname)
outUI <- tagList()
for (v in seq_along(input$var_subset)) {
if (input$var_subset[[v]] %in% var.factor) {
varlevel <- levels(as.factor(data.list$data[[input$var_subset[[v]]]]))
outUI[[v]] <- selectInput(session$ns(paste0("val_subset", v)), paste0("Subset value: ", input$var_subset[[v]]),
choices = varlevel, multiple = T,
selected = varlevel[1]
)
} else {
val <- stats::quantile(data.list$data[[input$var_subset[[v]]]], na.rm = T)
outUI[[v]] <- sliderInput(session$ns(paste0("val_subset", v)), paste0("Subset range: ", input$var_subset[[v]]),
min = val[1], max = val[5],
value = c(val[2], val[4])
)
}
}
outUI
})
})
data.info <- reactive({
req(!is.null(input$check_binary))
out <- data.table::data.table(data.list$data)
out[, (data.list$conti_original) := lapply(.SD, function(x) {
as.numeric(as.vector(x))
}), .SDcols = data.list$conti_original]
if (!is.null(input$factor_vname)) {
out[, (input$factor_vname) := lapply(.SD, as.factor), .SDcols = input$factor_vname]
}
req(input$cluster_vname)
if (input$cluster_vname == "None") {
cluster.survey <- as.formula("~ 1")
} else {
cluster.survey <- as.formula(paste("~", input$cluster_vname))
out <- out[!is.na(get(input$cluster_vname))]
}
if (input$strata_vname == "None") {
strata.survey <- NULL
} else {
strata.survey <- as.formula(paste("~", input$strata_vname))
out <- out[!is.na(get(input$strata_vname))]
}
if (input$weights_vname == "None") {
weights.survey <- NULL
} else {
weights.survey <- as.formula(paste("~", input$weights_vname))
out <- out[!is.na(get(input$weights_vname))]
}
# surveydata <- survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out)
# surveydata <- tryCatch(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out),
# error = function(e){return(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out, nest = T))})
out.label <- mk.lev(out)
if (!is.null(input$check_binary) & input$check_binary) {
validate(
need(length(input$var_binary) > 0, "No variables to dichotomize")
)
sym.ineq <- c("\u2264", "\u2265", "\u003c", "\u003e")
names(sym.ineq) <- sym.ineq[4:1]
sym.ineq2 <- c("le", "ge", "l", "g")
names(sym.ineq2) <- sym.ineq
for (v in seq_along(input$var_binary)) {
req(input[[paste0("con_binary", v)]])
req(input[[paste0("cut_binary", v)]])
if (input[[paste0("con_binary", v)]] == "\u2264") {
out[, BinaryGroupRandom := factor(1 - as.integer(get(input$var_binary[[v]]) <= input[[paste0("cut_binary", v)]]))]
} else if (input[[paste0("con_binary", v)]] == "\u2265") {
out[, BinaryGroupRandom := factor(1 - as.integer(get(input$var_binary[[v]]) >= input[[paste0("cut_binary", v)]]))]
} else if (input[[paste0("con_binary", v)]] == "\u003c") {
out[, BinaryGroupRandom := factor(1 - as.integer(get(input$var_binary[[v]]) < input[[paste0("cut_binary", v)]]))]
} else {
out[, BinaryGroupRandom := factor(1 - as.integer(get(input$var_binary[[v]]) > input[[paste0("cut_binary", v)]]))]
}
cn.new <- paste0(input$var_binary[[v]], "_group_", sym.ineq2[input[[paste0("con_binary", v)]]], input[[paste0("cut_binary", v)]])
data.table::setnames(out, "BinaryGroupRandom", cn.new)
label.binary <- mk.lev(out[, .SD, .SDcols = cn.new])
label.binary[, var_label := paste0(input$var_binary[[v]], "_group")]
label.binary[, val_label := paste0(c(input[[paste0("con_binary", v)]], sym.ineq[input[[paste0("con_binary", v)]]]), " ", input[[paste0("cut_binary", v)]])]
out.label <- rbind(out.label, label.binary)
}
# surveydata <- tryCatch(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out),
# error = function(e){return(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out, nest = T))})
}
if (!is.null(input$check_ref)) {
if (input$check_ref) {
validate(
need(length(input$var_ref) > 0, "No variables to change reference")
)
for (v in seq_along(input$var_ref)) {
req(input[[paste0("con_ref", v)]])
out[[input$var_ref[[v]]]] <- stats::relevel(out[[input$var_ref[[v]]]], ref = input[[paste0("con_ref", v)]])
out.label[variable == input$var_ref[[v]], ":="(level = levels(out[[input$var_ref[[v]]]]), val_label = levels(out[[input$var_ref[[v]]]]))]
}
}
}
if (!is.null(input$check_subset)) {
if (input$check_subset) {
validate(
need(length(input$var_subset) > 0, "No variables for subsetting"),
need(all(sapply(1:length(input$var_subset), function(x) {
length(input[[paste0("val_subset", x)]])
})), "No value for subsetting")
)
var.factor <- c(data.list$factor_original, input$factor_vname)
for (v in seq_along(input$var_subset)) {
if (input$var_subset[[v]] %in% var.factor) {
out <- out[get(input$var_subset[[v]]) %in% input[[paste0("val_subset", v)]]]
# surveydata <- survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out)
# surveydata <- tryCatch(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out),
# error = function(e){return(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out, nest = T))})
# var.factor <- c(data()$factor_original, input$factor_vname)
out[, (var.factor) := lapply(.SD, factor), .SDcols = var.factor]
out.label2 <- mk.lev(out)[, c("variable", "level")]
data.table::setkey(out.label, "variable", "level")
data.table::setkey(out.label2, "variable", "level")
out.label <- out.label[out.label2]
} else {
out <- out[get(input$var_subset[[v]]) >= input[[paste0("val_subset", v)]][1] & get(input$var_subset[[v]]) <= input[[paste0("val_subset", v)]][2]]
# surveydata <- survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out)
# surveydata <- tryCatch(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out),
# error = function(e){return(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out, nest = T))})
# var.factor <- c(data()$factor_original, input$factor_vname)
out[, (var.factor) := lapply(.SD, factor), .SDcols = var.factor]
out.label2 <- mk.lev(out)[, c("variable", "level")]
data.table::setkey(out.label, "variable", "level")
data.table::setkey(out.label2, "variable", "level")
out.label <- out.label[out.label2]
}
}
}
}
# out.label[, var_label := ref[out.label$variable, name.old]]
for (vn in ref[["name.new"]]) {
w <- which(ref[["name.new"]] == vn)
out.label[variable == vn, var_label := ref[["name.old"]][w]]
}
surveydata <- tryCatch(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out),
error = function(e) {
return(survey::svydesign(id = cluster.survey, strata = strata.survey, weights = weights.survey, data = out, nest = T))
}
)
return(list(data = out, label = out.label, survey = surveydata))
})
data <- reactive(data.info()$data)
data.label <- reactive(data.info()$label)
design.survey <- reactive(data.info()$survey)
output$data <- renderDT({
datatable(data(),
rownames = F, editable = F, extensions = "Buttons", caption = "Data",
options = c(jstable::opt.data("data"), list(scrollX = TRUE))
)
})
output$data_label <- renderDT({
datatable(data.label(),
rownames = F, editable = F, extensions = "Buttons", caption = "Label of data",
options = c(jstable::opt.data("label"), list(scrollX = TRUE))
)
})
out_untb1 <- callModule(tb1module2, "tb1", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit, showAllLevels = T)
output$untable1 <- renderDT({
tb <- out_untb1()$table
cap <- out_untb1()$caption
out.tb1 <- datatable(tb,
rownames = T, extensions = "Buttons", caption = cap,
options = c(
jstable::opt.tb1("tb1"),
list(columnDefs = list(list(visible = FALSE, targets = which(colnames(tb) %in% c("test", "sig"))))),
list(scrollX = TRUE)
)
)
if ("sig" %in% colnames(tb)) {
out.tb1 <- out.tb1 %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
}
return(out.tb1)
})
out_tb1 <- callModule(tb1module2, "tb1", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit, design.survey = design.survey, showAllLevels = T)
output$table1 <- renderDT({
tb <- out_tb1()$table
cap <- out_tb1()$caption
out.tb1 <- datatable(tb,
rownames = T, extensions = "Buttons", caption = cap,
options = c(
jstable::opt.tb1("tb1"),
list(columnDefs = list(list(visible = FALSE, targets = which(colnames(tb) %in% c("test", "sig"))))),
list(scrollX = TRUE)
)
)
if ("sig" %in% colnames(tb)) {
out.tb1 <- out.tb1 %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
}
return(out.tb1)
})
out_linear <- callModule(regressModule2, "linear", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit, design.survey = design.survey, default.unires = F)
output$lineartable <- renderDT({
hide <- which(colnames(out_linear()$table) == "sig")
datatable(out_linear()$table,
rownames = T, extensions = "Buttons", caption = out_linear()$caption,
options = c(
jstable::opt.tbreg(out_linear()$caption),
list(columnDefs = list(list(visible = FALSE, targets = hide))),
list(scrollX = TRUE)
)
) %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
})
out_logistic <- callModule(logisticModule2, "logistic", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit, design.survey = design.survey, default.unires = F)
output$logistictable <- renderDT({
hide <- which(colnames(out_logistic()$table) == "sig")
datatable(out_logistic()$table,
rownames = T, extensions = "Buttons", caption = out_logistic()$caption,
options = c(
jstable::opt.tbreg(out_logistic()$caption),
list(columnDefs = list(list(visible = FALSE, targets = hide))),
list(scrollX = TRUE)
)
) %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
})
out_cox <- callModule(coxModule, "cox", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit, design.survey = design.survey, default.unires = F)
output$coxtable <- renderDT({
hide <- which(colnames(out_cox()$table) == c("sig"))
datatable(out_cox()$table,
rownames = T, extensions = "Buttons", caption = out_cox()$caption,
options = c(
opt.tbreg(out_cox()$caption),
list(columnDefs = list(list(visible = FALSE, targets = hide)))
)
) %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
})
out_ggpairs <- callModule(ggpairsModule2, "ggpairs", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
output$ggpairs_plot <- renderPlot({
print(out_ggpairs())
})
out_kaplan <- callModule(kaplanModule, "kaplan", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit, design.survey = design.survey)
output$kaplan_plot <- renderPlot({
print(out_kaplan())
})
out_roc <- callModule(rocModule, "roc", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, nfactor.limit = nfactor.limit)
output$plot_roc <- renderPlot({
print(out_roc()$plot)
})
output$table_roc <- renderDT({
datatable(out_roc()$tb,
rownames = F, editable = F, extensions = "Buttons",
caption = "ROC results",
options = c(jstable::opt.tbreg("roctable"), list(scrollX = TRUE))
)
})
out_timeroc <- callModule(timerocModule, "timeroc", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, nfactor.limit = nfactor.limit)
output$plot_timeroc <- renderPlot({
print(out_timeroc()$plot)
})
output$table_timeroc <- renderDT({
datatable(out_timeroc()$tb,
rownames = F, editable = F, extensions = "Buttons", caption = "ROC results",
options = c(jstable::opt.tbreg("timeroctable"), list(scrollX = TRUE))
)
})
session$onSessionEnded(function() {
stopApp()
})
}
# viewer <- dialogViewer("Descriptive statistics", width = 1100, height = 850)
viewer <- browserViewer(browser = getOption("browser"))
runGadget(ui, server, viewer = viewer)
}
#' @title jsSurveyAddin: Rstudio addin of jsSurveyGadget
#' @description Rstudio addin of jsSurveyGadget
#' @return Rstudio addin of jsSurveyGadget
#' @details Rstudio addin of jsSurveyGadget
#' @examples
#' if (interactive()) {
#' jsSurveydAddin()
#' }
#' @seealso
#' \code{\link[rstudioapi]{rstudio-editors}}
#' @rdname jsSurveyAddin
#' @export
#' @importFrom rstudioapi getActiveDocumentContext
jsSurveyAddin <- function() {
context <- rstudioapi::getActiveDocumentContext()
# Set the default data to use based on the selection.
dataString <- context$selection[[1]]$text
data <- get(dataString, envir = .GlobalEnv)
# viewer <- dialogViewer("Subset", width = 1000, height = 800)
jsSurveyGadget(data, nfactor.limit = 20)
}
#' @title jsSurveyExtAddin: RStudio Addin for survey data analysis with external data.
#' @description RStudio Addin for survey data analysis with external csv/xlsx/sas7bdat/sav/dta file.
#' @param nfactor.limit nlevels limit for categorical variables, Default: 20
#' @param max.filesize Maximum file size to upload (MB), Default: 2048 (2 GB)
#' @return RStudio Addin for survey data analysis with external data.
#' @details RStudio Addin for survey data analysis with external csv/xlsx/sas7bdat/sav/dta file.
#' @examples
#' if (interactive()) {
#' jsSurveyExtAddin()
#' }
#' @seealso
#' \code{\link[data.table]{fwrite}}
#' \code{\link[jstable]{opt.tb1}},\code{\link[jstable]{opt.tbreg}}
#' @rdname jsSurveyExtAddin
#' @export
#' @importFrom data.table fwrite
#' @importFrom jstable opt.tb1 opt.tbreg
#' @importFrom DT datatable %>% formatStyle styleEqual renderDT DTOutput
#' @importFrom shinycustomloader withLoader
#' @importFrom jstable opt.data opt.tb1 opt.tbreg
#' @importFrom utils data
#' @import shiny
jsSurveyExtAddin <- function(nfactor.limit = 20, max.filesize = 2048) {
data.example <- utils::data("nhanes", package = "survey")
options(shiny.maxRequestSize = max.filesize * 1024^2, survey.lonely.psu = "certainty")
ui <- navbarPage(
"Survey data analysis",
tabPanel("Data",
icon = icon("table"),
sidebarLayout(
sidebarPanel(
uiOutput("import"),
downloadButton("downloadData", "Example data")
),
mainPanel(
tabsetPanel(
type = "pills",
tabPanel("Data", withLoader(DTOutput("data"), type = "html", loader = "loader6")),
tabPanel("Label", withLoader(DTOutput("data_label", width = "100%"), type = "html", loader = "loader6"))
),
htmlOutput("naomit")
)
)
),
tabPanel("Table 1",
icon = icon("percentage"),
sidebarLayout(
sidebarPanel(
tb1moduleUI("tb1")
),
mainPanel(
tabsetPanel(
type = "pills",
tabPanel(
"Unweighted",
withLoader(DTOutput("untable1"), type = "html", loader = "loader6"),
wellPanel(
h5("Normal continuous variables are summarized with Mean (SD) and t-test(2 groups) or ANOVA(> 2 groups)"),
h5("Non-normal continuous variables are summarized with median [IQR or min,max] and kruskal-wallis test"),
h5("Categorical variables are summarized with table")
)
),
tabPanel(
"Weighted",
withLoader(DTOutput("table1"), type = "html", loader = "loader6"),
wellPanel(
h5("Normal continuous variables are summarized with Mean (SD) and complex survey regression"),
h5("Non-normal continuous variables are summarized with median [IQR or min,max] and complex sampling rank test"),
h5("Categorical variables are summarized with table and svychisq test")
)
)
)
)
)
),
navbarMenu("Survey regression",
icon = icon("list-alt"),
tabPanel(
"Linear",
sidebarLayout(
sidebarPanel(
regressModuleUI("linear")
),
mainPanel(
withLoader(DTOutput("lineartable"), type = "html", loader = "loader6")
)
)
),
tabPanel(
"Binomial",
sidebarLayout(
sidebarPanel(
regressModuleUI("logistic")
),
mainPanel(
withLoader(DTOutput("logistictable"), type = "html", loader = "loader6")
)
)
),
tabPanel(
"Cox model",
sidebarLayout(
sidebarPanel(
coxUI("cox")
),
mainPanel(
withLoader(DTOutput("coxtable"), type = "html", loader = "loader6")
)
)
)
),
navbarMenu("Plot",
icon = icon("bar-chart-o"),
tabPanel(
"Scatter plot",
sidebarLayout(
sidebarPanel(
ggpairsModuleUI1("ggpairs")
),
mainPanel(
withLoader(plotOutput("ggpairs_plot"), type = "html", loader = "loader6"),
ggpairsModuleUI2("ggpairs")
)
)
),
tabPanel(
"Kaplan-meier plot",
sidebarLayout(
sidebarPanel(
kaplanUI("kaplan")
),
mainPanel(
optionUI("kaplan"),
withLoader(plotOutput("kaplan_plot"), type = "html", loader = "loader6"),
ggplotdownUI("kaplan")
)
)
)
),
navbarMenu("ROC analysis",
icon = icon("check"),
tabPanel(
"ROC",
sidebarLayout(
sidebarPanel(
rocUI("roc")
),
mainPanel(
withLoader(plotOutput("plot_roc"), type = "html", loader = "loader6"),
ggplotdownUI("roc"),
withLoader(DTOutput("table_roc"), type = "html", loader = "loader6")
)
)
),
tabPanel(
"Time-dependent ROC",
sidebarLayout(
sidebarPanel(
timerocUI("timeroc")
),
mainPanel(
withLoader(plotOutput("plot_timeroc"), type = "html", loader = "loader6"),
ggplotdownUI("timeroc"),
withLoader(DTOutput("table_timeroc"), type = "html", loader = "loader6")
)
)
)
)
)
server <- function(input, output, session) {
output$downloadData <- downloadHandler(
filename = function() {
paste("example_survey", ".csv", sep = "")
},
content = function(file) {
data.table::fwrite(get(data.example), file)
}
)
output$import <- renderUI({
FileSurveyInput("datafile")
})
data.info <- callModule(FileSurvey, "datafile", nfactor.limit = nfactor.limit)
data <- reactive(data.info()$data)
data.label <- reactive(data.info()$label)
id.weight.survey <- reactive(data.info()$id.weight.survey)
design.survey <- reactive(data.info()$survey)
output$data <- renderDT({
datatable(data(),
rownames = F, editable = F, extensions = "Buttons", caption = "Data",
options = c(opt.data("data"), list(scrollX = TRUE))
)
})
output$data_label <- renderDT({
datatable(data.label(),
rownames = F, editable = F, extensions = "Buttons", caption = "Label of data",
options = c(opt.data("label"), list(scrollX = TRUE))
)
})
output$naomit <- renderText({
data.info()$naomit
})
out_untb1 <- callModule(tb1module2, "tb1", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
output$untable1 <- renderDT({
tb <- out_untb1()$table
cap <- out_untb1()$caption
out.tb1 <- datatable(tb,
rownames = T, extensions = "Buttons", caption = cap,
options = c(
jstable::opt.tb1("tb1"),
list(columnDefs = list(list(visible = FALSE, targets = which(colnames(tb) %in% c("test", "sig"))))),
list(scrollX = TRUE)
)
)
if ("sig" %in% colnames(tb)) {
out.tb1 <- out.tb1 %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
}
return(out.tb1)
})
out_tb1 <- callModule(tb1module2, "tb1", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, nfactor.limit = nfactor.limit)
output$table1 <- renderDT({
tb <- out_tb1()$table
cap <- out_tb1()$caption
out.tb1 <- datatable(tb,
rownames = T, extensions = "Buttons", caption = cap,
options = c(
opt.tb1("tb1"),
list(columnDefs = list(list(visible = FALSE, targets = which(colnames(tb) %in% c("test", "sig"))))),
list(scrollX = TRUE)
)
)
if ("sig" %in% colnames(tb)) {
out.tb1 <- out.tb1 %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
}
return(out.tb1)
})
out_linear <- callModule(regressModule2, "linear", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, default.unires = F, nfactor.limit = nfactor.limit)
output$lineartable <- renderDT({
hide <- which(colnames(out_linear()$table) == "sig")
datatable(out_linear()$table,
rownames = T, extensions = "Buttons", caption = out_linear()$caption,
options = c(
opt.tbreg(out_linear()$caption),
list(columnDefs = list(list(visible = FALSE, targets = hide))),
list(scrollX = TRUE)
)
) %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
})
out_logistic <- callModule(logisticModule2, "logistic", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, default.unires = F, nfactor.limit = nfactor.limit)
output$logistictable <- renderDT({
hide <- which(colnames(out_logistic()$table) == "sig")
datatable(out_logistic()$table,
rownames = T, extensions = "Buttons", caption = out_logistic()$caption,
options = c(
opt.tbreg(out_logistic()$caption),
list(columnDefs = list(list(visible = FALSE, targets = hide))),
list(scrollX = TRUE)
)
) %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
})
out_cox <- callModule(coxModule, "cox", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, default.unires = F, nfactor.limit = nfactor.limit)
output$coxtable <- renderDT({
hide <- which(colnames(out_cox()$table) == c("sig"))
datatable(out_cox()$table,
rownames = T, extensions = "Buttons", caption = out_cox()$caption,
options = c(
opt.tbreg(out_cox()$caption),
list(columnDefs = list(list(visible = FALSE, targets = hide)))
)
) %>% formatStyle("sig", target = "row", backgroundColor = styleEqual("**", "yellow"))
})
out_ggpairs <- callModule(ggpairsModule2, "ggpairs", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
output$ggpairs_plot <- renderPlot({
print(out_ggpairs())
})
out_kaplan <- callModule(kaplanModule, "kaplan", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, nfactor.limit = nfactor.limit)
output$kaplan_plot <- renderPlot({
print(out_kaplan())
})
out_roc <- callModule(rocModule, "roc", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, nfactor.limit = nfactor.limit)
output$plot_roc <- renderPlot({
print(out_roc()$plot)
})
output$table_roc <- renderDT({
datatable(out_roc()$tb,
rownames = F, editable = F, extensions = "Buttons",
caption = "ROC results",
options = c(jstable::opt.tbreg("roctable"), list(scrollX = TRUE))
)
})
out_timeroc <- callModule(timerocModule, "timeroc", data = data, data_label = data.label, data_varStruct = NULL, design.survey = design.survey, nfactor.limit = nfactor.limit)
output$plot_timeroc <- renderPlot({
print(out_timeroc()$plot)
})
output$table_timeroc <- renderDT({
datatable(out_timeroc()$tb,
rownames = F, editable = F, extensions = "Buttons", caption = "ROC results",
options = c(jstable::opt.tbreg("roctable"), list(scrollX = TRUE))
)
})
session$onSessionEnded(function() {
stopApp()
})
}
# viewer <- dialogViewer("Descriptive statistics", width = 1100, height = 850)
viewer <- browserViewer(browser = getOption("browser"))
runGadget(ui, server, viewer = viewer)
}
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