moved app to correctly include in package and allow load with dataset

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: webResearch
 Title: Browser Based Data Analysis
-Version: 0.0.0.9000
+Version: 24.11.1
 Authors@R: 
     person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154"))
@@ -14,7 +14,6 @@ Imports:
     bslib,
     dplyr,
     glue,
-    gt,
     gtsummary,
     haven,
     here,

NAMESPACE

@@ -2,10 +2,11 @@
 
 export(argsstring2list)
 export(baseline_table)
-export(file_extension)
 export(getfun)
+export(panel_space)
 export(read_input)
 export(regression_model)
 export(regression_table)
+export(shiny_webResearch)
 export(write_quarto)
 importFrom(stats,as.formula)

R/app.R

@@ -0,0 +1,34 @@
+#' Test version of the shiny_cast function to launch the app with a data set in
+#' the environment.
+#'
+#' @param data optional data set to provide for analysis
+#' @param ... arguments passed on to `shiny::runApp()`
+#'
+#' @return shiny app
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' mtcars |> shiny_webResearch(launch.browser = TRUE)
+#' }
+shiny_webResearch <- function(data = NULL, ...) {
+  appDir <- system.file("apps", "data_analysis", package = "webResearch")
+  if (appDir == "") {
+    stop("Could not find example directory. Try re-installing `webResearch`.", call. = FALSE)
+  }
+
+  G <- .GlobalEnv
+  assign("webResearch_data", data, envir = G)
+  a <- shiny::runApp(appDir = appDir, ...)
+  return(invisible(a))
+}
+
+
+#' Wrapping nav_spacer to avoid errors on dependencies when packaging
+#'
+#' @return bslib object
+#' @export
+#'
+panel_space <- function() {
+  bslib::nav_spacer()
+}

R/baseline_table.R

@@ -13,7 +13,7 @@
 #' mtcars |> baseline_table(fun.args = list(by = "gear"))
 baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) {
   if (!is.null(vars)) {
-    data <- dplyr::select(dplyr::all_of(vars))
+    data <- data |> dplyr::select(dplyr::all_of(vars))
   }
 
   out <- do.call(fun, c(list(data = data), fun.args))

R/helpers.R

@@ -48,24 +48,6 @@ write_quarto <- function(data,fileformat,qmd.file=here::here("analyses.qmd"),fil
   )
 }
 
-#' Helper to import files correctly
-#'
-#' @param filenames file names
-#'
-#' @return character vector
-#' @export
-#'
-#' @examples
-#' file_extension(list.files(here::here(""))[[2]])[[1]]
-#' file_extension(c("file.cd..ks", "file"))
-file_extension <- function(filenames) {
-  sub(
-    pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "",
-    filenames,
-    perl = TRUE
-  )
-}
-
 #' Flexible file import based on extension
 #'
 #' @param file file name
@@ -77,7 +59,7 @@ file_extension <- function(filenames) {
 #' @examples
 #' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
 read_input <- function(file, consider.na = c("NA", '""', "")) {
-  ext <- file_extension(file)
+  ext <- tools::file_ext(file)
 
   if (ext == "csv") {
     df <- readr::read_csv(file = file, na = consider.na)
@@ -86,10 +68,12 @@ read_input <- function(file, consider.na = c("NA", '""', "")) {
   } else if (ext == "dta") {
     df <- haven::read_dta(file = file)
   } else if (ext == "ods") {
-    df <- readODS::read_ods(file = file)
+    df <- readODS::read_ods(path = file)
+  } else if (ext == "rds") {
+    df <- readr::read_rds(file = file)
   } else {
     stop("Input file format has to be on of:
-             '.csv', '.xls', '.xlsx', '.dta' or '.ods'")
+             '.csv', '.xls', '.xlsx', '.dta', '.ods' or '.rds'")
   }
 
   df

R/regression_model.R

@@ -4,7 +4,7 @@
 #' @param fun Name of function as character vector or function to use for model creation.
 #' @param vars character vector of variables to include
 #' @param outcome.str Name of outcome variable. Character vector.
-#' @param auto.mode Make assumptions on function dependent on outcome data format.
+#' @param auto.mode Make assumptions on function dependent on outcome data format. Overwrites other arguments.
 #' @param formula.str Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.
 #' @param args.list List of arguments passed to 'fun' with 'do.call'.
 #'
@@ -15,16 +15,18 @@
 #'
 #' @examples
 #' gtsummary::trial |>
-#'   regression_model(outcome.str = "age",)
+#'   regression_model(outcome.str = "age")
 #' gtsummary::trial |>
 #'   regression_model(
 #'     outcome.str = "age",
+#'     auto.mode = FALSE,
 #'     fun = "stats::lm",
 #'     formula.str = "{outcome.str}~.",
 #'     args.list = NULL
 #'   )
 #' gtsummary::trial |> regression_model(
 #'   outcome.str = "trt",
+#'   auto.mode = FALSE,
 #'   fun = "stats::glm",
 #'   args.list = list(family = binomial(link = "logit"))
 #' )
@@ -35,9 +37,11 @@ regression_model <- function(data,
                              args.list = NULL,
                              fun = NULL,
                              vars = NULL) {
-  if (formula.str==""){
+  if (!is.null(formula.str)) {
+    if (formula.str == "") {
       formula.str <- NULL
     }
+  }
 
   if (!is.null(formula.str)) {
     formula.str <- glue::glue(formula.str)
@@ -66,7 +70,7 @@ regression_model <- function(data,
     } else if (is.factor(data[[outcome.str]])) {
       if (length(levels(data[[outcome.str]])) == 2) {
         fun <- "stats::glm"
-        args.list <- list(family = binomial(link = "logit"))
+        args.list <- list(family = stats::binomial(link = "logit"))
       } else if (length(levels(data[[outcome.str]])) > 2) {
         fun <- "MASS::polr"
         args.list <- list(

R/regression_table.R

@@ -13,7 +13,7 @@
 #'     outcome.str = "stage",
 #'     fun = "MASS::polr"
 #'   ) |>
-#'   regression_table(args.list = list(exponentiate = TRUE))
+#'   regression_table(args.list = list("exponentiate" = TRUE))
 #' gtsummary::trial |>
 #'   regression_model(
 #'     outcome.str = "age",
@@ -32,8 +32,10 @@
 regression_table <- function(data, args.list = NULL, fun = "gtsummary::tbl_regression") {
 
   if (any(c(length(class(data))!=1, class(data)!="lm"))){
+    if (!"exponentiate" %in% names(args.list)){
       args.list <- c(args.list,list(exponentiate=TRUE))
     }
+  }
 
   out <- do.call(getfun(fun), c(list(x = data), args.list))
   return(out)

app/ui.R

@@ -1,140 +0,0 @@
-require(shiny)
-require(bslib)
-# require(ggplot2)
-# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/index_from_raw.R")
-# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/plot_index.R")
-# source(here::here("R/index_from_raw.R"))
-# source(here::here("R/plot_index.R"))
-
-# ui <- fluidPage(
-
-cards <- list(
-  bslib::card(
-    max_height = "200px",
-    full_screen = TRUE,
-    bslib::card_header("Data overview"),
-    shiny::uiOutput("data.input")
-  ),
-  bslib::card(
-    # max_height = "200px",
-    full_screen = TRUE,
-    bslib::card_header("Baseline characteristics"),
-    gt::gt_output(outputId = "table1")
-  ),
-  bslib::card(
-    full_screen = TRUE,
-    bslib::card_header("Multivariable regression table"),
-    gt::gt_output(outputId = "table2")
-  )
-)
-
-panels <- list(
-  bslib::nav_panel(title="Data overview",
-                   shiny::uiOutput("data.input")),
-  bslib::nav_panel(title="Baseline characteristics",
-                   gt::gt_output(outputId = "table1")),
-  bslib::nav_panel(title="Multivariable regression table",
-                   gt::gt_output(outputId = "table2"))
-)
-
-
-ui <- bslib::page_sidebar(
-  theme = bslib::bs_theme(bootswatch = "minty"),
-  title = "webResearcher for easy data analysis",
-  window_title = "webResearcher",
-  header = h6("Welcome to the webResearcher tool. This is an early alpha version to act as a proof-of-concept and in no way intended for wider public use."),
-
-  # sidebarPanel(
-  sidebar = bslib::sidebar(
-    open = "open",
-    h4("Upload your dataset"),
-
-    # Input: Select a file ----
-    fileInput(
-      inputId = "file",
-      label = "Choose data file",
-      multiple = FALSE,
-      accept = c(
-        "text/csv",
-        "text/comma-separated-values,text/plain",
-        ".csv",
-        ".xlsx",
-        ".xls",
-        ".dta",
-        ".ods"
-      )
-    ),
-    conditionalPanel(
-      condition = "output.uploaded=='yes'",
-      h4("Parameter specifications"),
-      radioButtons(
-        inputId = "regression_auto",
-        label = "Automatically choose function",
-        inline = TRUE,
-        choiceNames = c(
-          "Yes",
-          "No"
-        ),
-        choiceValues = c(1, 2)
-      ),
-      conditionalPanel(
-        condition = "input.regression_auto==2",
-        textInput(
-          inputId = "regression_formula",
-          label = "Formula string to render with 'glue::glue'",
-          value = NULL
-        ),
-        textInput(
-          inputId = "regression_fun",
-          label = "Function to use for analysis (needs pasckage and name)",
-          value = "stats::lm"
-        ),
-        textInput(
-          inputId = "regression_args",
-          label = "Arguments to pass to the function (provided as a string)",
-          value = ""
-        )
-      ),
-      helpText(em("Please specify relevant columns from your data, and press 'Load data'")),
-      uiOutput("outcome_var"),
-      radioButtons(
-        inputId = "all",
-        label = "Specify covariables",
-        inline = TRUE, selected = 2,
-        choiceNames = c(
-          "Yes",
-          "No"
-        ),
-        choiceValues = c(1, 2)
-      ),
-      conditionalPanel(
-        condition = "input.all==1",
-        uiOutput("include_vars")
-      ),
-      actionButton("load", "Analyse", class = "btn-primary")
-    )
-     # ,
-     #
-     # # Horizontal line ----
-     # tags$hr(),
-     # h4("Download results"),
-     #
-     # # Button
-     # downloadButton(outputId="report",
-     #                label= "Download",
-     #                icon = shiny::icon("download"))
-  ),
-  bslib::navset_card_underline(
-    title="Data and results",
-    panels[[1]],
-    panels[[2]],
-    panels[[3]]
-  )
-
-  # layout_columns(
-  #   cards[[1]]
-  # ),
-  # layout_columns(
-  #   cards[[2]], cards[[3]]
-  # )
-)

inst/apps/data_analysis/functions.R

@@ -1,7 +1,54 @@
 
 
 ########
-#### Current file: R//baseline_table.R 
+#### Current file: /Users/au301842/webResearch/R//app.R 
+########
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+shiny_webResearch <-  function(data=NULL,...){
+  appDir <- system.file("apps", "data_analysis", package = "webResearch")
+  if (appDir == "") {
+    stop("Could not find example directory. Try re-installing `webResearch`.", call. = FALSE)
+  }
+
+  G <- .GlobalEnv
+  assign("webResearch_data", data, envir=G)
+  a=shiny::runApp(appDir = appDir, ...)
+  return(invisible(a))
+}
+
+
+
+
+
+
+
+
+
+page_panels <- function(data){
+bslib::navset_card_underline(
+  title="Data and results",
+  data[[1]],
+  data[[2]],
+  data[[3]]
+)
+}
+
+
+########
+#### Current file: /Users/au301842/webResearch/R//baseline_table.R 
 ########
 
 
@@ -19,7 +66,7 @@
 
 baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary, vars = NULL) {
   if (!is.null(vars)) {
-    data <- dplyr::select(dplyr::all_of(vars))
+    data <- data |> dplyr::select(dplyr::all_of(vars))
   }
 
   out <- do.call(fun, c(list(data = data), fun.args))
@@ -29,7 +76,7 @@ baseline_table <- function(data, fun.args = NULL, fun = gtsummary::tbl_summary,
 
 
 ########
-#### Current file: R//helpers.R 
+#### Current file: /Users/au301842/webResearch/R//helpers.R 
 ########
 
 
@@ -92,26 +139,8 @@ write_quarto <- function(data,fileformat,qmd.file=here::here("analyses.qmd"),fil
 
 
 
-file_extension <- function(filenames) {
-  sub(
-    pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "",
-    filenames,
-    perl = TRUE
-  )
-}
-
-
-
-
-
-
-
-
-
-
-
 read_input <- function(file, consider.na = c("NA", '""', "")) {
-  ext <- file_extension(file)
+  ext <- tools::file_ext(file)
 
   if (ext == "csv") {
     df <- readr::read_csv(file = file, na = consider.na)
@@ -120,7 +149,7 @@ read_input <- function(file, consider.na = c("NA", '""', "")) {
   } else if (ext == "dta") {
     df <- haven::read_dta(file = file)
   } else if (ext == "ods") {
-    df <- readODS::read_ods(file = file)
+    df <- readODS::read_ods(path = file)
   } else {
     stop("Input file format has to be on of:
              '.csv', '.xls', '.xlsx', '.dta' or '.ods'")
@@ -145,7 +174,7 @@ argsstring2list <- function(string){
 
 
 ########
-#### Current file: R//regression_model.R 
+#### Current file: /Users/au301842/webResearch/R//regression_model.R 
 ########
 
 
@@ -175,6 +204,8 @@ argsstring2list <- function(string){
 
 
 
+
+
 
 
 
@@ -185,9 +216,11 @@ regression_model <- function(data,
                              args.list = NULL,
                              fun = NULL,
                              vars = NULL) {
-  if (formula.str==""){
+  if (!is.null(formula.str)) {
+    if (formula.str == "") {
       formula.str <- NULL
     }
+  }
 
   if (!is.null(formula.str)) {
     formula.str <- glue::glue(formula.str)
@@ -216,7 +249,7 @@ regression_model <- function(data,
     } else if (is.factor(data[[outcome.str]])) {
       if (length(levels(data[[outcome.str]])) == 2) {
         fun <- "stats::glm"
-        args.list <- list(family = binomial(link = "logit"))
+        args.list <- list(family = stats::binomial(link = "logit"))
       } else if (length(levels(data[[outcome.str]])) > 2) {
         fun <- "MASS::polr"
         args.list <- list(
@@ -252,7 +285,7 @@ regression_model <- function(data,
 
 
 ########
-#### Current file: R//regression_table.R 
+#### Current file: /Users/au301842/webResearch/R//regression_table.R 
 ########
 
 
@@ -289,8 +322,10 @@ regression_model <- function(data,
 regression_table <- function(data, args.list = NULL, fun = "gtsummary::tbl_regression") {
 
   if (any(c(length(class(data))!=1, class(data)!="lm"))){
+    if (!"exponentiate" %in% names(args.list)){
       args.list <- c(args.list,list(exponentiate=TRUE))
     }
+  }
 
   out <- do.call(getfun(fun), c(list(x = data), args.list))
   return(out)

inst/apps/data_analysis/rsconnect/shinyapps.io/agdamsbo/webResearch.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 13276335
-bundleId: 9334619
+bundleId: 9370648
 url: https://agdamsbo.shinyapps.io/webResearch/
 version: 1

inst/apps/data_analysis/server.R

@@ -1,13 +1,13 @@
 # project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
 # source(here::here("app/functions.R"))
 
-source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
+# source("https://raw.githubusercontent.com/agdamsbo/webResearch/refs/heads/main/app/functions.R")
 
 library(readr)
 library(MASS)
 library(stats)
-library(gt)
 library(gtsummary)
+library(gt)
 library(openxlsx2)
 library(haven)
 library(readODS)
@@ -19,23 +19,31 @@ library(quarto)
 library(here)
 library(broom)
 library(broom.helpers)
-
+if (!requireNamespace("webResearch")) {
+  devtools::install_github("agdamsbo/webResearch", quiet = TRUE, upgrade = "never")
+}
+library(webResearch)
 
 server <- function(input, output, session) {
   v <- shiny::reactiveValues(
     list = NULL,
-    ds = NULL
+    ds = NULL,
+    input = exists("webResearch_data"),
+    local_temp = NULL
   )
 
   ds <- shiny::reactive({
     # input$file1 will be NULL initially. After the user selects
     # and uploads a file, head of that data file by default,
     # or all rows if selected, will be shown.
-
+    if (v$input) {
+      out <- webResearch_data
+    } else {
       shiny::req(input$file)
-
+      out <- read_input(input$file$datapath)
+    }
     v$ds <- "present"
-    return(read_input(input$file$datapath))
+    return(out)
   })
 
   output$include_vars <- shiny::renderUI({
@@ -59,7 +67,6 @@ server <- function(input, output, session) {
   })
 
   output$data.input <- shiny::renderTable({
-    shiny::req(input$file)
     ds()
   })
 
@@ -80,10 +87,18 @@ server <- function(input, output, session) {
         by.var <- NULL
       }
 
+      if (is.null(input$include_vars)) {
+        base_vars <- NULL
+      } else {
+        base_vars <- c(input$include_vars, input$outcome_var)
+      }
+
+
       v$list <- list(
         data = data,
         table1 = data |>
           baseline_table(
+            vars = base_vars,
             fun.args =
               list(
                 by = by.var
@@ -124,6 +139,16 @@ server <- function(input, output, session) {
 
   shiny::outputOptions(output, "uploaded", suspendWhenHidden = FALSE)
 
+  output$has_input <- shiny::reactive({
+    if (v$input) {
+      "yes"
+    } else {
+      "no"
+    }
+  })
+
+  shiny::outputOptions(output, "has_input", suspendWhenHidden = FALSE)
+
   #####
   #### Generating output
   #####
@@ -136,14 +161,21 @@ server <- function(input, output, session) {
   #   }
   # )
 
+
+  # Could be rendered with other tables or should show progress
+  # Investigate quarto render problems
+  # On temp file handling: https://github.com/quarto-dev/quarto-cli/issues/3992
   output$report <- downloadHandler(
     filename = "analyses.html",
     content = function(file) {
+      local.temp <- paste0("temp.", tools::file_ext(file))
       v$list |>
         write_quarto(
-          file = file,
+          file = local.temp,
-          qmd.file = "www/analyses.qmd"
+          qmd.file = file.path(getwd(), "www/analyses.qmd")
         )
+      v$local_temp <- local.temp
+      file.rename(v$local_temp, file)
     }
   )
 

inst/apps/data_analysis/ui.R

@@ -0,0 +1,159 @@
+library(shiny)
+library(bslib)
+requireNamespace("gt")
+# require(ggplot2)
+# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/index_from_raw.R")
+# source("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/R/plot_index.R")
+# source(here::here("R/index_from_raw.R"))
+# source(here::here("R/plot_index.R"))
+
+# ui <- fluidPage(
+
+cards <- list(
+  bslib::card(
+    max_height = "200px",
+    full_screen = TRUE,
+    bslib::card_header("Data overview"),
+    shiny::uiOutput("data.input")
+  ),
+  bslib::card(
+    # max_height = "200px",
+    full_screen = TRUE,
+    bslib::card_header("Baseline characteristics"),
+    gt::gt_output(outputId = "table1")
+  ),
+  bslib::card(
+    full_screen = TRUE,
+    bslib::card_header("Multivariable regression table"),
+    gt::gt_output(outputId = "table2")
+  )
+)
+
+panels <- list(
+  bslib::nav_panel(
+    title = "Data overview",
+    shiny::uiOutput("data.input")
+  ),
+  bslib::nav_panel(
+    title = "Baseline characteristics",
+    gt::gt_output(outputId = "table1")
+  ),
+  bslib::nav_panel(
+    title = "Multivariable regression table",
+    gt::gt_output(outputId = "table2")
+  )
+)
+
+
+ui <- bslib::page(
+  theme = bslib::bs_theme(bootswatch = "minty"),
+  title = "webResearcher for easy data analysis",
+  bslib::page_navbar(
+    title = "webResearcher",
+    header = h6("Welcome to the webResearcher tool. This is an early alpha version to act as a proof-of-concept and in no way intended for wider public use."),
+
+    # sidebarPanel(
+    sidebar = bslib::sidebar(
+      open = "open",
+      shiny::h4("Upload your dataset"),
+      shiny::conditionalPanel(
+        condition = "output.has_input=='yes'",
+        # Input: Select a file ----
+        shiny::helpText("Analyses are performed on provided data")
+      ),
+      shiny::conditionalPanel(
+        condition = "output.has_input=='no'",
+        # Input: Select a file ----
+        shiny::fileInput(
+          inputId = "file",
+          label = "Choose data file",
+          multiple = FALSE,
+          accept = c(
+            "text/csv",
+            "text/comma-separated-values,text/plain",
+            ".csv",
+            ".xlsx",
+            ".xls",
+            ".dta",
+            ".ods",
+            ".rds"
+          )
+        )
+      ),
+      shiny::conditionalPanel(
+        condition = "output.uploaded=='yes'",
+        shiny::h4("Parameter specifications"),
+        shiny::radioButtons(
+          inputId = "regression_auto",
+          label = "Automatically choose function",
+          inline = TRUE,
+          choiceNames = c(
+            "Yes",
+            "No"
+          ),
+          choiceValues = c(1, 2)
+        ),
+        shiny::conditionalPanel(
+          condition = "input.regression_auto==2",
+          shiny::textInput(
+            inputId = "regression_formula",
+            label = "Formula string to render with 'glue::glue'",
+            value = NULL
+          ),
+          shiny::textInput(
+            inputId = "regression_fun",
+            label = "Function to use for analysis (needs pasckage and name)",
+            value = "stats::lm"
+          ),
+          shiny::textInput(
+            inputId = "regression_args",
+            label = "Arguments to pass to the function (provided as a string)",
+            value = ""
+          )
+        ),
+        shiny::helpText(em("Please specify relevant columns from your data, and press 'Load data'")),
+        shiny::uiOutput("outcome_var"),
+        shiny::radioButtons(
+          inputId = "all",
+          label = "Specify covariables",
+          inline = TRUE, selected = 2,
+          choiceNames = c(
+            "Yes",
+            "No"
+          ),
+          choiceValues = c(1, 2)
+        ),
+        shiny::conditionalPanel(
+          condition = "input.all==1",
+          shiny::uiOutput("include_vars")
+        ),
+        shiny::actionButton("load", "Analyse", class = "btn-primary"),
+        #
+        # # Horizontal line ----
+        tags$hr(),
+        h4("Download results"),
+
+        shiny::helpText("The download currently works, but the output is not correctly formatted. Work in progress!"),
+
+        # Button
+        downloadButton(
+          outputId = "report",
+          label = "Download",
+          icon = shiny::icon("download")
+        )
+
+      )
+    ),
+    bslib::nav_spacer(),
+    panels[[1]],
+    panels[[2]],
+    panels[[3]]
+
+    # layout_columns(
+    #   cards[[1]]
+    # ),
+    # layout_columns(
+    #   cards[[2]], cards[[3]]
+    # )
+  )
+)

inst/apps/data_analysis/www/analyses_files/libs/quarto-html/quarto-syntax-highlighting.css

@@ -0,0 +1,205 @@
+/* quarto syntax highlight colors */
+:root {
+  --quarto-hl-ot-color: #003B4F;
+  --quarto-hl-at-color: #657422;
+  --quarto-hl-ss-color: #20794D;
+  --quarto-hl-an-color: #5E5E5E;
+  --quarto-hl-fu-color: #4758AB;
+  --quarto-hl-st-color: #20794D;
+  --quarto-hl-cf-color: #003B4F;
+  --quarto-hl-op-color: #5E5E5E;
+  --quarto-hl-er-color: #AD0000;
+  --quarto-hl-bn-color: #AD0000;
+  --quarto-hl-al-color: #AD0000;
+  --quarto-hl-va-color: #111111;
+  --quarto-hl-bu-color: inherit;
+  --quarto-hl-ex-color: inherit;
+  --quarto-hl-pp-color: #AD0000;
+  --quarto-hl-in-color: #5E5E5E;
+  --quarto-hl-vs-color: #20794D;
+  --quarto-hl-wa-color: #5E5E5E;
+  --quarto-hl-do-color: #5E5E5E;
+  --quarto-hl-im-color: #00769E;
+  --quarto-hl-ch-color: #20794D;
+  --quarto-hl-dt-color: #AD0000;
+  --quarto-hl-fl-color: #AD0000;
+  --quarto-hl-co-color: #5E5E5E;
+  --quarto-hl-cv-color: #5E5E5E;
+  --quarto-hl-cn-color: #8f5902;
+  --quarto-hl-sc-color: #5E5E5E;
+  --quarto-hl-dv-color: #AD0000;
+  --quarto-hl-kw-color: #003B4F;
+}
+
+/* other quarto variables */
+:root {
+  --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
+}
+
+pre > code.sourceCode > span {
+  color: #003B4F;
+}
+
+code span {
+  color: #003B4F;
+}
+
+code.sourceCode > span {
+  color: #003B4F;
+}
+
+div.sourceCode,
+div.sourceCode pre.sourceCode {
+  color: #003B4F;
+}
+
+code span.ot {
+  color: #003B4F;
+  font-style: inherit;
+}
+
+code span.at {
+  color: #657422;
+  font-style: inherit;
+}
+
+code span.ss {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.an {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.fu {
+  color: #4758AB;
+  font-style: inherit;
+}
+
+code span.st {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.cf {
+  color: #003B4F;
+  font-weight: bold;
+  font-style: inherit;
+}
+
+code span.op {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.er {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.bn {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.al {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.va {
+  color: #111111;
+  font-style: inherit;
+}
+
+code span.bu {
+  font-style: inherit;
+}
+
+code span.ex {
+  font-style: inherit;
+}
+
+code span.pp {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.in {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.vs {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.wa {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+code span.do {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+code span.im {
+  color: #00769E;
+  font-style: inherit;
+}
+
+code span.ch {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.dt {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.fl {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.co {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.cv {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+code span.cn {
+  color: #8f5902;
+  font-style: inherit;
+}
+
+code span.sc {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.dv {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.kw {
+  color: #003B4F;
+  font-weight: bold;
+  font-style: inherit;
+}
+
+.prevent-inlining {
+  content: "</";
+}
+
+/*# sourceMappingURL=debc5d5d77c3f9108843748ff7464032.css.map */

inst/apps/data_analysis/www/analyses_files/libs/quarto-html/quarto.js

@@ -0,0 +1,908 @@
+const sectionChanged = new CustomEvent("quarto-sectionChanged", {
+  detail: {},
+  bubbles: true,
+  cancelable: false,
+  composed: false,
+});
+
+const layoutMarginEls = () => {
+  // Find any conflicting margin elements and add margins to the
+  // top to prevent overlap
+  const marginChildren = window.document.querySelectorAll(
+    ".column-margin.column-container > *, .margin-caption, .aside"
+  );
+
+  let lastBottom = 0;
+  for (const marginChild of marginChildren) {
+    if (marginChild.offsetParent !== null) {
+      // clear the top margin so we recompute it
+      marginChild.style.marginTop = null;
+      const top = marginChild.getBoundingClientRect().top + window.scrollY;
+      if (top < lastBottom) {
+        const marginChildStyle = window.getComputedStyle(marginChild);
+        const marginBottom = parseFloat(marginChildStyle["marginBottom"]);
+        const margin = lastBottom - top + marginBottom;
+        marginChild.style.marginTop = `${margin}px`;
+      }
+      const styles = window.getComputedStyle(marginChild);
+      const marginTop = parseFloat(styles["marginTop"]);
+      lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
+    }
+  }
+};
+
+window.document.addEventListener("DOMContentLoaded", function (_event) {
+  // Recompute the position of margin elements anytime the body size changes
+  if (window.ResizeObserver) {
+    const resizeObserver = new window.ResizeObserver(
+      throttle(() => {
+        layoutMarginEls();
+        if (
+          window.document.body.getBoundingClientRect().width < 990 &&
+          isReaderMode()
+        ) {
+          quartoToggleReader();
+        }
+      }, 50)
+    );
+    resizeObserver.observe(window.document.body);
+  }
+
+  const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
+  const sidebarEl = window.document.getElementById("quarto-sidebar");
+  const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
+  const marginSidebarEl = window.document.getElementById(
+    "quarto-margin-sidebar"
+  );
+  // function to determine whether the element has a previous sibling that is active
+  const prevSiblingIsActiveLink = (el) => {
+    const sibling = el.previousElementSibling;
+    if (sibling && sibling.tagName === "A") {
+      return sibling.classList.contains("active");
+    } else {
+      return false;
+    }
+  };
+
+  // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior)
+  function fireSlideEnter(e) {
+    const event = window.document.createEvent("Event");
+    event.initEvent("slideenter", true, true);
+    window.document.dispatchEvent(event);
+  }
+  const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
+  tabs.forEach((tab) => {
+    tab.addEventListener("shown.bs.tab", fireSlideEnter);
+  });
+
+  // fire slideEnter for tabby tab activations (for htmlwidget resize behavior)
+  document.addEventListener("tabby", fireSlideEnter, false);
+
+  // Track scrolling and mark TOC links as active
+  // get table of contents and sidebar (bail if we don't have at least one)
+  const tocLinks = tocEl
+    ? [...tocEl.querySelectorAll("a[data-scroll-target]")]
+    : [];
+  const makeActive = (link) => tocLinks[link].classList.add("active");
+  const removeActive = (link) => tocLinks[link].classList.remove("active");
+  const removeAllActive = () =>
+    [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
+
+  // activate the anchor for a section associated with this TOC entry
+  tocLinks.forEach((link) => {
+    link.addEventListener("click", () => {
+      if (link.href.indexOf("#") !== -1) {
+        const anchor = link.href.split("#")[1];
+        const heading = window.document.querySelector(
+          `[data-anchor-id="${anchor}"]`
+        );
+        if (heading) {
+          // Add the class
+          heading.classList.add("reveal-anchorjs-link");
+
+          // function to show the anchor
+          const handleMouseout = () => {
+            heading.classList.remove("reveal-anchorjs-link");
+            heading.removeEventListener("mouseout", handleMouseout);
+          };
+
+          // add a function to clear the anchor when the user mouses out of it
+          heading.addEventListener("mouseout", handleMouseout);
+        }
+      }
+    });
+  });
+
+  const sections = tocLinks.map((link) => {
+    const target = link.getAttribute("data-scroll-target");
+    if (target.startsWith("#")) {
+      return window.document.getElementById(decodeURI(`${target.slice(1)}`));
+    } else {
+      return window.document.querySelector(decodeURI(`${target}`));
+    }
+  });
+
+  const sectionMargin = 200;
+  let currentActive = 0;
+  // track whether we've initialized state the first time
+  let init = false;
+
+  const updateActiveLink = () => {
+    // The index from bottom to top (e.g. reversed list)
+    let sectionIndex = -1;
+    if (
+      window.innerHeight + window.pageYOffset >=
+      window.document.body.offsetHeight
+    ) {
+      // This is the no-scroll case where last section should be the active one
+      sectionIndex = 0;
+    } else {
+      // This finds the last section visible on screen that should be made active
+      sectionIndex = [...sections].reverse().findIndex((section) => {
+        if (section) {
+          return window.pageYOffset >= section.offsetTop - sectionMargin;
+        } else {
+          return false;
+        }
+      });
+    }
+    if (sectionIndex > -1) {
+      const current = sections.length - sectionIndex - 1;
+      if (current !== currentActive) {
+        removeAllActive();
+        currentActive = current;
+        makeActive(current);
+        if (init) {
+          window.dispatchEvent(sectionChanged);
+        }
+        init = true;
+      }
+    }
+  };
+
+  const inHiddenRegion = (top, bottom, hiddenRegions) => {
+    for (const region of hiddenRegions) {
+      if (top <= region.bottom && bottom >= region.top) {
+        return true;
+      }
+    }
+    return false;
+  };
+
+  const categorySelector = "header.quarto-title-block .quarto-category";
+  const activateCategories = (href) => {
+    // Find any categories
+    // Surround them with a link pointing back to:
+    // #category=Authoring
+    try {
+      const categoryEls = window.document.querySelectorAll(categorySelector);
+      for (const categoryEl of categoryEls) {
+        const categoryText = categoryEl.textContent;
+        if (categoryText) {
+          const link = `${href}#category=${encodeURIComponent(categoryText)}`;
+          const linkEl = window.document.createElement("a");
+          linkEl.setAttribute("href", link);
+          for (const child of categoryEl.childNodes) {
+            linkEl.append(child);
+          }
+          categoryEl.appendChild(linkEl);
+        }
+      }
+    } catch {
+      // Ignore errors
+    }
+  };
+  function hasTitleCategories() {
+    return window.document.querySelector(categorySelector) !== null;
+  }
+
+  function offsetRelativeUrl(url) {
+    const offset = getMeta("quarto:offset");
+    return offset ? offset + url : url;
+  }
+
+  function offsetAbsoluteUrl(url) {
+    const offset = getMeta("quarto:offset");
+    const baseUrl = new URL(offset, window.location);
+
+    const projRelativeUrl = url.replace(baseUrl, "");
+    if (projRelativeUrl.startsWith("/")) {
+      return projRelativeUrl;
+    } else {
+      return "/" + projRelativeUrl;
+    }
+  }
+
+  // read a meta tag value
+  function getMeta(metaName) {
+    const metas = window.document.getElementsByTagName("meta");
+    for (let i = 0; i < metas.length; i++) {
+      if (metas[i].getAttribute("name") === metaName) {
+        return metas[i].getAttribute("content");
+      }
+    }
+    return "";
+  }
+
+  async function findAndActivateCategories() {
+    const currentPagePath = offsetAbsoluteUrl(window.location.href);
+    const response = await fetch(offsetRelativeUrl("listings.json"));
+    if (response.status == 200) {
+      return response.json().then(function (listingPaths) {
+        const listingHrefs = [];
+        for (const listingPath of listingPaths) {
+          const pathWithoutLeadingSlash = listingPath.listing.substring(1);
+          for (const item of listingPath.items) {
+            if (
+              item === currentPagePath ||
+              item === currentPagePath + "index.html"
+            ) {
+              // Resolve this path against the offset to be sure
+              // we already are using the correct path to the listing
+              // (this adjusts the listing urls to be rooted against
+              // whatever root the page is actually running against)
+              const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
+              const baseUrl = window.location;
+              const resolvedPath = new URL(relative, baseUrl);
+              listingHrefs.push(resolvedPath.pathname);
+              break;
+            }
+          }
+        }
+
+        // Look up the tree for a nearby linting and use that if we find one
+        const nearestListing = findNearestParentListing(
+          offsetAbsoluteUrl(window.location.pathname),
+          listingHrefs
+        );
+        if (nearestListing) {
+          activateCategories(nearestListing);
+        } else {
+          // See if the referrer is a listing page for this item
+          const referredRelativePath = offsetAbsoluteUrl(document.referrer);
+          const referrerListing = listingHrefs.find((listingHref) => {
+            const isListingReferrer =
+              listingHref === referredRelativePath ||
+              listingHref === referredRelativePath + "index.html";
+            return isListingReferrer;
+          });
+
+          if (referrerListing) {
+            // Try to use the referrer if possible
+            activateCategories(referrerListing);
+          } else if (listingHrefs.length > 0) {
+            // Otherwise, just fall back to the first listing
+            activateCategories(listingHrefs[0]);
+          }
+        }
+      });
+    }
+  }
+  if (hasTitleCategories()) {
+    findAndActivateCategories();
+  }
+
+  const findNearestParentListing = (href, listingHrefs) => {
+    if (!href || !listingHrefs) {
+      return undefined;
+    }
+    // Look up the tree for a nearby linting and use that if we find one
+    const relativeParts = href.substring(1).split("/");
+    while (relativeParts.length > 0) {
+      const path = relativeParts.join("/");
+      for (const listingHref of listingHrefs) {
+        if (listingHref.startsWith(path)) {
+          return listingHref;
+        }
+      }
+      relativeParts.pop();
+    }
+
+    return undefined;
+  };
+
+  const manageSidebarVisiblity = (el, placeholderDescriptor) => {
+    let isVisible = true;
+    let elRect;
+
+    return (hiddenRegions) => {
+      if (el === null) {
+        return;
+      }
+
+      // Find the last element of the TOC
+      const lastChildEl = el.lastElementChild;
+
+      if (lastChildEl) {
+        // Converts the sidebar to a menu
+        const convertToMenu = () => {
+          for (const child of el.children) {
+            child.style.opacity = 0;
+            child.style.overflow = "hidden";
+            child.style.pointerEvents = "none";
+          }
+
+          nexttick(() => {
+            const toggleContainer = window.document.createElement("div");
+            toggleContainer.style.width = "100%";
+            toggleContainer.classList.add("zindex-over-content");
+            toggleContainer.classList.add("quarto-sidebar-toggle");
+            toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
+            toggleContainer.id = placeholderDescriptor.id;
+            toggleContainer.style.position = "fixed";
+
+            const toggleIcon = window.document.createElement("i");
+            toggleIcon.classList.add("quarto-sidebar-toggle-icon");
+            toggleIcon.classList.add("bi");
+            toggleIcon.classList.add("bi-caret-down-fill");
+
+            const toggleTitle = window.document.createElement("div");
+            const titleEl = window.document.body.querySelector(
+              placeholderDescriptor.titleSelector
+            );
+            if (titleEl) {
+              toggleTitle.append(
+                titleEl.textContent || titleEl.innerText,
+                toggleIcon
+              );
+            }
+            toggleTitle.classList.add("zindex-over-content");
+            toggleTitle.classList.add("quarto-sidebar-toggle-title");
+            toggleContainer.append(toggleTitle);
+
+            const toggleContents = window.document.createElement("div");
+            toggleContents.classList = el.classList;
+            toggleContents.classList.add("zindex-over-content");
+            toggleContents.classList.add("quarto-sidebar-toggle-contents");
+            for (const child of el.children) {
+              if (child.id === "toc-title") {
+                continue;
+              }
+
+              const clone = child.cloneNode(true);
+              clone.style.opacity = 1;
+              clone.style.pointerEvents = null;
+              clone.style.display = null;
+              toggleContents.append(clone);
+            }
+            toggleContents.style.height = "0px";
+            const positionToggle = () => {
+              // position the element (top left of parent, same width as parent)
+              if (!elRect) {
+                elRect = el.getBoundingClientRect();
+              }
+              toggleContainer.style.left = `${elRect.left}px`;
+              toggleContainer.style.top = `${elRect.top}px`;
+              toggleContainer.style.width = `${elRect.width}px`;
+            };
+            positionToggle();
+
+            toggleContainer.append(toggleContents);
+            el.parentElement.prepend(toggleContainer);
+
+            // Process clicks
+            let tocShowing = false;
+            // Allow the caller to control whether this is dismissed
+            // when it is clicked (e.g. sidebar navigation supports
+            // opening and closing the nav tree, so don't dismiss on click)
+            const clickEl = placeholderDescriptor.dismissOnClick
+              ? toggleContainer
+              : toggleTitle;
+
+            const closeToggle = () => {
+              if (tocShowing) {
+                toggleContainer.classList.remove("expanded");
+                toggleContents.style.height = "0px";
+                tocShowing = false;
+              }
+            };
+
+            // Get rid of any expanded toggle if the user scrolls
+            window.document.addEventListener(
+              "scroll",
+              throttle(() => {
+                closeToggle();
+              }, 50)
+            );
+
+            // Handle positioning of the toggle
+            window.addEventListener(
+              "resize",
+              throttle(() => {
+                elRect = undefined;
+                positionToggle();
+              }, 50)
+            );
+
+            window.addEventListener("quarto-hrChanged", () => {
+              elRect = undefined;
+            });
+
+            // Process the click
+            clickEl.onclick = () => {
+              if (!tocShowing) {
+                toggleContainer.classList.add("expanded");
+                toggleContents.style.height = null;
+                tocShowing = true;
+              } else {
+                closeToggle();
+              }
+            };
+          });
+        };
+
+        // Converts a sidebar from a menu back to a sidebar
+        const convertToSidebar = () => {
+          for (const child of el.children) {
+            child.style.opacity = 1;
+            child.style.overflow = null;
+            child.style.pointerEvents = null;
+          }
+
+          const placeholderEl = window.document.getElementById(
+            placeholderDescriptor.id
+          );
+          if (placeholderEl) {
+            placeholderEl.remove();
+          }
+
+          el.classList.remove("rollup");
+        };
+
+        if (isReaderMode()) {
+          convertToMenu();
+          isVisible = false;
+        } else {
+          // Find the top and bottom o the element that is being managed
+          const elTop = el.offsetTop;
+          const elBottom =
+            elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
+
+          if (!isVisible) {
+            // If the element is current not visible reveal if there are
+            // no conflicts with overlay regions
+            if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+              convertToSidebar();
+              isVisible = true;
+            }
+          } else {
+            // If the element is visible, hide it if it conflicts with overlay regions
+            // and insert a placeholder toggle (or if we're in reader mode)
+            if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+              convertToMenu();
+              isVisible = false;
+            }
+          }
+        }
+      }
+    };
+  };
+
+  const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
+  for (const tabEl of tabEls) {
+    const id = tabEl.getAttribute("data-bs-target");
+    if (id) {
+      const columnEl = document.querySelector(
+        `${id} .column-margin, .tabset-margin-content`
+      );
+      if (columnEl)
+        tabEl.addEventListener("shown.bs.tab", function (event) {
+          const el = event.srcElement;
+          if (el) {
+            const visibleCls = `${el.id}-margin-content`;
+            // walk up until we find a parent tabset
+            let panelTabsetEl = el.parentElement;
+            while (panelTabsetEl) {
+              if (panelTabsetEl.classList.contains("panel-tabset")) {
+                break;
+              }
+              panelTabsetEl = panelTabsetEl.parentElement;
+            }
+
+            if (panelTabsetEl) {
+              const prevSib = panelTabsetEl.previousElementSibling;
+              if (
+                prevSib &&
+                prevSib.classList.contains("tabset-margin-container")
+              ) {
+                const childNodes = prevSib.querySelectorAll(
+                  ".tabset-margin-content"
+                );
+                for (const childEl of childNodes) {
+                  if (childEl.classList.contains(visibleCls)) {
+                    childEl.classList.remove("collapse");
+                  } else {
+                    childEl.classList.add("collapse");
+                  }
+                }
+              }
+            }
+          }
+
+          layoutMarginEls();
+        });
+    }
+  }
+
+  // Manage the visibility of the toc and the sidebar
+  const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
+    id: "quarto-toc-toggle",
+    titleSelector: "#toc-title",
+    dismissOnClick: true,
+  });
+  const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
+    id: "quarto-sidebarnav-toggle",
+    titleSelector: ".title",
+    dismissOnClick: false,
+  });
+  let tocLeftScrollVisibility;
+  if (leftTocEl) {
+    tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
+      id: "quarto-lefttoc-toggle",
+      titleSelector: "#toc-title",
+      dismissOnClick: true,
+    });
+  }
+
+  // Find the first element that uses formatting in special columns
+  const conflictingEls = window.document.body.querySelectorAll(
+    '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
+  );
+
+  // Filter all the possibly conflicting elements into ones
+  // the do conflict on the left or ride side
+  const arrConflictingEls = Array.from(conflictingEls);
+  const leftSideConflictEls = arrConflictingEls.filter((el) => {
+    if (el.tagName === "ASIDE") {
+      return false;
+    }
+    return Array.from(el.classList).find((className) => {
+      return (
+        className !== "column-body" &&
+        className.startsWith("column-") &&
+        !className.endsWith("right") &&
+        !className.endsWith("container") &&
+        className !== "column-margin"
+      );
+    });
+  });
+  const rightSideConflictEls = arrConflictingEls.filter((el) => {
+    if (el.tagName === "ASIDE") {
+      return true;
+    }
+
+    const hasMarginCaption = Array.from(el.classList).find((className) => {
+      return className == "margin-caption";
+    });
+    if (hasMarginCaption) {
+      return true;
+    }
+
+    return Array.from(el.classList).find((className) => {
+      return (
+        className !== "column-body" &&
+        !className.endsWith("container") &&
+        className.startsWith("column-") &&
+        !className.endsWith("left")
+      );
+    });
+  });
+
+  const kOverlapPaddingSize = 10;
+  function toRegions(els) {
+    return els.map((el) => {
+      const boundRect = el.getBoundingClientRect();
+      const top =
+        boundRect.top +
+        document.documentElement.scrollTop -
+        kOverlapPaddingSize;
+      return {
+        top,
+        bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
+      };
+    });
+  }
+
+  let hasObserved = false;
+  const visibleItemObserver = (els) => {
+    let visibleElements = [...els];
+    const intersectionObserver = new IntersectionObserver(
+      (entries, _observer) => {
+        entries.forEach((entry) => {
+          if (entry.isIntersecting) {
+            if (visibleElements.indexOf(entry.target) === -1) {
+              visibleElements.push(entry.target);
+            }
+          } else {
+            visibleElements = visibleElements.filter((visibleEntry) => {
+              return visibleEntry !== entry;
+            });
+          }
+        });
+
+        if (!hasObserved) {
+          hideOverlappedSidebars();
+        }
+        hasObserved = true;
+      },
+      {}
+    );
+    els.forEach((el) => {
+      intersectionObserver.observe(el);
+    });
+
+    return {
+      getVisibleEntries: () => {
+        return visibleElements;
+      },
+    };
+  };
+
+  const rightElementObserver = visibleItemObserver(rightSideConflictEls);
+  const leftElementObserver = visibleItemObserver(leftSideConflictEls);
+
+  const hideOverlappedSidebars = () => {
+    marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
+    sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
+    if (tocLeftScrollVisibility) {
+      tocLeftScrollVisibility(
+        toRegions(leftElementObserver.getVisibleEntries())
+      );
+    }
+  };
+
+  window.quartoToggleReader = () => {
+    // Applies a slow class (or removes it)
+    // to update the transition speed
+    const slowTransition = (slow) => {
+      const manageTransition = (id, slow) => {
+        const el = document.getElementById(id);
+        if (el) {
+          if (slow) {
+            el.classList.add("slow");
+          } else {
+            el.classList.remove("slow");
+          }
+        }
+      };
+
+      manageTransition("TOC", slow);
+      manageTransition("quarto-sidebar", slow);
+    };
+    const readerMode = !isReaderMode();
+    setReaderModeValue(readerMode);
+
+    // If we're entering reader mode, slow the transition
+    if (readerMode) {
+      slowTransition(readerMode);
+    }
+    highlightReaderToggle(readerMode);
+    hideOverlappedSidebars();
+
+    // If we're exiting reader mode, restore the non-slow transition
+    if (!readerMode) {
+      slowTransition(!readerMode);
+    }
+  };
+
+  const highlightReaderToggle = (readerMode) => {
+    const els = document.querySelectorAll(".quarto-reader-toggle");
+    if (els) {
+      els.forEach((el) => {
+        if (readerMode) {
+          el.classList.add("reader");
+        } else {
+          el.classList.remove("reader");
+        }
+      });
+    }
+  };
+
+  const setReaderModeValue = (val) => {
+    if (window.location.protocol !== "file:") {
+      window.localStorage.setItem("quarto-reader-mode", val);
+    } else {
+      localReaderMode = val;
+    }
+  };
+
+  const isReaderMode = () => {
+    if (window.location.protocol !== "file:") {
+      return window.localStorage.getItem("quarto-reader-mode") === "true";
+    } else {
+      return localReaderMode;
+    }
+  };
+  let localReaderMode = null;
+
+  const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
+  const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
+
+  // Walk the TOC and collapse/expand nodes
+  // Nodes are expanded if:
+  // - they are top level
+  // - they have children that are 'active' links
+  // - they are directly below an link that is 'active'
+  const walk = (el, depth) => {
+    // Tick depth when we enter a UL
+    if (el.tagName === "UL") {
+      depth = depth + 1;
+    }
+
+    // It this is active link
+    let isActiveNode = false;
+    if (el.tagName === "A" && el.classList.contains("active")) {
+      isActiveNode = true;
+    }
+
+    // See if there is an active child to this element
+    let hasActiveChild = false;
+    for (child of el.children) {
+      hasActiveChild = walk(child, depth) || hasActiveChild;
+    }
+
+    // Process the collapse state if this is an UL
+    if (el.tagName === "UL") {
+      if (tocOpenDepth === -1 && depth > 1) {
+        // toc-expand: false
+        el.classList.add("collapse");
+      } else if (
+        depth <= tocOpenDepth ||
+        hasActiveChild ||
+        prevSiblingIsActiveLink(el)
+      ) {
+        el.classList.remove("collapse");
+      } else {
+        el.classList.add("collapse");
+      }
+
+      // untick depth when we leave a UL
+      depth = depth - 1;
+    }
+    return hasActiveChild || isActiveNode;
+  };
+
+  // walk the TOC and expand / collapse any items that should be shown
+  if (tocEl) {
+    updateActiveLink();
+    walk(tocEl, 0);
+  }
+
+  // Throttle the scroll event and walk peridiocally
+  window.document.addEventListener(
+    "scroll",
+    throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
+      if (!isReaderMode()) {
+        hideOverlappedSidebars();
+      }
+    }, 5)
+  );
+  window.addEventListener(
+    "resize",
+    throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
+      if (!isReaderMode()) {
+        hideOverlappedSidebars();
+      }
+    }, 10)
+  );
+  hideOverlappedSidebars();
+  highlightReaderToggle(isReaderMode());
+});
+
+// grouped tabsets
+window.addEventListener("pageshow", (_event) => {
+  function getTabSettings() {
+    const data = localStorage.getItem("quarto-persistent-tabsets-data");
+    if (!data) {
+      localStorage.setItem("quarto-persistent-tabsets-data", "{}");
+      return {};
+    }
+    if (data) {
+      return JSON.parse(data);
+    }
+  }
+
+  function setTabSettings(data) {
+    localStorage.setItem(
+      "quarto-persistent-tabsets-data",
+      JSON.stringify(data)
+    );
+  }
+
+  function setTabState(groupName, groupValue) {
+    const data = getTabSettings();
+    data[groupName] = groupValue;
+    setTabSettings(data);
+  }
+
+  function toggleTab(tab, active) {
+    const tabPanelId = tab.getAttribute("aria-controls");
+    const tabPanel = document.getElementById(tabPanelId);
+    if (active) {
+      tab.classList.add("active");
+      tabPanel.classList.add("active");
+    } else {
+      tab.classList.remove("active");
+      tabPanel.classList.remove("active");
+    }
+  }
+
+  function toggleAll(selectedGroup, selectorsToSync) {
+    for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
+      const active = selectedGroup === thisGroup;
+      for (const tab of tabs) {
+        toggleTab(tab, active);
+      }
+    }
+  }
+
+  function findSelectorsToSyncByLanguage() {
+    const result = {};
+    const tabs = Array.from(
+      document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
+    );
+    for (const item of tabs) {
+      const div = item.parentElement.parentElement.parentElement;
+      const group = div.getAttribute("data-group");
+      if (!result[group]) {
+        result[group] = {};
+      }
+      const selectorsToSync = result[group];
+      const value = item.innerHTML;
+      if (!selectorsToSync[value]) {
+        selectorsToSync[value] = [];
+      }
+      selectorsToSync[value].push(item);
+    }
+    return result;
+  }
+
+  function setupSelectorSync() {
+    const selectorsToSync = findSelectorsToSyncByLanguage();
+    Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
+      Object.entries(tabSetsByValue).forEach(([value, items]) => {
+        items.forEach((item) => {
+          item.addEventListener("click", (_event) => {
+            setTabState(group, value);
+            toggleAll(value, selectorsToSync[group]);
+          });
+        });
+      });
+    });
+    return selectorsToSync;
+  }
+
+  const selectorsToSync = setupSelectorSync();
+  for (const [group, selectedName] of Object.entries(getTabSettings())) {
+    const selectors = selectorsToSync[group];
+    // it's possible that stale state gives us empty selections, so we explicitly check here.
+    if (selectors) {
+      toggleAll(selectedName, selectors);
+    }
+  }
+});
+
+function throttle(func, wait) {
+  let waiting = false;
+  return function () {
+    if (!waiting) {
+      func.apply(this, arguments);
+      waiting = true;
+      setTimeout(function () {
+        waiting = false;
+      }, wait);
+    }
+  };
+}
+
+function nexttick(func) {
+  return setTimeout(func, 0);
+}

inst/apps/data_analysis/www/analyses_files/libs/quarto-html/tippy.css

@@ -0,0 +1 @@
+.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}

man/file_extension.Rd

@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/helpers.R
-\name{file_extension}
-\alias{file_extension}
-\title{Helper to import files correctly}
-\usage{
-file_extension(filenames)
-}
-\arguments{
-\item{filenames}{file names}
-}
-\value{
-character vector
-}
-\description{
-Helper to import files correctly
-}
-\examples{
-file_extension(list.files(here::here(""))[[2]])[[1]]
-file_extension(c("file.cd..ks", "file"))
-}

man/panel_space.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/app.R
+\name{panel_space}
+\alias{panel_space}
+\title{Wrapping nav_spacer to avoid errors on dependencies when packaging}
+\usage{
+panel_space()
+}
+\value{
+bslib object
+}
+\description{
+Wrapping nav_spacer to avoid errors on dependencies when packaging
+}

man/regression_model.Rd

@@ -19,7 +19,7 @@ regression_model(
 
 \item{outcome.str}{Name of outcome variable. Character vector.}
 
-\item{auto.mode}{Make assumptions on function dependent on outcome data format.}
+\item{auto.mode}{Make assumptions on function dependent on outcome data format. Overwrites other arguments.}
 
 \item{formula.str}{Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.}
 
@@ -41,12 +41,14 @@ gtsummary::trial |>
 gtsummary::trial |>
   regression_model(
     outcome.str = "age",
+    auto.mode = FALSE,
     fun = "stats::lm",
     formula.str = "{outcome.str}~.",
     args.list = NULL
   )
 gtsummary::trial |> regression_model(
   outcome.str = "trt",
+  auto.mode = FALSE,
   fun = "stats::glm",
   args.list = list(family = binomial(link = "logit"))
 )

man/regression_table.Rd

@@ -25,7 +25,7 @@ gtsummary::trial |>
     outcome.str = "stage",
     fun = "MASS::polr"
   ) |>
-  regression_table(args.list = list(exponentiate = TRUE))
+  regression_table(args.list = list("exponentiate" = TRUE))
 gtsummary::trial |>
   regression_model(
     outcome.str = "age",

man/shiny_webResearch.Rd

@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/app.R
+\name{shiny_webResearch}
+\alias{shiny_webResearch}
+\title{Test version of the shiny_cast function to launch the app with a data set in
+the environment.}
+\usage{
+shiny_webResearch(data = NULL, ...)
+}
+\arguments{
+\item{data}{optional data set to provide for analysis}
+
+\item{...}{arguments passed on to \code{shiny::runApp()}}
+}
+\value{
+shiny app
+}
+\description{
+Test version of the shiny_cast function to launch the app with a data set in
+the environment.
+}
+\examples{
+\dontrun{
+mtcars |> shiny_webResearch(launch.browser = TRUE)
+}
+}

publish_shiny.R

@@ -1,18 +0,0 @@
-# Prep for shiny
-# system2("cat ./R/index_from_raw.R ./R/plot_index.R ./R/read_file.R > ./R/functions.R")
-
-project.aid::merge_scripts(list.files("R/",full.names = TRUE),dest = here::here("app/functions.R"))
-
-# Typical shiny
-shiny::runApp(appDir = here::here("app/"))
-shiny::runApp(appDir = here::here("app/"), launch.browser = TRUE)
-
-project.aid::deploy_shiny(
-  path="app/",
-  account.name = "agdamsbo",
-  name.app = "webResearch",
-  name.token = "rsconnect_agdamsbo_token",
-  name.secret = "rsconnect_agdamsbo_secret"
-)
-
-