--- /dev/null
+ui <- htmlTemplate("index.html")
+
+server <- function(input, output) {
+ source("scripts/data.R", local = TRUE)
+ source("scripts/estimators.R", local = TRUE)
+
+ react_values <- reactiveValues()
+
+ data_logic(input, output, react_values)
+ estimators_logic(input, output, react_values)
+}
+
+shinyApp(ui, server)
--- /dev/null
+<!DOCTYPE html>
+<html>
+ <head>
+ {{ bootstrapLib(theme = bslib::bs_theme(primary = "red")) }}
+ {{ headContent() }}
+ <title>Rnaught Web</title>
+ <link rel="stylesheet" type="text/css" href="styles.css">
+ <!-- Enable tooltips. -->
+ <script>
+ $(document).ready(function(){
+ $('[data-bs-toggle="tooltip"]').tooltip();
+ });
+ </script>
+ </head>
+ <body class="d-flex flex-column h-100">
+ <noscript>
+ <strong>This application requires JavaScript.</strong>
+ </noscript>
+ {{ htmlTemplate("templates/navbar.html") }}
+ {{ htmlTemplate("templates/tabs.html") }}
+ {{ htmlTemplate("templates/content.html") }}
+ {{ htmlTemplate("templates/footer.html") }}
+ </body>
+</html>
--- /dev/null
+# Main logic block for data-related interactions.
+data_logic <- function(input, output, react_values) {
+ # Initialize a data frame to hold the datasets.
+ react_values$data_table <- data.frame(
+ Name = character(0),
+ `Time units` = character(0),
+ `Case counts` = character(0),
+ check.names = FALSE
+ )
+
+ render_plot(input, output)
+ single_entry(input, output, react_values)
+ bulk_entry(input, output, react_values)
+ render_data(output, react_values)
+ delete_data(input, react_values)
+ export_data(output, react_values)
+}
+
+# Convert the input case counts string to an integer vector.
+tokenize_counts <- function(counts_str) {
+ suppressWarnings(as.integer(unlist(strsplit(trimws(counts_str), ","))))
+}
+
+# Render the preview plot for single entry data.
+render_plot <- function(input, output) {
+ observe({
+ counts <- tokenize_counts(input$data_counts)
+ if (length(counts) > 0 && !anyNA(counts) && all(counts >= 0)) {
+ output$data_plot <- renderPlot(
+ plot(seq_along(counts) - 1, counts, type = "o", pch = 16, col = "red",
+ xlab = input$data_units, ylab = "Cases", cex.lab = 1.5,
+ xlim = c(0, max(length(counts) - 1, 1)), ylim = c(0, max(counts, 1))
+ )
+ )
+ } else {
+ output$data_plot <- renderPlot(
+ plot(NULL, xlim = c(0, 10), ylim = c(0, 10),
+ xlab = input$data_units, ylab = "Cases", cex.lab = 1.5
+ )
+ )
+ }
+ })
+}
+
+# Add a single dataset to the existing table.
+single_entry <- function(input, output, react_values) {
+ observeEvent(input$data_single, {
+ valid <- TRUE
+
+ # Ensure the dataset name is neither blank nor a duplicate.
+ name <- trimws(input$data_name)
+ if (name == "") {
+ output$data_name_warn <- renderText("The dataset name cannot be blank.")
+ valid <- FALSE
+ } else if (name %in% react_values$data_table[, 1]) {
+ output$data_name_warn <- renderText(
+ "There is already a dataset with the specified name."
+ )
+ valid <- FALSE
+ } else {
+ output$data_name_warn <- renderText("")
+ }
+
+ # Ensure the case counts are specified as a comma-separated of one or more
+ # non-negative integers.
+ counts <- tokenize_counts(input$data_counts)
+ if (length(counts) == 0) {
+ output$data_counts_warn <- renderText("Case counts cannot be blank.")
+ valid <- FALSE
+ } else if (anyNA(counts) || any(counts < 0)) {
+ output$data_counts_warn <- renderText(
+ "Case counts can only contain non-negative integers."
+ )
+ valid <- FALSE
+ } else {
+ output$data_counts_warn <- renderText("")
+ }
+
+ if (valid) {
+ # Add the new dataset to the data table.
+ new_row <- data.frame(name, input$data_units, toString(counts))
+ colnames(new_row) <- c("Name", "Time units", "Case counts")
+ react_values$data_table <- rbind(react_values$data_table, new_row)
+
+ # Evaluate all existing estimators on the new dataset and update the
+ # corresponding row in the estimates table.
+ update_estimates_rows(new_row, react_values)
+
+ showNotification("Dataset added successfully.",
+ duration = 3, id = "notify-success"
+ )
+ }
+ })
+}
+
+# Add multiple datasets to the existing table.
+bulk_entry <- function(input, output, react_values) {
+ observeEvent(input$data_bulk, {
+ tryCatch(
+ {
+ datasets <- read.csv(text = input$data_area, header = FALSE, sep = ",")
+
+ names <- trimws(datasets[, 1])
+ units <- trimws(datasets[, 2])
+ counts <- apply(datasets[, 3:ncol(datasets)], 1,
+ function(row) {
+ row <- suppressWarnings(as.integer(row))
+ toString(row[!is.na(row) & row >= 0])
+ }
+ )
+
+ warning_text <- ""
+
+ # Ensure the dataset names are neither blank nor duplicates.
+ if (anyNA(names) || any(names == "")) {
+ warning_text <- paste0(warning_text, sep = "<br>",
+ "Each row must begin with a non-blank dataset name."
+ )
+ } else {
+ if (length(unique(names)) != length(names)) {
+ warning_text <- paste0(warning_text, sep = "<br>",
+ "The rows contain duplicate dataset names."
+ )
+ }
+ if (any(names %in% react_values$data_table[, 1])) {
+ warning_text <- paste0(warning_text, sep = "<br>",
+ "The rows contain dataset names which already exist."
+ )
+ }
+ }
+
+ # Ensure the second entry in each row is a time unit equal to
+ # "Days" or "Weeks".
+ if (!all(units %in% c("Days", "Weeks"))) {
+ warning_text <- paste0(warning_text, sep = "<br>",
+ "The second entry in each row must be either 'Days' or 'Weeks'."
+ )
+ }
+
+ # Ensure the counts in each row have at least one non-negative integer.
+ if (any(counts == "")) {
+ warning_text <- paste0(warning_text, sep = "<br>",
+ "Each row must contain at least one non-negative integer."
+ )
+ }
+
+ output$data_area_warn <- renderUI(HTML(warning_text))
+
+ if (warning_text == "") {
+ # Add the new datasets to the data table.
+ new_rows <- data.frame(names, units, counts)
+ colnames(new_rows) <- c("Name", "Time units", "Case counts")
+ react_values$data_table <- rbind(react_values$data_table, new_rows)
+
+ # Evaluate all existing estimators on the new dataset and update the
+ # corresponding row in the estimates table.
+ update_estimates_rows(new_rows, react_values)
+
+ showNotification("Datasets added successfully.",
+ duration = 3, id = "notify-success"
+ )
+ }
+ },
+ error = function(e) {
+ output$data_area_warn <- renderText(
+ "The input does not match the required format."
+ )
+ }
+ )
+ })
+}
+
+# Render the data table when new datasets are added.
+render_data <- function(output, react_values) {
+ observe({
+ output$data_table <- DT::renderDataTable(react_values$data_table)
+ })
+}
+
+# Delete rows in the data table,
+# and the corresponding rows in the estimates table.
+delete_data <- function(input, react_values) {
+ observeEvent(input$data_delete, {
+ new_table <- react_values$data_table[-input$data_table_rows_selected, ]
+ if (nrow(new_table) > 0) {
+ rownames(new_table) <- seq_len(nrow(new_table))
+ }
+ react_values$data_table <- new_table
+
+ if (ncol(react_values$estimates_table) == 1) {
+ react_values$estimates_table <- data.frame(
+ Datasets = react_values$data_table[, 1]
+ )
+ } else {
+ react_values$estimates_table <-
+ react_values$estimates_table[-input$data_table_rows_selected, ]
+ }
+ })
+}
+
+# Export data table as a CSV file.
+export_data <- function(output, react_values) {
+ output$data_export <- downloadHandler(
+ filename = function() {
+ paste0("Rnaught_data_", format(Sys.time(), "%y-%m-%d_%H-%M-%S"), ".csv")
+ },
+ content = function(file) {
+ write.csv(react_values$data_table, file, row.names = FALSE)
+ }
+ )
+}
+
+# When new datasets are added, evaluate all existing estimators on them and
+# add new rows to the estimates table.
+update_estimates_rows <- function(datasets, react_values) {
+ new_rows <- data.frame(
+ matrix(nrow = nrow(datasets), ncol = ncol(react_values$estimates_table))
+ )
+ colnames(new_rows) <- colnames(react_values$estimates_table)
+
+ for (row in seq_len(nrow(datasets))) {
+ new_rows[row, 1] <- datasets[row, 1]
+
+ if (length(react_values$estimators) > 0) {
+ for (col in 2:ncol(react_values$estimates_table)) {
+ new_rows[row, col] <- eval_estimator(
+ react_values$estimators[[col - 1]], datasets[row, ]
+ )
+ }
+ }
+ }
+
+ react_values$estimates_table <- rbind(
+ react_values$estimates_table, new_rows
+ )
+}
--- /dev/null
+estimators_logic <- function(input, output, react_values) {
+ # Initialize a data frame to hold estimates.
+ react_values$estimates_table <- data.frame(Dataset = character(0))
+ # Initialize a list to hold added estimators.
+ react_values$estimators <- list()
+
+ add_id(input, output, react_values)
+ add_idea(input, output, react_values)
+ add_seq_bayes(input, output, react_values)
+ add_wp(input, output, react_values)
+
+ render_estimates(output, react_values)
+ delete_estimators(input, react_values)
+ export_estimates(output, react_values)
+}
+
+# If an estimator is added, ensure it is not a duplicate and add it to the list
+# of estimators. This function should be called at the end of each
+# estimator-specific 'add' function, after validating their parameters.
+add_estimator <- function(method, new_estimator, output, react_values) {
+ num_estimators <- length(react_values$estimators)
+
+ # Check whether the new estimator is a duplicate, and warn if so.
+ for (i in seq_len(num_estimators)) {
+ if (identical(new_estimator, react_values$estimators[[i]])) {
+ showNotification("Error: This estimator has already been added.",
+ duration = 3, id = "notify-error"
+ )
+ return()
+ }
+ }
+
+ # Add the new estimator to the list of estimators.
+ react_values$estimators[[num_estimators + 1]] <- new_estimator
+
+ showNotification("Estimator added successfully.",
+ duration = 3, id = "notify-success"
+ )
+
+ # Evaluate all the new estimator on all existing datasets and create a new
+ # column in the estimates table.
+ update_estimates_col(new_estimator, react_values)
+}
+
+# Ensure serial intervals are specified as positive numbers.
+validate_mu <- function(method, input, output) {
+ mu <- suppressWarnings(as.numeric(trimws(input[[paste0("mu_", method)]])))
+ if (is.na(mu) || mu <= 0) {
+ output[[paste0("mu_", method, "_warn")]] <- renderText(
+ "The serial interval must be a positive number."
+ )
+ return(NULL)
+ }
+ output[[paste0("mu_", method, "_warn")]] <- renderText("")
+ mu
+}
+
+# Incidence Decay (ID).
+add_id <- function(input, output, react_values) {
+ observeEvent(input$add_id, {
+ mu <- validate_mu("id", input, output)
+ if (!is.null(mu)) {
+ new_estimator <- list(
+ method = "id", mu = mu, mu_units = input$mu_id_units
+ )
+ add_estimator("id", new_estimator, output, react_values)
+ }
+ })
+}
+
+# Incidence Decay and Exponential Adjustment (IDEA).
+add_idea <- function(input, output, react_values) {
+ observeEvent(input$add_idea, {
+ mu <- validate_mu("idea", input, output)
+ if (!is.null(mu)) {
+ new_estimator <- list(
+ method = "idea", mu = mu, mu_units = input$mu_idea_units
+ )
+ add_estimator("idea", new_estimator, output, react_values)
+ }
+ })
+}
+
+# Sequential Bayes (seqB).
+add_seq_bayes <- function(input, output, react_values) {
+ observeEvent(input$add_seq_bayes, {
+ mu <- validate_mu("seq_bayes", input, output)
+
+ kappa <- trimws(input$kappa)
+ kappa <- if (kappa == "") 20 else suppressWarnings(as.numeric(kappa))
+
+ if (is.na(kappa) || kappa <= 0) {
+ output$kappa_warn <- renderText(
+ "The maximum prior must be a positive number."
+ )
+ } else if (!is.null(mu)) {
+ output$kappa_warn <- renderText("")
+ new_estimator <- list(
+ method = "seq_bayes", mu = mu,
+ mu_units = input$mu_seq_bayes_units, kappa = kappa
+ )
+ add_estimator("seq_bayes", new_estimator, output, react_values)
+ }
+ })
+}
+
+# White and Pagano (WP).
+add_wp <- function(input, output, react_values) {
+ observeEvent(input$add_wp, {
+ if (input$wp_mu_known == "Yes") {
+ mu <- validate_mu("wp", input, output)
+ if (!is.null(mu)) {
+ new_estimator <- list(method = "wp",
+ mu = mu, mu_units = input$mu_wp_units
+ )
+ add_estimator("wp", new_estimator, output, react_values)
+ }
+ } else {
+ grid_length <- trimws(input$grid_length)
+ max_shape <- trimws(input$max_shape)
+ max_scale <- trimws(input$max_scale)
+
+ suppressWarnings({
+ grid_length <- if (grid_length == "") 100 else as.numeric(grid_length)
+ max_shape <- if (max_shape == "") 10 else as.numeric(max_shape)
+ max_scale <- if (max_scale == "") 10 else as.numeric(max_scale)
+ })
+
+ valid <- TRUE
+
+ if (is.na(grid_length) || grid_length <= 0) {
+ output$grid_length_warn <- renderText(
+ "The grid length must be a positive integer."
+ )
+ valid <- FALSE
+ } else {
+ output$grid_length_warn <- renderText("")
+ }
+
+ if (is.na(max_shape) || max_shape <= 0) {
+ output$max_shape_warn <- renderText(
+ "The maximum shape must be a positive number."
+ )
+ valid <- FALSE
+ } else {
+ output$max_shape_warn <- renderText("")
+ }
+
+ if (is.na(max_scale) || max_scale <= 0) {
+ output$max_scale_warn <- renderText(
+ "The maximum scale must be a positive number."
+ )
+ valid <- FALSE
+ } else {
+ output$max_scale_warn <- renderText("")
+ }
+
+ if (valid) {
+ new_estimator <- list(method = "wp", mu = NA, grid_length = grid_length,
+ max_shape = max_shape, max_scale = max_scale
+ )
+ add_estimator("wp", new_estimator, output, react_values)
+ }
+ }
+ })
+}
+
+# Convert an estimator's specified serial interval to match the time units of
+# the given dataset.
+convert_mu_units <- function(data_units, estimator_units, mu) {
+ if (data_units == "Days" && estimator_units == "Weeks") {
+ return(mu * 7)
+ } else if (data_units == "Weeks" && estimator_units == "Days") {
+ return(mu / 7)
+ }
+ mu
+}
+
+# Add a column to the estimates table when a new estimator is added.
+update_estimates_col <- function(estimator, react_values) {
+ dataset_rows <- seq_len(nrow(react_values$data_table))
+ estimates <- dataset_rows
+
+ for (row in dataset_rows) {
+ estimate <- eval_estimator(estimator, react_values$data_table[row, ])
+ estimates[row] <- estimate
+ }
+
+ estimates <- data.frame(estimates)
+ colnames(estimates) <- estimates_col_name(estimates, estimator)
+
+ react_values$estimates_table <- cbind(
+ react_values$estimates_table, estimates
+ )
+}
+
+# Evaluate the specified estimator on the given dataset.
+eval_estimator <- function(estimator, dataset) {
+ cases <- as.integer(unlist(strsplit(dataset[, 3], ",")))
+
+ if (estimator$method == "id") {
+ mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+ estimate <- round(Rnaught::id(cases, mu), 2)
+ } else if (estimator$method == "idea") {
+ mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+ estimate <- round(Rnaught::idea(cases, mu), 2)
+ } else if (estimator$method == "seq_bayes") {
+ mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+ estimate <- round(Rnaught::seq_bayes(cases, mu, estimator$kappa), 2)
+ } else if (estimator$method == "wp") {
+ if (is.na(estimator$mu)) {
+ estimate <- Rnaught::wp(cases, serial = TRUE,
+ grid_length = estimator$grid_length,
+ max_shape = estimator$max_shape, max_scale = estimator$max_scale
+ )
+ estimated_mu <- round(sum(estimate$supp * estimate$pmf), 2)
+ estimate <- paste0(round(estimate$r0, 2), " (μ = ", estimated_mu,
+ " ", tolower(dataset[, 2]), ")"
+ )
+ } else {
+ mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+ estimate <- round(Rnaught::wp(cases, mu), 2)
+ }
+ }
+
+ return(estimate)
+}
+
+# Create the column name of an estimator when it is
+# added to the estimates table.
+estimates_col_name <- function(estimates, estimator) {
+ if (estimator$method == "id") {
+ return(paste0("ID", " (μ = ", estimator$mu, " ",
+ tolower(estimator$mu_units), ")"
+ ))
+ } else if (estimator$method == "idea") {
+ return(paste0("IDEA", " (μ = ", estimator$mu, " ",
+ tolower(estimator$mu_units), ")"
+ ))
+ } else if (estimator$method == "seq_bayes") {
+ return(paste0("seqB", " (μ = ", estimator$mu, " ",
+ tolower(estimator$mu_units), ", κ = ", estimator$kappa, ")"
+ ))
+ } else if (estimator$method == "wp") {
+ if (is.na(estimator$mu)) {
+ return(paste0("WP (", estimator$grid_length, ", ",
+ round(estimator$max_shape, 3), ", ", round(estimator$max_scale, 3), ")"
+ ))
+ } else {
+ return(paste0("WP", " (μ = ", estimator$mu, " ",
+ tolower(estimator$mu_units), ")"
+ ))
+ }
+ }
+}
+
+# Render the estimates table whenever it is updated.
+render_estimates <- function(output, react_values) {
+ observe({
+ output$estimates_table <- DT::renderDataTable(react_values$estimates_table,
+ selection = list(target = "column", selectable = c(0)),
+ escape = FALSE, rownames = FALSE,
+ options = list(
+ columnDefs = list(list(className = "dt-left", targets = "_all"))
+ ),
+ )
+ })
+}
+
+# Delete columns from the estimates table,
+# as well as the corresponding estimators.
+delete_estimators <- function(input, react_values) {
+ observeEvent(input$estimators_delete, {
+ cols_selected <- input$estimates_table_columns_selected
+ react_values$estimators <- react_values$estimators[-cols_selected]
+ react_values$estimates_table[, cols_selected + 1] <- NULL
+ })
+}
+
+# Export estimates table as a CSV file.
+export_estimates <- function(output, react_values) {
+ output$estimates_export <- downloadHandler(
+ filename = function() {
+ paste0(
+ "Rnaught_estimates_", format(Sys.time(), "%y-%m-%d_%H-%M-%S"), ".csv"
+ )
+ },
+ content = function(file) {
+ output_table <- data.frame(
+ lapply(react_values$estimates_table, sub_entity)
+ )
+ colnames(output_table) <- sub_entity(
+ colnames(react_values$estimates_table)
+ )
+ write.csv(output_table, file, row.names = FALSE)
+ }
+ )
+}
+
+# Substitute HTML entity codes with natural names.
+sub_entity <- function(obj) {
+ obj <- gsub("μ", "mu", obj)
+ obj <- gsub("κ", "kappa", obj)
+ obj
+}
--- /dev/null
+<div class="container-fluid tab-content px-3 py-3">
+ <div id="about" class="tab-pane fade show active px-1">
+ {{ htmlTemplate("templates/content/about.html") }}
+ </div>
+ <div id="data" class="tab-pane fade">
+ {{ htmlTemplate("templates/content/data.html") }}
+ </div>
+ <div id="estimators" class="tab-pane fade">
+ {{ htmlTemplate("templates/content/estimators.html") }}
+ </div>
+ <div id="help" class="tab-pane fade">
+ {{ htmlTemplate("templates/content/help.html") }}
+ </div>
+</div>
--- /dev/null
+<h1>Welcome to the Rnaught web application!</h1>
+<p>
+ Rnaught is an R package and web application for estimating the
+ <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" target="_blank">basic reproduction number</a>
+ of infectious diseases. For information about using this application, view the
+ <span class="fw-bold text-primary">Help <span class="glyphicon glyphicon-question-sign"></span></span> tab.
+ To learn more about the package, visit the online
+ <a href="https://MI2YorkU.github.io/Rnaught" target="_blank">documentation</a> or
+ <a href="https://github.com/MI2YorkU/Rnaught" target="_blank">GitHub</a> repository.
+ Technical details about the estimators featured in this project can be found in the reference
+ <a href="https://doi.org/10.1371/journal.pone.0269306" target="_blank">article</a>.
+</p>
+
+<h4>What is the basic reproduction number?</h4>
+<p>
+ The basic reproduction number, denoted <em>R<sub>0</sub></em>, describes the expected number of infections caused by a
+ single infectious individual. It assumes that all individuals in a given population are susceptible to the disease,
+ and that no preventive measures (such as lockdowns or vaccinations) have been enforced. As such, it is a useful
+ indicator of the transmissibility of a disease during the early stages of its detection.
+</p>
+<p>
+ If <em>R<sub>0</sub></em> < 1, then the disease will eventually die out. On the other hand, if
+ <em>R<sub>0</sub></em> > 1, the rate at which the disease spreads is exponential. Typically, it is difficult to
+ determine <em>R<sub>0</sub></em> precisely, due to uncertainty in information relating to the spread of the disease.
+ Therefore, many estimation methods exist, each based on their own models and yielding different estimates. It is the
+ responsibility of public health officials to employ the most appropriate estimator given the situation at hand.
+</p>
--- /dev/null
+<nav class="nav nav-tabs">
+ <a class="nav-link active" data-bs-toggle="tab" href="#enter-data">Enter data</a>
+ <a class="nav-link" data-bs-toggle="tab" href="#view-data">View data</a>
+</nav>
+
+<div class="container-fluid tab-content">
+ <div id="enter-data" class="pt-3 tab-pane fade show active">
+ {{ htmlTemplate("templates/content/data/enter-data.html") }}
+ </div>
+ <div id="view-data" class="pt-3 tab-pane fade">
+ {{ htmlTemplate("templates/content/data/view-data.html") }}
+ </div>
+</div>
--- /dev/null
+<div class="row mb-5">
+ <form class="col-md">
+ {{ htmlTemplate("templates/content/data/enter-data/single-entry.html") }}
+ </form>
+ <div class="col-md mt-5 mt-md-0 d-flex flex-column align-items-center">
+ <h5>Data plot</h5>
+ {{ plotOutput(outputId = "data_plot") }}
+ </div>
+</div>
+<hr>
+<form>
+ {{ htmlTemplate("templates/content/data/enter-data/bulk-entry.html") }}
+</form>
--- /dev/null
+<h4 class="mb-3">Bulk entry</h4>
+<!-- Button to toggle help text. -->
+<button type="button" class="btn btn-outline-primary btn-sm" id="bulk-help-toggle"
+ data-bs-toggle="collapse" data-bs-target="#bulk-help">
+ Show required format
+</button>
+<!-- Help text for bulk input format. -->
+<div class="collapse mt-2" id="bulk-help">
+ <div class="card card-body border-primary">
+ <p>Enter one or more rows in the following format:</p>
+ <p class="overflow-x-scroll text-nowrap font-monospace">
+ <u>Dataset name</u>,<u>Time units</u>,<u>Case counts</u>
+ </p>
+ <p>
+ <u class="font-monospace">Time units</u> must be one of
+ <u class="font-monospace">Days</u> or
+ <u class="font-monospace">Weeks</u>, and
+ <u class="font-monospace">Case counts</u>
+ must be a comma-separated list of one or more non-negative integers.
+ </p>
+ <p>Example:</p>
+ <p class="overflow-x-scroll text-nowrap font-monospace lh-sm">
+ Montreal,Days,1,2,3,4,5,6,7,8,9,19<br>
+ Ottawa,Weeks,1,2,3,4,5,6,7,8,9,19<br>
+ Toronto,Days,1,2,3,4,5,6,7,8,9,19
+ </p>
+ </div>
+</div>
+<!-- Data input area. -->
+<div>
+ <textarea id="data_area" class="form-control shiny-input-textarea my-3" rows="3" wrap="off"></textarea>
+ <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small>
+</div>
+<!-- Submit data. -->
+<button id="data_bulk" type="button" class="btn btn-outline-primary btn-sm action-button">
+ <span class="glyphicon glyphicon-plus"></span> Add
+</button>
--- /dev/null
+<h4>Single entry</h4>
+<!-- Dataset name. -->
+<div class="my-3">
+ <label class="form-label" for="data_name">Dataset name</label>
+ <input name="data_name" class="form-control" type="text">
+ <small id="data_name_warn" class="form-text text-primary shiny-text-output"></small>
+</div>
+<!-- Case counts. -->
+<div class="mb-3">
+ <label class="form-label" for="data_counts">
+ Case counts
+ <sup data-bs-toggle="tooltip" data-bs-placement="right"
+ data-bs-title="Enter as a comma-separated list of non-negative integers (example: 0,1,1,2,3,5,8,13).">
+ [?]
+ </sup>
+ </label>
+ <input name="data_counts" class="form-control" type="text">
+ <small id="data_counts_warn" class="form-text text-primary shiny-text-output"></small>
+</div>
+<!-- Time units. -->
+<div class="mb-3">
+ <label class="form-label" for="data_units">Time units</label>
+ <div class="shiny-input-radiogroup" id="data_units">
+ <div class="form-check form-check-inline">
+ <label class="form-check-label">
+ <input type="radio" class="form-check-input me-2" name="data_units" value="Days">Days
+ </label>
+ </div>
+ <div class="form-check form-check-inline">
+ <label class="form-check-label">
+ <input type="radio" class="form-check-input me-2" name="data_units" value="Weeks" checked>Weeks
+ </label>
+ </div>
+ </div>
+</div>
+<!-- Submit data. -->
+<button id="data_single" type="button" class="btn btn-outline-primary btn-sm action-button">
+ <span class="glyphicon glyphicon-plus"></span> Add
+</button>
--- /dev/null
+<h4>Data table</h4>
+<!-- Data table. -->
+<div class="my-3">
+ {{ DT::dataTableOutput(outputId = "data_table") }}
+</div>
+<!-- Display inactive delete button when no rows are selected. -->
+<button type="button" class="btn btn-primary btn-sm text-white" disabled
+ data-display-if="'data_table_rows_selected' in input && input.data_table_rows_selected.length == 0">
+ <span class="glyphicon glyphicon-remove"></span> Delete row(s)
+</button>
+<!-- Display active delete button when at least one row is selected. -->
+<button id="data_delete" type="button" class="btn btn-primary btn-sm action-button text-white"
+ data-display-if="'data_table_rows_selected' in input && input.data_table_rows_selected.length != 0">
+ <span class="glyphicon glyphicon-remove"></span> Delete row(s)
+</button>
+<!-- Button to export data table as a CSV file. -->
+<a id="data_export" type="button" class="btn btn-outline-primary btn-sm shiny-download-link">
+ <span class="glyphicon glyphicon-download-alt"></span> Export table
+</a>
--- /dev/null
+<nav class="nav nav-tabs">
+ <a class="nav-link active" data-bs-toggle="tab" href="#add-estimators">Add estimators</a>
+ <a class="nav-link" data-bs-toggle="tab" href="#view-estimates">View estimates</a>
+</nav>
+
+<div class="container-fluid tab-content">
+ <div id="add-estimators" class="pt-3 tab-pane fade show active">
+ {{ htmlTemplate("templates/content/estimators/add-estimators.html") }}
+ </div>
+ <div id="view-estimates" class="pt-3 tab-pane fade">
+ {{ htmlTemplate("templates/content/estimators/view-estimates.html") }}
+ </div>
+</div>
--- /dev/null
+<div class="accordion accordion-flush" id="estimators-accordion">
+ {{
+ htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+ id = "id",
+ header = "Incidence Decay (ID)",
+ reference_label = "Fisman et al. (PloS One, 2013)",
+ reference_url = "https://doi.org/10.1371/journal.pone.0083622"
+ )
+ }}
+ {{
+ htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+ id = "idea",
+ header = "Incidence Decay and Exponential Adjustment (IDEA)",
+ reference_label = "Fisman et al. (PloS One, 2013)",
+ reference_url = "https://doi.org/10.1371/journal.pone.0083622"
+ )
+ }}
+ {{
+ htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+ id = "seq_bayes",
+ header = "Sequential Bayes (seqB)",
+ reference_label = "Bettencourt and Riberio (PloS One, 2008)",
+ reference_url = "https://doi.org/10.1371/journal.pone.0002185"
+ )
+ }}
+ {{
+ htmlTemplate("templates/content/estimators/add-estimators/components/panel.html",
+ id = "wp",
+ header = "White and Pagano (WP)",
+ reference_label = "White and Pagano (Statistics in Medicine, 2008)",
+ reference_url = "https://doi.org/10.1002/sim.3136"
+ )
+ }}
+</div>
--- /dev/null
+<!-- Serial interval label and help tooltip. -->
+<label class="form-label" for="mu_{{ id }}">
+ Serial interval (μ)
+ <sup data-bs-toggle="tooltip" data-bs-placement="right"
+ data-bs-title="The serial interval is the time between when an infected individual (the infector) becomes
+ symptomatic, to when another individual (who is infected by the infector) becomes symptomatic.">
+ [?]
+ </sup>
+</label>
+<div class="input-group">
+ <!-- Serial interval input field. -->
+ <input name="mu_{{ id }}" class="form-control" type="text">
+ <!-- Days/weeks dropdown. -->
+ <select name="mu_{{ id }}_units" class="form-select">
+ <option value="Days" selected>Days</option>
+ <option value="Weeks">Weeks</option>
+ </select>
+</div>
+<!-- Warning text for incorrect values. -->
+<small id="mu_{{ id }}_warn" class="form-text text-primary shiny-text-output"></small>
--- /dev/null
+<div class="accordion-item">
+ <h2 class="accordion-header">
+ <button class="accordion-button collapsed" type="button"
+ data-bs-toggle="collapse" data-bs-target="#{{ id }}">
+ <h4>{{ header }}</h4>
+ </button>
+ </h2>
+ <div id="{{ id }}" class="accordion-collapse collapse" data-bs-parent="#estimators-accordion">
+ <div class="accordion-body">
+ <p>Reference: <a href="{{ reference_url }}" target="_blank"><em>{{ reference_label }}</em></a></p>
+ <p>{{ htmlTemplate(paste0("templates/content/estimators/add-estimators/descriptions/", id, ".html")) }}</p>
+ <h5>Parameters</h5>
+ <form class="my-3">
+ {{ htmlTemplate(paste0("templates/content/estimators/add-estimators/parameters/", id, ".html")) }}
+ </form>
+ <button id="add_{{ id }}" type="button" class="btn btn-outline-primary btn-sm action-button">
+ <span class="glyphicon glyphicon-plus"></span> Add
+ </button>
+ </div>
+ </div>
+</div>
--- /dev/null
+This is a short description of the ID method.
--- /dev/null
+This is a short description of the IDEA method.
--- /dev/null
+This is a short description of the seqB method.
--- /dev/null
+This is a short description of the WP method.
--- /dev/null
+{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "id") }}
--- /dev/null
+{{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "idea") }}
--- /dev/null
+<div class="row">
+ <!-- Serial interval (mu). -->
+ <div class="col-md">
+ {{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "seq_bayes") }}
+ </div>
+ <!-- Maximum value of the uniform prior (kappa). -->
+ <div class="col-md mt-2 mt-md-0">
+ <!-- Label and help tooltip. -->
+ <label class="form-label" for="kappa">
+ Maximum prior (κ)
+ <sup data-bs-toggle="tooltip" data-bs-placement="right" data-bs-html="true"
+ data-bs-title="The initial maximum belief of <em>R<sub>0</sub></em>. The higher this value, the higher
+ <em>R<sub>0</sub></em> is believed to be prior to the estimation.">
+ [?]
+ </sup>
+ </label>
+ <!-- Input field. -->
+ <input name="kappa" class="form-control" type="text" placeholder="Default: 20">
+ <!-- Warning text for incorrect values. -->
+ <small id="kappa_warn" class="form-text text-primary shiny-text-output"></small>
+ </div>
+</div>
--- /dev/null
+<!-- Radio buttons to specify whether the serial interval is known. -->
+<label class="form-label" for="wp_mu_known">Is the serial interval known?</label>
+<div class="shiny-input-radiogroup" id="wp_mu_known">
+ <div class="form-check form-check-inline">
+ <label class="form-check-label">
+ <input type="radio" class="form-check-input me-2" name="wp_mu_known" value="Yes" checked>Yes
+ </label>
+ </div>
+ <div class="form-check form-check-inline">
+ <label class="form-check-label">
+ <input type="radio" class="form-check-input me-2" name="wp_mu_known" value="No">No
+ </label>
+ </div>
+</div>
+<!-- Show the input field for the serial interval if it is known. -->
+<div data-display-if="input.wp_mu_known == 'Yes'" class="mt-2 mt-md-0">
+ {{ htmlTemplate("templates/content/estimators/add-estimators/components/mu.html", id = "wp") }}
+</div>
+<!-- Show the input fields for the grid search parameters if the serial interval is unknown. -->
+<div data-display-if="input.wp_mu_known == 'No'" class="row">
+ <!-- Grid length. -->
+ <div class="col-md mt-2 mt-md-0">
+ <label class="form-label" for="grid_length">Grid length</label>
+ <input name="grid_length" class="form-control" type="text" placeholder="Default: 100">
+ <small id="grid_length_warn" class="form-text text-primary shiny-text-output"></small>
+ </div>
+ <!-- Maximum shape. -->
+ <div class="col-md mt-2 mt-md-0">
+ <label class="form-label" for="max_shape">Maximum shape</label>
+ <input name="max_shape" class="form-control" type="text" placeholder="Default: 10">
+ <small id="max_shape_warn" class="form-text text-primary shiny-text-output"></small>
+ </div>
+ <!-- Grid length. -->
+ <div class="col-md mt-2 mt-md-0">
+ <label class="form-label" for="max_scale">Maximum scale</label>
+ <input name="max_scale" class="form-control" type="text" placeholder="Default: 10">
+ <small id="max_scale_warn" class="form-text text-primary shiny-text-output"></small>
+ </div>
+</div>
--- /dev/null
+<h4>Estimates table</h4>
+<!-- Estimates table. -->
+<div class="my-3">
+ {{ DT::dataTableOutput(outputId = "estimates_table") }}
+</div>
+<!-- Display inactive delete button when no columns are selected. -->
+<button type="button" class="btn btn-primary btn-sm text-white" disabled
+ data-display-if="'estimates_table_columns_selected' in input &&
+ input.estimates_table_columns_selected.length == 0">
+ <span class="glyphicon glyphicon-remove"></span> Delete column(s)
+</button>
+<!-- Display active delete button when at least one column is selected. -->
+<button id="estimators_delete" type="button" class="btn btn-primary btn-sm action-button text-white"
+ data-display-if="'estimates_table_columns_selected' in input &&
+ input.estimates_table_columns_selected.length != 0">
+ <span class="glyphicon glyphicon-remove"></span> Delete column(s)
+</button>
+<!-- Button to export estimates table as a CSV file. -->
+<a id="estimates_export" type="button" class="btn btn-outline-primary btn-sm shiny-download-link">
+ <span class="glyphicon glyphicon-download-alt"></span> Export table
+</a>
--- /dev/null
+<div class="accordion accordion-flush" id="help-accordion">
+ {{
+ htmlTemplate("templates/content/help/panel.html",
+ id = "example-help-1",
+ header = "Example help 1"
+ )
+ }}
+ {{
+ htmlTemplate("templates/content/help/panel.html",
+ id = "example-help-2",
+ header = "Example help 2"
+ )
+ }}
+</div>
--- /dev/null
+Example help 1
--- /dev/null
+Example help 2
--- /dev/null
+<div class="accordion-item">
+ <h2 class="accordion-header">
+ <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#{{ id }}">
+ {{ header }}
+ </button>
+ </h2>
+ <div id="{{ id }}" class="accordion-collapse collapse" data-bs-parent="#help-accordion">
+ <div class="accordion-body">
+ {{ htmlTemplate(paste0("templates/content/help/", id, ".html")) }}
+ </div>
+ </div>
+</div>
--- /dev/null
+<footer class="container-fluid mt-auto text-center">
+ <em>
+ Released under the
+ <a href="https://www.gnu.org/licenses/agpl-3.0.html" target="_blank">AGPLv3</a>
+ or later.
+ </em>
+</footer>
--- /dev/null
+<nav class="navbar navbar-expand-sm">
+ <div class="container-fluid">
+ <!-- Project name and description. -->
+ <a class="navbar-brand text-primary" href="/">Rnaught Web</a>
+ <span class="navbar-text d-none d-md-block">
+ An estimation suite for <em>R<sub>0</sub></em>
+ </span>
+ <!-- Navigation toggler for smaller screens. -->
+ <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#nav-toggle">
+ <span class="glyphicon glyphicon-menu-hamburger text-primary"></span>
+ </button>
+ <!-- Navigation links. -->
+ <div class="collapse navbar-collapse justify-content-end" id="nav-toggle">
+ <div class="navbar-nav">
+ <a class="nav-link text-primary" href="https://MI2YorkU.github.io/Rnaught" target="_blank">
+ <span class="glyphicon glyphicon-book"></span> Documentation
+ </a>
+ <a class="nav-link text-primary" href="https://github.com/MI2Yorku/Rnaught" target="_blank">
+ <span class="glyphicon glyphicon-console"></span> Source
+ </a>
+ <a class="nav-link text-primary" href="https://doi.org/10.1371/journal.pone.0269306" target="_blank">
+ <span class="glyphicon glyphicon-education"></span> Article
+ </a>
+ </div>
+ </div>
+ </div>
+</nav>
--- /dev/null
+<nav class="nav nav-pills nav-fill">
+ <a class="nav-link rounded-0 active" data-bs-toggle="pill" href="#about">
+ About <span class="glyphicon glyphicon-info-sign"></span>
+ </a>
+ <a class="nav-link rounded-0" data-bs-toggle="pill" href="#data">
+ Data <span class="glyphicon glyphicon-list-alt"></span>
+ </a>
+ <a class="nav-link rounded-0" data-bs-toggle="pill" href="#estimators">
+ Estimators <span class="glyphicon glyphicon-random"></span>
+ </a>
+ <a class="nav-link rounded-0" data-bs-toggle="pill" href="#help">
+ Help <span class="glyphicon glyphicon-question-sign"></span>
+ </a>
+</nav>
--- /dev/null
+body {
+ min-height: 100vh;
+ height: 100%;
+ width: 100%;
+}
+
+noscript {
+ text-align: center;
+}
+
+.nav-pills .active {
+ color: white !important;
+}
+
+.action-button:hover, #bulk-help-toggle:hover, #data_export:hover {
+ color: white !important;
+}
+
+#data_plot {
+ margin-top: -0.5rem;
+}
+
+td.selected {
+ background-color: red;
+ color: white;
+}
git.nmode.ca / Rnaught / commitdiff
