diff options
Diffstat (limited to 'inst/web')
39 files changed, 1101 insertions, 0 deletions
diff --git a/inst/web/app.R b/inst/web/app.R new file mode 100644 index 0000000..639dc87 --- /dev/null +++ b/inst/web/app.R @@ -0,0 +1,13 @@ +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) diff --git a/inst/web/index.html b/inst/web/index.html new file mode 100644 index 0000000..504918d --- /dev/null +++ b/inst/web/index.html @@ -0,0 +1,19 @@ +<!DOCTYPE html> +<html> + <head> + {{ bootstrapLib(theme = bslib::bs_theme(primary = "black")) }} + {{ headContent() }} + <title>Rnaught Web</title> + <link rel="stylesheet" type="text/css" href="styles.css"> + <script src="script.js"></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> diff --git a/inst/web/scripts/data.R b/inst/web/scripts/data.R new file mode 100644 index 0000000..8f8694c --- /dev/null +++ b/inst/web/scripts/data.R @@ -0,0 +1,253 @@ +# Main logic block for data-related interactions. +data_logic <- function(input, output, react_values) { + # Initialize a data frame to hold the datasets. + react_values$data_table <- data.frame( + Name = character(0), + `Time units` = character(0), + `Case counts` = character(0), + check.names = FALSE + ) + + manual_entry(input, output, react_values) + upload_data(input, output, react_values) + load_samples(input, output, react_values) + render_data_table(output, react_values) + render_plot(input, output, react_values, "Days") + render_plot(input, output, react_values, "Weeks") + delete_data(input, react_values) + export_data(output, react_values) +} + +# Convert the input case counts string to an integer vector. +tokenize_counts <- function(counts_str) { + suppressWarnings(as.integer(unlist(strsplit(trimws(counts_str), ",")))) +} + +# Render the plots for daily and weekly data when the data table is updated. +render_plot <- function(input, output, react_values, time_units) { + observe({ + datasets <- react_values$data_table[ + which(react_values$data_table[["Time units"]] == time_units), + ] + + data_plot <- plotly::plot_ly(type = "scatter", mode = "lines") + if (nrow(datasets) > 0) { + for (i in seq_len(nrow(datasets))) { + counts <- tokenize_counts(datasets[i, 3]) + data_plot <- plotly::add_trace(data_plot, + x = seq_along(counts) - 1, y = counts, name = datasets[i, 1] + ) + } + } + + plot_title <- paste( + if (time_units == "Days") "Daily" else "Weekly", "case counts" + ) + + data_plot <- plotly::layout(data_plot, title = plot_title, + xaxis = list(title = time_units), yaxis = list(title = "Cases") + ) + + data_plot <- plotly::config(data_plot, displaylogo = FALSE, + toImageButtonOptions = list( + filename = paste0("Rnaught_data_", tolower(time_units), "_plot") + ) + ) + + output[[paste0("data_plot_", tolower(time_units))]] <- + plotly::renderPlotly(data_plot) + }) +} + +# Validate and add manually-entered datasets. +manual_entry <- function(input, output, react_values) { + observeEvent(input$data_bulk, { + validate_data(input, output, react_values, "data_area") + }) +} + +# Validate and add datasets from a CSV file. +upload_data <- function(input, output, react_values) { + observeEvent(input$data_upload, { + validate_data(input, output, react_values, "data_upload") + }) +} + +# Validate datasets and update the data table. +validate_data <- function(input, output, react_values, data_source) { + tryCatch( + { + if (data_source == "data_area") { + datasets <- read.csv(text = input$data_area, header = FALSE, sep = ",") + } else if (data_source == "data_upload") { + datasets <- read.csv( + file = input$data_upload$datapath, header = FALSE, sep = "," + ) + } + + names <- trimws(datasets[, 1]) + units <- trimws(datasets[, 2]) + counts <- apply(data.frame(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, + "Each row must begin with a non-blank dataset name.<br>" + ) + } else { + if (length(unique(names)) != length(names)) { + warning_text <- paste0(warning_text, + "The rows contain duplicate dataset names.<br>" + ) + } + if (any(names %in% react_values$data_table[, 1])) { + warning_text <- paste0(warning_text, + "The rows contain dataset names which already exist.<br>" + ) + } + } + + # Ensure the second entry in each row is a time unit equal to + # "Days" or "Weeks". + if (!all(units %in% c("Days", "Weeks"))) { + warning_text <- paste0(warning_text, + "The second entry in each row must be either 'Days' or 'Weeks'.<br>" + ) + } + + # Ensure the counts in each row have at least one non-negative integer. + if (any(counts == "")) { + warning_text <- paste0(warning_text, + "Each row must contain at least one non-negative integer.<br>" + ) + } + + output[[paste0(data_source, "_warn")]] <- renderUI(HTML(warning_text)) + + if (warning_text == "") { + # Add the new datasets to the data table. + new_rows <- data.frame(names, units, counts) + colnames(new_rows) <- c("Name", "Time units", "Case counts") + react_values$data_table <- rbind(react_values$data_table, new_rows) + + # Evaluate all existing estimators on the new datasets and update the + # corresponding columns in the estimates table. + update_estimates_cols(new_rows, react_values) + + showNotification("Datasets added successfully.", duration = 3) + } + }, + error = function(e) { + output[[paste0(data_source, "_warn")]] <- renderText( + "The input does not match the required format." + ) + } + ) +} + +# Load sample datasets. +load_samples <- function(input, output, react_values) { + observeEvent(input$data_samples, { + names <- c() + units <- c() + counts <- c() + + # COVID-19 Canada, March 2020 (weekly). + if (input$covid_canada) { + names <- c(names, "COVID-19 Canada 2020/03/03 - 2020/03/31") + units <- c(units, "Weeks") + counts <- c(counts, toString(Rnaught::COVIDCanada[seq(41, 69, 7), 2])) + } + # COVID-19 Ontario, March 2020 (weekly). + if (input$covid_ontario) { + names <- c(names, "COVID-19 Ontario 2020/03/03 - 2020/03/31") + units <- c(units, "Weeks") + counts <- c(counts, + toString(Rnaught::COVIDCanadaPT[seq(10176, 10204, 7), 3]) + ) + } + + if (length(names) == 0) { + output$data_samples_warn <- renderText( + "At least one sample dataset must be selected." + ) + } else if (any(names %in% react_values$data_table[, 1])) { + output$data_samples_warn <- renderText( + "At least one of the selected dataset names already exist." + ) + } else { + output$data_samples_warn <- renderText("") + + 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 sample datasets and update the + # corresponding columns in the estimates table. + update_estimates_cols(new_rows, react_values) + + showNotification("Datasets added successfully.", duration = 3) + } + }) +} + +# Render the data table when new datasets are added. +render_data_table <- function(output, react_values) { + observe({ + output$data_table <- DT::renderDataTable( + react_values$data_table, rownames = FALSE + ) + }) +} + +# Delete rows in the data table and the corresponding columns in the estimates +# table. +delete_data <- function(input, react_values) { + observeEvent(input$data_delete, { + rows_selected <- input$data_table_rows_selected + react_values$data_table <- react_values$data_table[-rows_selected, ] + react_values$estimates_table <- + react_values$estimates_table[, -(rows_selected + 2)] + }) +} + +# 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 columns to the estimates table. +update_estimates_cols <- function(datasets, react_values) { + new_cols <- data.frame( + matrix(nrow = nrow(react_values$estimates_table), ncol = nrow(datasets)) + ) + colnames(new_cols) <- datasets[, 1] + + if (nrow(new_cols) > 0) { + for (row in seq_len(nrow(new_cols))) { + estimator <- react_values$estimators[[row]] + for (col in seq_len(ncol(new_cols))) { + new_cols[row, col] <- eval_estimator(estimator, datasets[col, ]) + } + } + } + + react_values$estimates_table <- cbind( + react_values$estimates_table, new_cols + ) +} diff --git a/inst/web/scripts/estimators.R b/inst/web/scripts/estimators.R new file mode 100644 index 0000000..7c457ea --- /dev/null +++ b/inst/web/scripts/estimators.R @@ -0,0 +1,327 @@ +# Main logic block for estimator-related interactions. +estimators_logic <- function(input, output, react_values) { + # Initialize a data frame to hold estimates. + react_values$estimates_table <- data.frame( + Estimator = character(0), + `Serial interval` = character(0), + check.names = FALSE + + ) + # Initialize a list to hold added estimators. + react_values$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 + ) + return() + } + } + + # Add the new estimator to the list of estimators. + react_values$estimators[[num_estimators + 1]] <- new_estimator + + showNotification("Estimator added successfully.", duration = 3) + + # Evaluate the new estimator on all existing datasets and create a new row in + # the estimates table. + update_estimates_row(new_estimator, react_values) +} + +# Ensure serial intervals are specified as positive numbers. +validate_mu <- function(method, input, output) { + mu <- suppressWarnings(as.numeric(trimws(input[[paste0("mu_", method)]]))) + if (is.na(mu) || mu <= 0) { + output[[paste0("mu_", method, "_warn")]] <- renderText( + "The serial interval must be a positive number." + ) + return(NULL) + } + output[[paste0("mu_", method, "_warn")]] <- renderText("") + mu +} + +# Incidence Decay (ID). +add_id <- function(input, output, react_values) { + observeEvent(input$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$kappa) + kappa <- if (kappa == "") 20 else suppressWarnings(as.numeric(kappa)) + + if (is.na(kappa) || kappa < 1) { + output$kappa_warn <- renderText( + "The maximum prior must be a number greater than or equal to 1." + ) + } 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 row to the estimates table when a new estimator is added. +update_estimates_row <- function(estimator, react_values) { + dataset_rows <- seq_len(nrow(react_values$data_table)) + estimates <- c() + + if (nrow(react_values$data_table) > 0) { + estimates <- dataset_rows + for (row in dataset_rows) { + estimate <- eval_estimator(estimator, react_values$data_table[row, ]) + estimates[row] <- estimate + } + } + + new_row <- data.frame( + t(c(estimator_name(estimator), estimator_mu_text(estimator), estimates)) + ) + colnames(new_row) <- colnames(react_values$estimates_table) + + react_values$estimates_table <- rbind( + react_values$estimates_table, new_row + ) +} + +# Evaluate the specified estimator on the given dataset. +eval_estimator <- function(estimator, dataset) { + cases <- as.integer(unlist(strsplit(dataset[, 3], ","))) + + tryCatch( + { + 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$pmf), 2) + mu_units <- if (dataset[, 2] == "Days") "day(s)" else "week(s)" + estimate <- paste0( + round(estimate$r0, 2), " (SI = ", estimated_mu, " ", mu_units, ")" + ) + } else { + mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu) + estimate <- round(Rnaught::wp(cases, mu), 2) + } + } + + return(estimate) + }, error = function(e) { + showNotification( + paste0(toString(e), + " [Estimator: ", sub(" .*", "", estimator_name(estimator)), + ", Dataset: ", dataset[, 1], "]" + ), duration = 6 + ) + return("—") + } + ) +} + +# Create the name of an estimator to be added to the first column of the +# estimates table. +estimator_name <- function(estimator) { + if (estimator$method == "id") { + return("ID") + } else if (estimator$method == "idea") { + return("IDEA") + } else if (estimator$method == "seq_bayes") { + return(paste0("seqB", " (κ = ", estimator$kappa, ")")) + } else if (estimator$method == "wp") { + if (is.na(estimator$mu)) { + return(paste0("WP (", estimator$grid_length, ", ", + round(estimator$max_shape, 3), ", ", round(estimator$max_scale, 3), ")" + )) + } else { + return("WP") + } + } +} + +# Create the text to be displayed for the serial interval in the second column +# of the estimates table. +estimator_mu_text <- function(estimator) { + if (is.na(estimator$mu)) { + return("—") + } + mu_units <- if (estimator$mu_units == "Days") "day(s)" else "week(s)" + paste(estimator$mu, 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, + escape = FALSE, rownames = FALSE, + options = list( + columnDefs = list(list(className = "dt-left", targets = "_all")) + ), + ) + }) +} + +# Delete rows from the estimates table and the corresponding estimators. +delete_estimators <- function(input, react_values) { + observeEvent(input$estimators_delete, { + rows_selected <- input$estimates_table_rows_selected + react_values$estimators <- react_values$estimators[-rows_selected] + react_values$estimates_table <- + react_values$estimates_table[-rows_selected, ] + }) +} + +# 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("κ", "kappa", obj) + obj +} diff --git a/inst/web/templates/content.html b/inst/web/templates/content.html new file mode 100644 index 0000000..da69f08 --- /dev/null +++ b/inst/web/templates/content.html @@ -0,0 +1,14 @@ +<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="estimation" class="tab-pane fade"> + {{ htmlTemplate("templates/content/estimation.html") }} + </div> + <div id="help" class="tab-pane fade"> + {{ htmlTemplate("templates/content/help.html") }} + </div> +</div> diff --git a/inst/web/templates/content/about.html b/inst/web/templates/content/about.html new file mode 100644 index 0000000..73b75ea --- /dev/null +++ b/inst/web/templates/content/about.html @@ -0,0 +1,28 @@ +<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</em><sub>0</sub>, is defined as the expected number of infections caused + by a single infectious individual when introduced into a totally susceptible population. 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. It is a useful indicator of the transmissibility of an infectious disease during + the early stages of its spread and detection. +</p> +<p> + If <em>R</em><sub>0</sub> < 1, the disease will eventually die out. On the other hand, if + <em>R</em><sub>0</sub> > 1, the disease will spread (the higher the <em>R</em><sub>0</sub>, the faster this will + happen). Due to uncertainty of known data about the disease, it is difficult to determine <em>R</em><sub>0</sub> + precisely. Therefore, many estimation methods exist, each based on different assumptions and yielding different + estimates. It is the responsibility of users to employ the most appropriate estimator (or suite of estimators) given + the situation at hand. +</p> diff --git a/inst/web/templates/content/data.html b/inst/web/templates/content/data.html new file mode 100644 index 0000000..574f003 --- /dev/null +++ b/inst/web/templates/content/data.html @@ -0,0 +1,12 @@ +<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> diff --git a/inst/web/templates/content/data/enter-data.html b/inst/web/templates/content/data/enter-data.html new file mode 100644 index 0000000..254f1d7 --- /dev/null +++ b/inst/web/templates/content/data/enter-data.html @@ -0,0 +1,9 @@ +<form class="mb-5"> + {{ htmlTemplate("templates/content/data/enter-data/required-format.html") }} + {{ htmlTemplate("templates/content/data/enter-data/manual-entry.html") }} + {{ htmlTemplate("templates/content/data/enter-data/upload-data.html") }} +</form> +<hr> +<form> + {{ htmlTemplate("templates/content/data/enter-data/load-samples.html") }} +</form> diff --git a/inst/web/templates/content/data/enter-data/load-samples.html b/inst/web/templates/content/data/enter-data/load-samples.html new file mode 100644 index 0000000..2a4f013 --- /dev/null +++ b/inst/web/templates/content/data/enter-data/load-samples.html @@ -0,0 +1,19 @@ +<h4 class="mb-3">Load samples</h4> +<!-- Checkboxes for sample data. --> +{{ + checkboxInput(inputId = "covid_canada", label = "COVID-19 Canada, 2020/03/03 - 2020/03/31 (Weekly)", + value = FALSE, width = "100%" + ) +}} +{{ + checkboxInput(inputId = "covid_ontario", label = "COVID-19 Ontario, 2020/03/03 - 2020/03/31 (Weekly)", + value = FALSE, width = "100%" + ) +}} +<!-- Warning text. --> +<div> + <small id="data_samples_warn" class="form-text text-primary shiny-text-output"></small> +</div> +<button id="data_samples" type="button" class="btn btn-outline-primary btn-sm action-button mt-3"> + <span class="glyphicon glyphicon-plus"></span> Add +</button> diff --git a/inst/web/templates/content/data/enter-data/manual-entry.html b/inst/web/templates/content/data/enter-data/manual-entry.html new file mode 100644 index 0000000..a6319d9 --- /dev/null +++ b/inst/web/templates/content/data/enter-data/manual-entry.html @@ -0,0 +1,11 @@ +<!-- Data input area (manual entry). --> +<div class="my-4"> + <label class="form-label" for="data_area">Enter manually</label> + <textarea id="data_area" class="form-control" rows="3" wrap="off"></textarea> + <div> + <small id="data_area_warn" class="form-text text-primary shiny-html-output"></small> + </div> + <button id="data_bulk" type="button" class="btn btn-outline-primary btn-sm action-button mt-3"> + <span class="glyphicon glyphicon-plus"></span> Add + </button> +</div> diff --git a/inst/web/templates/content/data/enter-data/required-format.html b/inst/web/templates/content/data/enter-data/required-format.html new file mode 100644 index 0000000..724dd83 --- /dev/null +++ b/inst/web/templates/content/data/enter-data/required-format.html @@ -0,0 +1,25 @@ +<!-- Button to toggle help text. --> +<button type="button" class="btn btn-outline-primary btn-sm" id="data-format-toggle" + data-bs-toggle="collapse" data-bs-target="#data-format">Show required format</button> +<!-- Help text for data input format. --> +<div class="collapse mt-2" id="data-format"> + <div class="card card-body border-primary"> + <p>Manually enter rows or upload a CSV file 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"> + Disease A,Days,1,2,3,4,5,6,7,8,9<br> + Disease B,Weeks,3,1,4,1,5,2,9<br> + Disease C,Days,2,3,5,7,11,13,17,19 + </p> + </div> +</div> diff --git a/inst/web/templates/content/data/enter-data/upload-data.html b/inst/web/templates/content/data/enter-data/upload-data.html new file mode 100644 index 0000000..740047b --- /dev/null +++ b/inst/web/templates/content/data/enter-data/upload-data.html @@ -0,0 +1,12 @@ +<!-- File input for data upload (hidden). --> +<input class="form-control" type="file" id="data_upload" accept="text/csv,text/comma-separated-values,text/plain,.csv"> +<!-- Custom button to trigger file selector for data upload (visible). --> +<label class="form-label" for="data-upload-select">Upload a CSV file</label> +<div class="input-group"> + <button id="data-upload-select" type="button" class="btn btn-outline-primary btn-sm"> + <span class="glyphicon glyphicon-file"></span> Select file + </button> + <input type="text" id="data-upload-name" class="form-control" placeholder="No file selected" disabled> +</div> +<!-- Warning text. --> +<small id="data_upload_warn" class="form-text text-primary shiny-html-output"></small> diff --git a/inst/web/templates/content/data/view-data.html b/inst/web/templates/content/data/view-data.html new file mode 100644 index 0000000..880cf7f --- /dev/null +++ b/inst/web/templates/content/data/view-data.html @@ -0,0 +1,3 @@ +{{ htmlTemplate("templates/content/data/view-data/data-table.html") }} +<hr> +{{ htmlTemplate("templates/content/data/view-data/data-plots.html") }} diff --git a/inst/web/templates/content/data/view-data/data-plots.html b/inst/web/templates/content/data/view-data/data-plots.html new file mode 100644 index 0000000..5019088 --- /dev/null +++ b/inst/web/templates/content/data/view-data/data-plots.html @@ -0,0 +1,7 @@ +<h4>Data plots</h4> +<div class="container my-5"> + {{ plotly::plotlyOutput(outputId = "data_plot_days") }} +</div> +<div class="container"> + {{ plotly::plotlyOutput(outputId = "data_plot_weeks") }} +</div> diff --git a/inst/web/templates/content/data/view-data/data-table.html b/inst/web/templates/content/data/view-data/data-table.html new file mode 100644 index 0000000..590a5b9 --- /dev/null +++ b/inst/web/templates/content/data/view-data/data-table.html @@ -0,0 +1,18 @@ +<h4>Data table</h4> +<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> diff --git a/inst/web/templates/content/estimation.html b/inst/web/templates/content/estimation.html new file mode 100644 index 0000000..5764057 --- /dev/null +++ b/inst/web/templates/content/estimation.html @@ -0,0 +1,13 @@ +<nav class="nav nav-tabs"> + <a class="nav-link active" data-bs-toggle="tab" href="#about-estimators">About the estimators</a> + <a class="nav-link" data-bs-toggle="tab" href="#estimates">Compute and view estimates</a> +</nav> + +<div class="container-fluid tab-content"> + <div id="about-estimators" class="pt-3 tab-pane fade show active"> + {{ htmlTemplate("templates/content/estimation/about-estimators.html") }} + </div> + <div id="estimates" class="pt-3 tab-pane fade"> + {{ htmlTemplate("templates/content/estimation/estimates.html") }} + </div> +</div> diff --git a/inst/web/templates/content/estimation/about-estimators.html b/inst/web/templates/content/estimation/about-estimators.html new file mode 100644 index 0000000..db2898b --- /dev/null +++ b/inst/web/templates/content/estimation/about-estimators.html @@ -0,0 +1,31 @@ +<div class="accordion accordion-flush" id="estimation-accordion"> + {{ + htmlTemplate("templates/content/estimation/about-estimators/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/estimation/about-estimators/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/estimation/about-estimators/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/estimation/about-estimators/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> diff --git a/inst/web/templates/content/estimation/about-estimators/id.html b/inst/web/templates/content/estimation/about-estimators/id.html new file mode 100644 index 0000000..fc70b1c --- /dev/null +++ b/inst/web/templates/content/estimation/about-estimators/id.html @@ -0,0 +1,3 @@ +The Incidence Decay (ID) estimator uses the method of least squares to estimate <em>R</em><sub>0</sub>. +This method assumes the serial interval is known, and is built under the SIR assumption. +We note that the use of this method might result in the underestimation of <em>R</em><sub>0</sub>. diff --git a/inst/web/templates/content/estimation/about-estimators/idea.html b/inst/web/templates/content/estimation/about-estimators/idea.html new file mode 100644 index 0000000..67548f8 --- /dev/null +++ b/inst/web/templates/content/estimation/about-estimators/idea.html @@ -0,0 +1,4 @@ +The Incidence Decay and Exponential Adjustment (ID) estimator is an alternative formulation of the Incidence Decay (ID) model which includes a decay factor to reflect the often observed outbreak decline. +This addresses the potential underestimation of the <em>R</em><sub>0</sub> estimate when using the ID method. +The method of least squares is used to estimate <em>R</em><sub>0</sub>, and similar to the ID model, the serial interval is assumed to be known and this method is developed assuming the SIR model. +We note that, since we need to obtain a minimizer of the decay factor to solve the optimization problem, we require that the number of cases in the dataset be at least 2. diff --git a/inst/web/templates/content/estimation/about-estimators/panel.html b/inst/web/templates/content/estimation/about-estimators/panel.html new file mode 100644 index 0000000..98fe155 --- /dev/null +++ b/inst/web/templates/content/estimation/about-estimators/panel.html @@ -0,0 +1,14 @@ +<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/estimation/about-estimators/", id, ".html")) }}</p> + </div> + </div> +</div> diff --git a/inst/web/templates/content/estimation/about-estimators/seq_bayes.html b/inst/web/templates/content/estimation/about-estimators/seq_bayes.html new file mode 100644 index 0000000..8f66ab4 --- /dev/null +++ b/inst/web/templates/content/estimation/about-estimators/seq_bayes.html @@ -0,0 +1,9 @@ +The sequential Bayes (seqB) estimator uses a Bayesian approach to estimate <em>R</em><sub>0</sub> which updates the reproductive number estimate as data accumulates over time. +This approach is based on the SIR model, and assumes that the mean of the serial distribution (ie. the serial interval (SI)) is known. +It is assumed that infectious counts are observed at periodic times (ie. daily, weekly). +This method cannot handle datasets where there are no new infections observed in a time interval, thus, to remedy this, +some manipulation may be necessary to make the times at which infectious counts are observed sufficiently course (ie. weeks instead of days). +Further, this method is also inappropriate in situations where long intervals between cases are observed in the initial stages of the epidemic. +Finally, the <em>R</em><sub>0</sub> approximation behaves similarly to a branching process, which means that throughout, the population size “available” to be infected remains constant. +We note that this assumption does not hold for the SIR/SEIR/SEAIR compartmental models. +As such, seqB estimates should only really be considered early on in an epidemic, ie. before the inflection point of an epidemic, if the dataset being used follows these models. diff --git a/inst/web/templates/content/estimation/about-estimators/wp.html b/inst/web/templates/content/estimation/about-estimators/wp.html new file mode 100644 index 0000000..c6f4580 --- /dev/null +++ b/inst/web/templates/content/estimation/about-estimators/wp.html @@ -0,0 +1,6 @@ +The White and Pagano (WP) estimator uses maximum likelihood estimation to estimate <em>R</em><sub>0</sub>. +In this method, the serial interval (SI) is either known, or can be estimated along with <em>R</em><sub>0</sub>. +It is assumed that the number of infectious individuals are observable at discrete time points (ie. daily or weekly). +Further, this method also assumes an underlying branching process, which means that throughout, the population size “available” to be infected remains constant. +We note that this assumption does not hold for the SIR/SEIR/SEAIR compartmental models. +As such, WP estimates should only really be considered early on in an epidemic, ie. before the inflection point of an epidemic, if the dataset being used follows these models. diff --git a/inst/web/templates/content/estimation/estimates.html b/inst/web/templates/content/estimation/estimates.html new file mode 100644 index 0000000..bc9124e --- /dev/null +++ b/inst/web/templates/content/estimation/estimates.html @@ -0,0 +1,3 @@ +{{ htmlTemplate("templates/content/estimation/estimates/estimates-table.html") }} +<hr> +{{ htmlTemplate("templates/content/estimation/estimates/add-estimators.html") }} diff --git a/inst/web/templates/content/estimation/estimates/add-estimators.html b/inst/web/templates/content/estimation/estimates/add-estimators.html new file mode 100644 index 0000000..60111c7 --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators.html @@ -0,0 +1,16 @@ +<h4>Add estimators</h4> +<form class="my-3"> + <!-- Dropdown to select estimator. --> + <label class="form-label" for="estimator_select">Select estimator:</label> + <select name="estimator_select" class="form-select"> + <option value="id" selected>Incidence Decay (ID)</option> + <option value="idea">Incidence Decay and Exponential Adjustment (IDEA)</option> + <option value="seq_bayes">Sequential Bayes (seqB)</option> + <option value="wp">White and Pagano (WP)</option> + </select> + <!-- Parameters. --> + {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "id") }} + {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "idea") }} + {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "seq_bayes") }} + {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/parameters.html", id = "wp") }} +</form> diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/id.html b/inst/web/templates/content/estimation/estimates/add-estimators/id.html new file mode 100644 index 0000000..7c35e55 --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators/id.html @@ -0,0 +1 @@ +{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "id") }} diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/idea.html b/inst/web/templates/content/estimation/estimates/add-estimators/idea.html new file mode 100644 index 0000000..781349f --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators/idea.html @@ -0,0 +1 @@ +{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "idea") }} diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/mu.html b/inst/web/templates/content/estimation/estimates/add-estimators/mu.html new file mode 100644 index 0000000..8781574 --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators/mu.html @@ -0,0 +1,22 @@ +<!-- Serial interval label and help tooltip. --> +<label class="form-label" for="mu_{{ id }}"> + Serial interval + <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. --> +<div> + <small id="mu_{{ id }}_warn" class="form-text text-primary shiny-text-output"></small> +</div> diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/parameters.html b/inst/web/templates/content/estimation/estimates/add-estimators/parameters.html new file mode 100644 index 0000000..5250e31 --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators/parameters.html @@ -0,0 +1,7 @@ +<div class="my-4" data-display-if="input.estimator_select === '{{ id }}'"> + <h5>Parameters</h5> + {{ htmlTemplate(paste0("templates/content/estimation/estimates/add-estimators/", id, ".html")) }} + <button id="add_{{ id }}" type="button" class="btn btn-outline-primary btn-sm action-button mt-3"> + <span class="glyphicon glyphicon-plus"></span> Add + </button> +</div> diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html b/inst/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html new file mode 100644 index 0000000..028fabc --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators/seq_bayes.html @@ -0,0 +1,22 @@ +<div class="row"> + <!-- Serial interval (mu). --> + <div class="col-md"> + {{ htmlTemplate("templates/content/estimation/estimates/add-estimators/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</em><sub>0</sub>. The higher this value, the higher + <em>R</em><sub>0</sub> 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> diff --git a/inst/web/templates/content/estimation/estimates/add-estimators/wp.html b/inst/web/templates/content/estimation/estimates/add-estimators/wp.html new file mode 100644 index 0000000..511170f --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/add-estimators/wp.html @@ -0,0 +1,39 @@ +<!-- 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/estimation/estimates/add-estimators/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> diff --git a/inst/web/templates/content/estimation/estimates/estimates-table.html b/inst/web/templates/content/estimation/estimates/estimates-table.html new file mode 100644 index 0000000..4704d03 --- /dev/null +++ b/inst/web/templates/content/estimation/estimates/estimates-table.html @@ -0,0 +1,19 @@ +<h4>Estimates table</h4> +<!-- Estimates table. --> +<div class="my-3"> + {{ DT::dataTableOutput(outputId = "estimates_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="'estimates_table_rows_selected' in input && input.estimates_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="estimators_delete" type="button" class="btn btn-primary btn-sm action-button text-white" + data-display-if="'estimates_table_rows_selected' in input && input.estimates_table_rows_selected.length != 0"> + <span class="glyphicon glyphicon-remove"></span> Delete row(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> diff --git a/inst/web/templates/content/help.html b/inst/web/templates/content/help.html new file mode 100644 index 0000000..df4e887 --- /dev/null +++ b/inst/web/templates/content/help.html @@ -0,0 +1,8 @@ +<div class="accordion accordion-flush" id="help-accordion"> + {{ + htmlTemplate("templates/content/help/panel.html", + id = "serial-interval", + header = "What is the serial interval?" + ) + }} +</div> diff --git a/inst/web/templates/content/help/panel.html b/inst/web/templates/content/help/panel.html new file mode 100644 index 0000000..9eb6e2e --- /dev/null +++ b/inst/web/templates/content/help/panel.html @@ -0,0 +1,12 @@ +<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> diff --git a/inst/web/templates/content/help/serial-interval.html b/inst/web/templates/content/help/serial-interval.html new file mode 100644 index 0000000..e061115 --- /dev/null +++ b/inst/web/templates/content/help/serial-interval.html @@ -0,0 +1,9 @@ +<p>Reference: <a href="https://en.wikipedia.org/wiki/Serial_interval" target="_blank"><em>Wikipedia</em></a> +<p> + The serial interval (SI) is not one of the estimators. It is a parameter required by most of the estimators, and can + also be estimated by some of them (if not specified). +</p> +<p> + The SI is defined as the average time between successive infections in a chain of transmission (i.e., the time between + the infection of an infected individual and their subsequent transmissions). +</p> diff --git a/inst/web/templates/footer.html b/inst/web/templates/footer.html new file mode 100644 index 0000000..19d4b0c --- /dev/null +++ b/inst/web/templates/footer.html @@ -0,0 +1,7 @@ +<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> diff --git a/inst/web/templates/navbar.html b/inst/web/templates/navbar.html new file mode 100644 index 0000000..d447fba --- /dev/null +++ b/inst/web/templates/navbar.html @@ -0,0 +1,27 @@ +<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</em><sub>0</sub> + </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> diff --git a/inst/web/templates/tabs.html b/inst/web/templates/tabs.html new file mode 100644 index 0000000..351b480 --- /dev/null +++ b/inst/web/templates/tabs.html @@ -0,0 +1,14 @@ +<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="#estimation"> + Estimation <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> diff --git a/inst/web/www/script.js b/inst/web/www/script.js new file mode 100644 index 0000000..30066d1 --- /dev/null +++ b/inst/web/www/script.js @@ -0,0 +1,21 @@ +$(document).ready(() => { + // Enable tooltips. + $('[data-bs-toggle="tooltip"]').tooltip(); + + // Toggle the text in the bulk data help button. + $('#data-format-toggle').on('click', event => { + btn = $(event.target); + show_format = 'Show required format'; + btn.text(btn.text() === show_format ? 'Hide required format' : show_format); + }); + + // Trigger the file selector via a custom button. + $('#data-upload-select').on('click', () => { + $('#data_upload').trigger('click'); + }); + + // Display the name of the uploaded file. + $('#data_upload').on('change', event => { + $('#data-upload-name').attr('placeholder', event.target.files[0].name); + }); +}); diff --git a/inst/web/www/styles.css b/inst/web/www/styles.css new file mode 100644 index 0000000..a6fc3cd --- /dev/null +++ b/inst/web/www/styles.css @@ -0,0 +1,23 @@ +body { + min-height: 100vh; + height: 100%; + width: 100%; +} + +noscript { + text-align: center; +} + +.shiny-notification { + background-color: black; + color: white; +} + +.plotly-notifier .notifier-note { + background-color: black !important; + color: white !important; +} + +#data_upload { + display: none; +} |