diff options
Diffstat (limited to 'inst/app')
39 files changed, 0 insertions, 1101 deletions
diff --git a/inst/app/app.R b/inst/app/app.R deleted file mode 100644 index 639dc87..0000000 --- a/inst/app/app.R +++ /dev/null @@ -1,13 +0,0 @@ -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/app/index.html b/inst/app/index.html deleted file mode 100644 index 504918d..0000000 --- a/inst/app/index.html +++ /dev/null @@ -1,19 +0,0 @@ -<!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/app/scripts/data.R b/inst/app/scripts/data.R deleted file mode 100644 index 8f8694c..0000000 --- a/inst/app/scripts/data.R +++ /dev/null @@ -1,253 +0,0 @@ -# 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/app/scripts/estimators.R b/inst/app/scripts/estimators.R deleted file mode 100644 index 7c457ea..0000000 --- a/inst/app/scripts/estimators.R +++ /dev/null @@ -1,327 +0,0 @@ -# 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/app/templates/content.html b/inst/app/templates/content.html deleted file mode 100644 index da69f08..0000000 --- a/inst/app/templates/content.html +++ /dev/null @@ -1,14 +0,0 @@ -<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/app/templates/content/about.html b/inst/app/templates/content/about.html deleted file mode 100644 index 73b75ea..0000000 --- a/inst/app/templates/content/about.html +++ /dev/null @@ -1,28 +0,0 @@ -<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/app/templates/content/data.html b/inst/app/templates/content/data.html deleted file mode 100644 index 574f003..0000000 --- a/inst/app/templates/content/data.html +++ /dev/null @@ -1,12 +0,0 @@ -<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/app/templates/content/data/enter-data.html b/inst/app/templates/content/data/enter-data.html deleted file mode 100644 index 254f1d7..0000000 --- a/inst/app/templates/content/data/enter-data.html +++ /dev/null @@ -1,9 +0,0 @@ -<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/app/templates/content/data/enter-data/load-samples.html b/inst/app/templates/content/data/enter-data/load-samples.html deleted file mode 100644 index 2a4f013..0000000 --- a/inst/app/templates/content/data/enter-data/load-samples.html +++ /dev/null @@ -1,19 +0,0 @@ -<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/app/templates/content/data/enter-data/manual-entry.html b/inst/app/templates/content/data/enter-data/manual-entry.html deleted file mode 100644 index a6319d9..0000000 --- a/inst/app/templates/content/data/enter-data/manual-entry.html +++ /dev/null @@ -1,11 +0,0 @@ -<!-- 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/app/templates/content/data/enter-data/required-format.html b/inst/app/templates/content/data/enter-data/required-format.html deleted file mode 100644 index 724dd83..0000000 --- a/inst/app/templates/content/data/enter-data/required-format.html +++ /dev/null @@ -1,25 +0,0 @@ -<!-- 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/app/templates/content/data/enter-data/upload-data.html b/inst/app/templates/content/data/enter-data/upload-data.html deleted file mode 100644 index 740047b..0000000 --- a/inst/app/templates/content/data/enter-data/upload-data.html +++ /dev/null @@ -1,12 +0,0 @@ -<!-- 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/app/templates/content/data/view-data.html b/inst/app/templates/content/data/view-data.html deleted file mode 100644 index 880cf7f..0000000 --- a/inst/app/templates/content/data/view-data.html +++ /dev/null @@ -1,3 +0,0 @@ -{{ htmlTemplate("templates/content/data/view-data/data-table.html") }} -<hr> -{{ htmlTemplate("templates/content/data/view-data/data-plots.html") }} diff --git a/inst/app/templates/content/data/view-data/data-plots.html b/inst/app/templates/content/data/view-data/data-plots.html deleted file mode 100644 index 5019088..0000000 --- a/inst/app/templates/content/data/view-data/data-plots.html +++ /dev/null @@ -1,7 +0,0 @@ -<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/app/templates/content/data/view-data/data-table.html b/inst/app/templates/content/data/view-data/data-table.html deleted file mode 100644 index 590a5b9..0000000 --- a/inst/app/templates/content/data/view-data/data-table.html +++ /dev/null @@ -1,18 +0,0 @@ -<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/app/templates/content/estimation.html b/inst/app/templates/content/estimation.html deleted file mode 100644 index 5764057..0000000 --- a/inst/app/templates/content/estimation.html +++ /dev/null @@ -1,13 +0,0 @@ -<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/app/templates/content/estimation/about-estimators.html b/inst/app/templates/content/estimation/about-estimators.html deleted file mode 100644 index db2898b..0000000 --- a/inst/app/templates/content/estimation/about-estimators.html +++ /dev/null @@ -1,31 +0,0 @@ -<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/app/templates/content/estimation/about-estimators/id.html b/inst/app/templates/content/estimation/about-estimators/id.html deleted file mode 100644 index fc70b1c..0000000 --- a/inst/app/templates/content/estimation/about-estimators/id.html +++ /dev/null @@ -1,3 +0,0 @@ -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/app/templates/content/estimation/about-estimators/idea.html b/inst/app/templates/content/estimation/about-estimators/idea.html deleted file mode 100644 index 67548f8..0000000 --- a/inst/app/templates/content/estimation/about-estimators/idea.html +++ /dev/null @@ -1,4 +0,0 @@ -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/app/templates/content/estimation/about-estimators/panel.html b/inst/app/templates/content/estimation/about-estimators/panel.html deleted file mode 100644 index 98fe155..0000000 --- a/inst/app/templates/content/estimation/about-estimators/panel.html +++ /dev/null @@ -1,14 +0,0 @@ -<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/app/templates/content/estimation/about-estimators/seq_bayes.html b/inst/app/templates/content/estimation/about-estimators/seq_bayes.html deleted file mode 100644 index 8f66ab4..0000000 --- a/inst/app/templates/content/estimation/about-estimators/seq_bayes.html +++ /dev/null @@ -1,9 +0,0 @@ -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/app/templates/content/estimation/about-estimators/wp.html b/inst/app/templates/content/estimation/about-estimators/wp.html deleted file mode 100644 index c6f4580..0000000 --- a/inst/app/templates/content/estimation/about-estimators/wp.html +++ /dev/null @@ -1,6 +0,0 @@ -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/app/templates/content/estimation/estimates.html b/inst/app/templates/content/estimation/estimates.html deleted file mode 100644 index bc9124e..0000000 --- a/inst/app/templates/content/estimation/estimates.html +++ /dev/null @@ -1,3 +0,0 @@ -{{ htmlTemplate("templates/content/estimation/estimates/estimates-table.html") }} -<hr> -{{ htmlTemplate("templates/content/estimation/estimates/add-estimators.html") }} diff --git a/inst/app/templates/content/estimation/estimates/add-estimators.html b/inst/app/templates/content/estimation/estimates/add-estimators.html deleted file mode 100644 index 60111c7..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators.html +++ /dev/null @@ -1,16 +0,0 @@ -<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/app/templates/content/estimation/estimates/add-estimators/id.html b/inst/app/templates/content/estimation/estimates/add-estimators/id.html deleted file mode 100644 index 7c35e55..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators/id.html +++ /dev/null @@ -1 +0,0 @@ -{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "id") }} diff --git a/inst/app/templates/content/estimation/estimates/add-estimators/idea.html b/inst/app/templates/content/estimation/estimates/add-estimators/idea.html deleted file mode 100644 index 781349f..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators/idea.html +++ /dev/null @@ -1 +0,0 @@ -{{ htmlTemplate("templates/content/estimation/estimates/add-estimators/mu.html", id = "idea") }} diff --git a/inst/app/templates/content/estimation/estimates/add-estimators/mu.html b/inst/app/templates/content/estimation/estimates/add-estimators/mu.html deleted file mode 100644 index 8781574..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators/mu.html +++ /dev/null @@ -1,22 +0,0 @@ -<!-- 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/app/templates/content/estimation/estimates/add-estimators/parameters.html b/inst/app/templates/content/estimation/estimates/add-estimators/parameters.html deleted file mode 100644 index 5250e31..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators/parameters.html +++ /dev/null @@ -1,7 +0,0 @@ -<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/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html b/inst/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html deleted file mode 100644 index 028fabc..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators/seq_bayes.html +++ /dev/null @@ -1,22 +0,0 @@ -<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/app/templates/content/estimation/estimates/add-estimators/wp.html b/inst/app/templates/content/estimation/estimates/add-estimators/wp.html deleted file mode 100644 index 511170f..0000000 --- a/inst/app/templates/content/estimation/estimates/add-estimators/wp.html +++ /dev/null @@ -1,39 +0,0 @@ -<!-- 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/app/templates/content/estimation/estimates/estimates-table.html b/inst/app/templates/content/estimation/estimates/estimates-table.html deleted file mode 100644 index 4704d03..0000000 --- a/inst/app/templates/content/estimation/estimates/estimates-table.html +++ /dev/null @@ -1,19 +0,0 @@ -<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/app/templates/content/help.html b/inst/app/templates/content/help.html deleted file mode 100644 index df4e887..0000000 --- a/inst/app/templates/content/help.html +++ /dev/null @@ -1,8 +0,0 @@ -<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/app/templates/content/help/panel.html b/inst/app/templates/content/help/panel.html deleted file mode 100644 index 9eb6e2e..0000000 --- a/inst/app/templates/content/help/panel.html +++ /dev/null @@ -1,12 +0,0 @@ -<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/app/templates/content/help/serial-interval.html b/inst/app/templates/content/help/serial-interval.html deleted file mode 100644 index e061115..0000000 --- a/inst/app/templates/content/help/serial-interval.html +++ /dev/null @@ -1,9 +0,0 @@ -<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/app/templates/footer.html b/inst/app/templates/footer.html deleted file mode 100644 index 19d4b0c..0000000 --- a/inst/app/templates/footer.html +++ /dev/null @@ -1,7 +0,0 @@ -<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/app/templates/navbar.html b/inst/app/templates/navbar.html deleted file mode 100644 index d447fba..0000000 --- a/inst/app/templates/navbar.html +++ /dev/null @@ -1,27 +0,0 @@ -<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/app/templates/tabs.html b/inst/app/templates/tabs.html deleted file mode 100644 index 351b480..0000000 --- a/inst/app/templates/tabs.html +++ /dev/null @@ -1,14 +0,0 @@ -<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/app/www/script.js b/inst/app/www/script.js deleted file mode 100644 index 30066d1..0000000 --- a/inst/app/www/script.js +++ /dev/null @@ -1,21 +0,0 @@ -$(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/app/www/styles.css b/inst/app/www/styles.css deleted file mode 100644 index a6fc3cd..0000000 --- a/inst/app/www/styles.css +++ /dev/null @@ -1,23 +0,0 @@ -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; -} |