Update web app entry point

- Rename 'app' -> 'web' - Return shiny app object in entry point function
author: Naeem Model <me@nmode.ca> 2025-01-06 23:55:43 +0000
committer: Naeem Model <me@nmode.ca> 2025-01-06 23:55:43 +0000
commit: e920b3e514e717fc05ed524267d3b53e272fec51 (patch)
tree: 353cfb36aca946d69da6d6dcacc0cb66177050ef /inst/app
parent: 2d34b71c7a8da7fd0fac59b934145286b2be7b1f (diff)
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$method == "seq_bayes") {
-    return(paste0("seqB", " (&#954; = ", estimator$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("&#954;", "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> &lt; 1, the disease will eventually die out. On the other hand, if
-  <em>R</em><sub>0</sub> &gt; 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 (&#954;)
-      <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;
-}
author	Naeem Model <me@nmode.ca>	2025-01-06 23:55:43 +0000
committer	Naeem Model <me@nmode.ca>	2025-01-06 23:55:43 +0000
commit	e920b3e514e717fc05ed524267d3b53e272fec51 (patch)
tree	353cfb36aca946d69da6d6dcacc0cb66177050ef /inst/app
parent	2d34b71c7a8da7fd0fac59b934145286b2be7b1f (diff)