Update web app entry point

- Rename 'app' -> 'web'
- Return shiny app object in entry point function

1 files changed, 327 insertions, 0 deletions

diff --git a/inst/web/scripts/estimators.R b/inst/web/scripts/estimators.R
new file mode 100644
index 0000000..7c457ea
--- /dev/null
+++ b/inst/web/scripts/estimators.R
@@ -0,0 +1,327 @@
+# Main logic block for estimator-related interactions.
+estimators_logic <- function(input, output, react_values) {
+  # Initialize a data frame to hold estimates.
+  react_values$estimates_table <- data.frame(
+    Estimator = character(0),
+    `Serial interval` = character(0),
+    check.names = FALSE
+
+  )
+  # Initialize a list to hold added estimators.
+  react_values$estimators <- list()
+
+  add_id(input, output, react_values)
+  add_idea(input, output, react_values)
+  add_seq_bayes(input, output, react_values)
+  add_wp(input, output, react_values)
+
+  render_estimates(output, react_values)
+  delete_estimators(input, react_values)
+  export_estimates(output, react_values)
+}
+
+# If an estimator is added, ensure it is not a duplicate and add it to the list
+# of estimators. This function should be called at the end of each
+# estimator-specific 'add' function, after validating their parameters.
+add_estimator <- function(method, new_estimator, output, react_values) {
+  num_estimators <- length(react_values$estimators)
+
+  # Check whether the new estimator is a duplicate, and warn if so.
+  for (i in seq_len(num_estimators)) {
+    if (identical(new_estimator, react_values$estimators[[i]])) {
+      showNotification(
+        "Error: This estimator has already been added.", duration = 3
+      )
+      return()
+    }
+  }
+
+  # Add the new estimator to the list of estimators.
+  react_values$estimators[[num_estimators + 1]] <- new_estimator
+
+  showNotification("Estimator added successfully.", duration = 3)
+
+  # Evaluate the new estimator on all existing datasets and create a new row in
+  # the estimates table.
+  update_estimates_row(new_estimator, react_values)
+}
+
+# Ensure serial intervals are specified as positive numbers.
+validate_mu <- function(method, input, output) {
+  mu <- suppressWarnings(as.numeric(trimws(input[[paste0("mu_", method)]])))
+  if (is.na(mu) || mu <= 0) {
+    output[[paste0("mu_", method, "_warn")]] <- renderText(
+      "The serial interval must be a positive number."
+    )
+    return(NULL)
+  }
+  output[[paste0("mu_", method, "_warn")]] <- renderText("")
+  mu
+}
+
+# Incidence Decay (ID).
+add_id <- function(input, output, react_values) {
+  observeEvent(input$add_id, {
+    mu <- validate_mu("id", input, output)
+    if (!is.null(mu)) {
+      new_estimator <- list(
+        method = "id", mu = mu, mu_units = input$mu_id_units
+      )
+      add_estimator("id", new_estimator, output, react_values)
+    }
+  })
+}
+
+# Incidence Decay and Exponential Adjustment (IDEA).
+add_idea <- function(input, output, react_values) {
+  observeEvent(input$add_idea, {
+    mu <- validate_mu("idea", input, output)
+    if (!is.null(mu)) {
+      new_estimator <- list(
+        method = "idea", mu = mu, mu_units = input$mu_idea_units
+      )
+      add_estimator("idea", new_estimator, output, react_values)
+    }
+  })
+}
+
+# Sequential Bayes (seqB).
+add_seq_bayes <- function(input, output, react_values) {
+  observeEvent(input$add_seq_bayes, {
+    mu <- validate_mu("seq_bayes", input, output)
+
+    kappa <- trimws(input$kappa)
+    kappa <- if (kappa == "") 20 else suppressWarnings(as.numeric(kappa))
+
+    if (is.na(kappa) || kappa < 1) {
+      output$kappa_warn <- renderText(
+        "The maximum prior must be a number greater than or equal to 1."
+      )
+    } else if (!is.null(mu)) {
+      output$kappa_warn <- renderText("")
+      new_estimator <- list(
+        method = "seq_bayes", mu = mu,
+        mu_units = input$mu_seq_bayes_units, kappa = kappa
+      )
+      add_estimator("seq_bayes", new_estimator, output, react_values)
+    }
+  })
+}
+
+# White and Pagano (WP).
+add_wp <- function(input, output, react_values) {
+  observeEvent(input$add_wp, {
+    if (input$wp_mu_known == "Yes") {
+      mu <- validate_mu("wp", input, output)
+      if (!is.null(mu)) {
+        new_estimator <- list(method = "wp",
+          mu = mu, mu_units = input$mu_wp_units
+        )
+        add_estimator("wp", new_estimator, output, react_values)
+      }
+    } else {
+      grid_length <- trimws(input$grid_length)
+      max_shape <- trimws(input$max_shape)
+      max_scale <- trimws(input$max_scale)
+
+      suppressWarnings({
+        grid_length <- if (grid_length == "") 100 else as.numeric(grid_length)
+        max_shape <- if (max_shape == "") 10 else as.numeric(max_shape)
+        max_scale <- if (max_scale == "") 10 else as.numeric(max_scale)
+      })
+
+      valid <- TRUE
+
+      if (is.na(grid_length) || grid_length <= 0) {
+        output$grid_length_warn <- renderText(
+          "The grid length must be a positive integer."
+        )
+        valid <- FALSE
+      } else {
+        output$grid_length_warn <- renderText("")
+      }
+
+      if (is.na(max_shape) || max_shape <= 0) {
+        output$max_shape_warn <- renderText(
+          "The maximum shape must be a positive number."
+        )
+        valid <- FALSE
+      } else {
+        output$max_shape_warn <- renderText("")
+      }
+
+      if (is.na(max_scale) || max_scale <= 0) {
+        output$max_scale_warn <- renderText(
+          "The maximum scale must be a positive number."
+        )
+        valid <- FALSE
+      } else {
+        output$max_scale_warn <- renderText("")
+      }
+
+      if (valid) {
+        new_estimator <- list(method = "wp", mu = NA, grid_length = grid_length,
+          max_shape = max_shape, max_scale = max_scale
+        )
+        add_estimator("wp", new_estimator, output, react_values)
+      }
+    }
+  })
+}
+
+# Convert an estimator's specified serial interval to match the time units of
+# the given dataset.
+convert_mu_units <- function(data_units, estimator_units, mu) {
+  if (data_units == "Days" && estimator_units == "Weeks") {
+    return(mu * 7)
+  } else if (data_units == "Weeks" && estimator_units == "Days") {
+    return(mu / 7)
+  }
+  mu
+}
+
+# Add a row to the estimates table when a new estimator is added.
+update_estimates_row <- function(estimator, react_values) {
+  dataset_rows <- seq_len(nrow(react_values$data_table))
+  estimates <- c()
+
+  if (nrow(react_values$data_table) > 0) {
+    estimates <- dataset_rows
+    for (row in dataset_rows) {
+      estimate <- eval_estimator(estimator, react_values$data_table[row, ])
+      estimates[row] <- estimate
+    }
+  }
+
+  new_row <- data.frame(
+    t(c(estimator_name(estimator), estimator_mu_text(estimator), estimates))
+  )
+  colnames(new_row) <- colnames(react_values$estimates_table)
+
+  react_values$estimates_table <- rbind(
+    react_values$estimates_table, new_row
+  )
+}
+
+# Evaluate the specified estimator on the given dataset.
+eval_estimator <- function(estimator, dataset) {
+  cases <- as.integer(unlist(strsplit(dataset[, 3], ",")))
+
+  tryCatch(
+    {
+      if (estimator$method == "id") {
+        mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+        estimate <- round(Rnaught::id(cases, mu), 2)
+      } else if (estimator$method == "idea") {
+        mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+        estimate <- round(Rnaught::idea(cases, mu), 2)
+      } else if (estimator$method == "seq_bayes") {
+        mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+        estimate <- round(Rnaught::seq_bayes(cases, mu, estimator$kappa), 2)
+      } else if (estimator$method == "wp") {
+        if (is.na(estimator$mu)) {
+          estimate <- Rnaught::wp(cases, serial = TRUE,
+            grid_length = estimator$grid_length,
+            max_shape = estimator$max_shape, max_scale = estimator$max_scale
+          )
+          estimated_mu <- round(sum(estimate$supp * estimate$pmf), 2)
+          mu_units <- if (dataset[, 2] == "Days") "day(s)" else "week(s)"
+          estimate <- paste0(
+            round(estimate$r0, 2), " (SI = ", estimated_mu, " ", mu_units, ")"
+          )
+        } else {
+          mu <- convert_mu_units(dataset[, 2], estimator$mu_units, estimator$mu)
+          estimate <- round(Rnaught::wp(cases, mu), 2)
+        }
+      }
+
+      return(estimate)
+    }, error = function(e) {
+      showNotification(
+        paste0(toString(e),
+          " [Estimator: ", sub(" .*", "", estimator_name(estimator)),
+          ", Dataset: ", dataset[, 1], "]"
+        ), duration = 6
+      )
+      return("—")
+    }
+  )
+}
+
+# Create the name of an estimator to be added to the first column of the
+# estimates table.
+estimator_name <- function(estimator) {
+  if (estimator$method == "id") {
+    return("ID")
+  } else if (estimator$method == "idea") {
+    return("IDEA")
+  } else if (estimator$method == "seq_bayes") {
+    return(paste0("seqB", " (&#954; = ", estimator$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
+}