1 files changed, 236 insertions, 0 deletions
diff --git a/inst/app/scripts/data.R b/inst/app/scripts/data.R
new file mode 100644
index 0000000..06cb256
--- /dev/null
+++ b/inst/app/scripts/data.R
@@ -0,0 +1,236 @@
+# Main logic block for data-related interactions.
+data_logic <- function(input, output, react_values) {
+  # Initialize a data frame to hold the datasets.
+  react_values$data_table <- data.frame(
+    Name = character(0),
+    `Time units` = character(0),
+    `Case counts` = character(0),
+    check.names = FALSE
+  )
+
+  render_plot(input, output)
+  single_entry(input, output, react_values)
+  bulk_entry(input, output, react_values)
+  render_data(output, react_values)
+  delete_data(input, react_values)
+  export_data(output, react_values)
+}
+
+# Convert the input case counts string to an integer vector.
+tokenize_counts <- function(counts_str) {
+  suppressWarnings(as.integer(unlist(strsplit(trimws(counts_str), ","))))
+}
+
+# Render the preview plot for single entry data.
+render_plot <- function(input, output) {
+  observe({
+    counts <- tokenize_counts(input$data_counts)
+    if (length(counts) > 0 && !anyNA(counts) && all(counts >= 0)) {
+      output$data_plot <- renderPlot(
+        plot(seq_along(counts) - 1, counts, type = "o", pch = 16, col = "red",
+          xlab = input$data_units, ylab = "Cases", cex.lab = 1.5,
+          xlim = c(0, max(length(counts) - 1, 1)), ylim = c(0, max(counts, 1))
+        )
+      )
+    } else {
+      output$data_plot <- renderPlot(
+        plot(NULL, xlim = c(0, 10), ylim = c(0, 10),
+          xlab = input$data_units, ylab = "Cases", cex.lab = 1.5
+        )
+      )
+    }
+  })
+}
+
+# Add a single dataset to the existing table.
+single_entry <- function(input, output, react_values) {
+  observeEvent(input$data_single, {
+    valid <- TRUE
+
+    # Ensure the dataset name is neither blank nor a duplicate.
+    name <- trimws(input$data_name)
+    if (name == "") {
+      output$data_name_warn <- renderText("The dataset name cannot be blank.")
+      valid <- FALSE
+    } else if (name %in% react_values$data_table[, 1]) {
+      output$data_name_warn <- renderText(
+        "There is already a dataset with the specified name."
+      )
+      valid <- FALSE
+    } else {
+      output$data_name_warn <- renderText("")
+    }
+
+    # Ensure the case counts are specified as a comma-separated of one or more
+    # non-negative integers.
+    counts <- tokenize_counts(input$data_counts)
+    if (length(counts) == 0) {
+      output$data_counts_warn <- renderText("Case counts cannot be blank.")
+      valid <- FALSE
+    } else if (anyNA(counts) || any(counts < 0)) {
+      output$data_counts_warn <- renderText(
+        "Case counts can only contain non-negative integers."
+      )
+      valid <- FALSE
+    } else {
+      output$data_counts_warn <- renderText("")
+    }
+
+    if (valid) {
+      # Add the new dataset to the data table.
+      new_row <- data.frame(name, input$data_units, toString(counts))
+      colnames(new_row) <- c("Name", "Time units", "Case counts")
+      react_values$data_table <- rbind(react_values$data_table, new_row)
+
+      # Evaluate all existing estimators on the new dataset and update the
+      # corresponding row in the estimates table.
+      update_estimates_rows(new_row, react_values)
+
+      showNotification("Dataset added successfully.",
+        duration = 3, id = "notify-success"
+      )
+    }
+  })
+}
+
+# Add multiple datasets to the existing table.
+bulk_entry <- function(input, output, react_values) {
+  observeEvent(input$data_bulk, {
+    tryCatch(
+      {
+        datasets <- read.csv(text = input$data_area, header = FALSE, sep = ",")
+
+        names <- trimws(datasets[, 1])
+        units <- trimws(datasets[, 2])
+        counts <- apply(datasets[, 3:ncol(datasets)], 1,
+          function(row) {
+            row <- suppressWarnings(as.integer(row))
+            toString(row[!is.na(row) & row >= 0])
+          }
+        )
+
+        warning_text <- ""
+
+        # Ensure the dataset names are neither blank nor duplicates.
+        if (anyNA(names) || any(names == "")) {
+          warning_text <- paste0(warning_text, sep = "<br>",
+            "Each row must begin with a non-blank dataset name."
+          )
+        } else {
+          if (length(unique(names)) != length(names)) {
+            warning_text <- paste0(warning_text, sep = "<br>",
+              "The rows contain duplicate dataset names."
+            )
+          }
+          if (any(names %in% react_values$data_table[, 1])) {
+            warning_text <- paste0(warning_text, sep = "<br>",
+              "The rows contain dataset names which already exist."
+            )
+          }
+        }
+
+        # Ensure the second entry in each row is a time unit equal to
+        # "Days" or "Weeks".
+        if (!all(units %in% c("Days", "Weeks"))) {
+          warning_text <- paste0(warning_text, sep = "<br>",
+            "The second entry in each row must be either 'Days' or 'Weeks'."
+          )
+        }
+
+        # Ensure the counts in each row have at least one non-negative integer.
+        if (any(counts == "")) {
+          warning_text <- paste0(warning_text, sep = "<br>",
+            "Each row must contain at least one non-negative integer."
+          )
+        }
+
+        output$data_area_warn <- renderUI(HTML(warning_text))
+
+        if (warning_text == "") {
+          # Add the new datasets to the data table.
+          new_rows <- data.frame(names, units, counts)
+          colnames(new_rows) <- c("Name", "Time units", "Case counts")
+          react_values$data_table <- rbind(react_values$data_table, new_rows)
+
+          # Evaluate all existing estimators on the new dataset and update the
+          # corresponding row in the estimates table.
+          update_estimates_rows(new_rows, react_values)
+
+          showNotification("Datasets added successfully.",
+            duration = 3, id = "notify-success"
+          )
+        }
+      },
+      error = function(e) {
+        output$data_area_warn <- renderText(
+          "The input does not match the required format."
+        )
+      }
+    )
+  })
+}
+
+# Render the data table when new datasets are added.
+render_data <- function(output, react_values) {
+  observe({
+    output$data_table <- DT::renderDataTable(react_values$data_table)
+  })
+}
+
+# Delete rows in the data table,
+# and the corresponding rows in the estimates table.
+delete_data <- function(input, react_values) {
+  observeEvent(input$data_delete, {
+    new_table <- react_values$data_table[-input$data_table_rows_selected, ]
+    if (nrow(new_table) > 0) {
+      rownames(new_table) <- seq_len(nrow(new_table))
+    }
+    react_values$data_table <- new_table
+
+    if (ncol(react_values$estimates_table) == 1) {
+      react_values$estimates_table <- data.frame(
+        Datasets = react_values$data_table[, 1]
+      )
+    } else {
+      react_values$estimates_table <-
+        react_values$estimates_table[-input$data_table_rows_selected, ]
+    }
+  })
+}
+
+# Export data table as a CSV file.
+export_data <- function(output, react_values) {
+  output$data_export <- downloadHandler(
+    filename = function() {
+      paste0("Rnaught_data_", format(Sys.time(), "%y-%m-%d_%H-%M-%S"), ".csv")
+    },
+    content = function(file) {
+      write.csv(react_values$data_table, file, row.names = FALSE)
+    }
+  )
+}
+
+# When new datasets are added, evaluate all existing estimators on them and
+# add new rows to the estimates table.
+update_estimates_rows <- function(datasets, react_values) {
+  new_rows <- data.frame(
+    matrix(nrow = nrow(datasets), ncol = ncol(react_values$estimates_table))
+  )
+  colnames(new_rows) <- colnames(react_values$estimates_table)
+
+  for (row in seq_len(nrow(datasets))) {
+    new_rows[row, 1] <- datasets[row, 1]
+
+    if (length(react_values$estimators) > 0) {
+      for (col in 2:ncol(react_values$estimates_table)) {
+        new_rows[row, col] <- eval_estimator(
+          react_values$estimators[[col - 1]], datasets[row, ]
+        )
+      }
+    }
+  }
+
+  react_values$estimates_table <- rbind(
+    react_values$estimates_table, new_rows
+  )
+}