Sample data and Upload data

diff --git a/data.R b/data.R
new file mode 100644 (file)
index 0000000..a07372a
--- /dev/null
+++ b/data.R
@@ -0,0 +1,363 @@
+# Main logic block for data-related interactions.\r
+data_logic <- function(input, output, react_values) {\r
+  # Initialize a data frame to hold the datasets.\r
+  react_values$data_table <- data.frame(\r
+    Name = character(0),\r
+    `Time units` = character(0),\r
+    `Case counts` = character(0),\r
+    check.names = FALSE\r
+  )\r
+  \r
+  render_plot(input, output)\r
+  single_entry(input, output, react_values)\r
+  bulk_entry(input, output, react_values)\r
+  upload_entry(input, output, react_values)\r
+  sample_entry(input, output, react_values)\r
+  render_data(output, react_values)\r
+  delete_data(input, react_values)\r
+  export_data(output, react_values)\r
+}\r
+\r
+warnings <- function(df, df_elems) {\r
+  \r
+  warning_text <- ''\r
+  \r
+  # Ensure the dataset names are neither blank nor duplicates.\r
+  if (anyNA(df_elems[[1]]) || any(df_elems[[1]] == "")) {\r
+    warning_text <- paste0(warning_text, sep = "<br>",\r
+                           "Each row must begin with a non-blank dataset name."\r
+    )\r
+  } \r
+  \r
+  if (length(unique(df_elems[[1]])) != length(df_elems[[1]])) {\r
+    warning_text <- paste0(warning_text, sep = "<br>",\r
+                           "The rows contain duplicate dataset names."\r
+    )\r
+  }\r
+  \r
+  if (any(df_elems[[1]] %in% react_values$data_table[, 1])) {\r
+    warning_text <- paste0(warning_text, sep = "<br>",\r
+                           "The rows contain dataset names which already exist."\r
+    )\r
+  }\r
+  # Ensure the second entry in each row is a time unit equal to\r
+  # "Days" or "Weeks".\r
+  if (!all(df_elems[[2]] %in% c("Days", "Weeks"))) {\r
+    warning_text <- paste0(warning_text, sep = "<br>",\r
+                           "The second entry in each row must be either 'Days' or 'Weeks'."\r
+    )\r
+  }\r
+  # Ensure the counts in each row have at least one non-negative integer.\r
+  if (any(df_elems[[3]] == "")) {\r
+    warning_text <- paste0(warning_text, sep = "<br>",\r
+                           "Each row must contain at least one non-negative integer."\r
+    )\r
+  }\r
+  return(warning_text)\r
+}\r
+\r
+\r
+# Convert the input case counts string to an integer vector.\r
+tokenize_counts <- function(counts_str) {\r
+  suppressWarnings(as.integer(unlist(strsplit(trimws(counts_str), ","))))\r
+}\r
+\r
+# Render the preview plot for single entry data.\r
+render_plot <- function(input, output) {\r
+  observe({\r
+    counts <- tokenize_counts(input$data_counts)\r
+    if (length(counts) > 0 && !anyNA(counts) && all(counts >= 0)) {\r
+      output$data_plot <- renderPlot(\r
+        plot(seq_along(counts) - 1, counts, type = "o", pch = 16, col = "black",\r
+             xlab = input$data_units, ylab = "Cases", cex.lab = 1.5,\r
+             xlim = c(0, max(length(counts) - 1, 1)), ylim = c(0, max(counts, 1))\r
+        )\r
+      )\r
+    } else {\r
+      output$data_plot <- renderPlot(\r
+        plot(NULL, xlim = c(0, 10), ylim = c(0, 10),\r
+             xlab = input$data_units, ylab = "Cases", cex.lab = 1.5\r
+        )\r
+      )\r
+    }\r
+  })\r
+}\r
+\r
+# Add a single dataset to the existing table.\r
+single_entry <- function(input, output, react_values) {\r
+  observeEvent(input$data_single, {\r
+    valid <- TRUE\r
+    \r
+    # Ensure the dataset name is neither blank nor a duplicate.\r
+    name <- trimws(input$data_name)\r
+    if (name == "") {\r
+      output$data_name_warn <- renderText("The dataset name cannot be blank.")\r
+      valid <- FALSE\r
+    } else if (name %in% react_values$data_table[, 1]) {\r
+      output$data_name_warn <- renderText(\r
+        "There is already a dataset with the specified name."\r
+      )\r
+      valid <- FALSE\r
+    } else {\r
+      output$data_name_warn <- renderText("")\r
+    }\r
+    \r
+    # Ensure the case counts are specified as a comma-separated of one or more\r
+    # non-negative integers.\r
+    counts <- tokenize_counts(input$data_counts)\r
+    if (length(counts) == 0) {\r
+      output$data_counts_warn <- renderText("Case counts cannot be blank.")\r
+      valid <- FALSE\r
+    } else if (anyNA(counts) || any(counts < 0)) {\r
+      output$data_counts_warn <- renderText(\r
+        "Case counts can only contain non-negative integers."\r
+      )\r
+      valid <- FALSE\r
+    } else {\r
+      output$data_counts_warn <- renderText("")\r
+    }\r
+    \r
+    if (valid) {\r
+      # Add the new dataset to the data table.\r
+      new_row <- data.frame(name, input$data_units, toString(counts))\r
+      colnames(new_row) <- c("Name", "Time units", "Case counts")\r
+      react_values$data_table <- rbind(react_values$data_table, new_row)\r
+      \r
+      # Evaluate all existing estimators on the new dataset and update the\r
+      # corresponding row in the estimates table.\r
+      update_estimates_rows(new_row, react_values)\r
+      \r
+      showNotification("Dataset added successfully.",\r
+                       duration = 3, id = "notify-success"\r
+      )\r
+    }\r
+  })\r
+}\r
+\r
+# Add multiple datasets to the existing table.\r
+bulk_entry <- function(input, output, react_values) {\r
+  observeEvent(input$data_bulk, {\r
+    tryCatch(\r
+      {\r
+        datasets <- read.csv(text = input$data_area, header = FALSE, sep = ",")\r
+        \r
+        names <- trimws(datasets[, 1])\r
+        units <- trimws(datasets[, 2])\r
+        counts <- apply(datasets[, 3:ncol(datasets)], 1,\r
+                        function(row) {\r
+                          row <- suppressWarnings(as.integer(row))\r
+                          toString(row[!is.na(row) & row >= 0])\r
+                        }\r
+        )\r
+        output$data_area_warn <- renderText("")\r
+        warning_text <- warnings(datasets, list(names, units, counts))\r
+        \r
+        if (warning_text == "") {\r
+          # Add the new datasets to the data table.\r
+          new_rows <- data.frame(names, units, counts)\r
+          colnames(new_rows) <- c("Name", "Time units", "Case counts")\r
+          react_values$data_table <- rbind(react_values$data_table, new_rows)\r
+          \r
+          # Evaluate all existing estimators on the new dataset and update the\r
+          # corresponding row in the estimates table.\r
+          update_estimates_rows(new_rows, react_values)\r
+          \r
+          showNotification("Datasets added successfully.",\r
+                           duration = 3, id = "notify-success"\r
+          )\r
+        } else {\r
+          output$data_area_warn <- renderUI(HTML(warning_text))\r
+        }\r
+      },\r
+      error = function(e) {\r
+        output$data_area_warn <- renderText(\r
+          "The input does not match the required format."\r
+        )\r
+      }\r
+    )\r
+  })\r
+}\r
+\r
+# Upload datasets to the existing table.\r
+upload_entry <- function(input, output, react_values) {\r
+  observeEvent(input$data_load, {\r
+    tryCatch(\r
+      {\r
+        df <- read.csv(file = input$upload_csv$datapath)\r
+        names <- trimws(df[, 1])\r
+        units <- trimws(df[, 2])\r
+        counts <- sapply(tokenize_counts(df[, 3:ncol(df)]),\r
+                         function(row) {\r
+                           row <- suppressWarnings(as.integer(row))\r
+                           toString(row[!is.na(row) & row >= 0])\r
+                         }\r
+        )\r
+        output$data_load_warn <- renderText("")\r
+        warning_text <- ''\r
+        warning_text <- warnings(df, list(names, units, counts))\r
+        \r
+        if (warning_text == "") {\r
+          \r
+          # Add the new datasets to the data table.\r
+          new_rows <- read.csv(file = input$upload_csv$datapath)\r
+          colnames(new_rows) <- c("Name", "Time units", "Case counts")\r
+          react_values$data_table <- rbind(react_values$data_table, new_rows)\r
+          \r
+          # Evaluate all existing estimators on the new dataset and update the\r
+          # corresponding row in the estimates table.\r
+          update_estimates_rows(new_rows, react_values)\r
+          \r
+          showNotification("Datasets added successfully.",\r
+                           duration = 3, id = "notify-success")\r
+          \r
+          \r
+        } else {\r
+          output$data_load_warn <- renderUI(HTML(warning_text))        \r
+        }\r
+      },\r
+      error = function(e) {\r
+        output$data_load_warn <- renderText(\r
+          "The input does not match the required format."\r
+        )\r
+      }\r
+    )\r
+  })\r
+}\r
+\r
+# Add sample datasets to the existing table.\r
+sample_entry <- function(input, output, react_values) {\r
+  observeEvent(input$sample_entry, {\r
+    tryCatch(\r
+      {\r
+        # datasets <- read.csv(text = input$sample, header = FALSE, sep = ",")\r
+        \r
+        names <- c()\r
+        units <- c()\r
+        counts <-c()\r
+        \r
+        if (input$march){\r
+          names <- append(names, c("Covid-19 March 2020"))\r
+          units<-append(units, c("Daily"))\r
+          counts<-append(counts,c(covid_cases[1]))}\r
+        if (input$april){ names <- append(names, c("Covid-19 April 2020"))\r
+        units<-append(units, c("Daily"))\r
+        counts<-append(counts,c(covid_cases[2]))}\r
+        if (input$may){ names <- append(names, c("Covid-19 May 2020"))\r
+        units<-append(units, c("Daily"))\r
+        counts<-append(counts,c(covid_cases[3]))}\r
+        \r
+        \r
+        if (input$june){ names <- append(names, c("Covid-19 June 2020"))\r
+        units<-append(units, c("Daily"))\r
+        counts<-append(counts,c(covid_cases[4]))}\r
+        \r
+        if (input$july){ names <- append(names, c("Covid-19 July 2020"))\r
+        units<-append(units, c("Daily"))\r
+        counts<-append(counts,c(covid_cases[5]))}\r
+        \r
+        warning_text <- ""\r
+        \r
+        # Ensure the dataset names are not duplicates.\r
+        \r
+        \r
+        if (any(names %in% react_values$data_table[, 1])) {\r
+          warning_text <- paste0(warning_text, sep = "<br>",\r
+                                 "The rows contain dataset names which already exist."\r
+          )\r
+          \r
+        }\r
+        \r
+        \r
+        output$sample_area_warn <- renderUI(HTML(warning_text))\r
+        \r
+        if (warning_text == "") {\r
+          # Add the new datasets to the data table.\r
+          \r
+          new_rows <- data.frame(names, units, counts)\r
+          colnames(new_rows) <- c("Name", "Time units", "Case counts")\r
+          react_values$data_table <- rbind(react_values$data_table, new_rows)\r
+          \r
+          # Evaluate all existing estimators on the new dataset and update the\r
+          # corresponding row in the estimates table.\r
+          update_estimates_rows(new_rows, react_values)\r
+          \r
+          showNotification("Datasets added successfully.",\r
+                           duration = 3, id = "notify-success"\r
+          )\r
+        }\r
+      }\r
+    )\r
+  })\r
+}\r
+\r
+# Render the data table when new datasets are added.\r
+render_data <- function(output, react_values) {\r
+  observe({\r
+    output$data_table <- DT::renderDataTable(react_values$data_table)\r
+  })\r
+}\r
+\r
+# Delete rows in the data table,\r
+# and the corresponding rows in the estimates table.\r
+delete_data <- function(input, react_values) {\r
+  observeEvent(input$data_delete, {\r
+    new_table <- react_values$data_table[-input$data_table_rows_selected, ]\r
+    if (nrow(new_table) > 0) {\r
+      rownames(new_table) <- seq_len(nrow(new_table))\r
+    }\r
+    react_values$data_table <- new_table\r
+    \r
+    if (ncol(react_values$estimates_table) == 1) {\r
+      react_values$estimates_table <- data.frame(\r
+        Datasets = react_values$data_table[, 1]\r
+      )\r
+    } else {\r
+      react_values$estimates_table <-\r
+        react_values$estimates_table[-input$data_table_rows_selected, ]\r
+    }\r
+  })\r
+}\r
+\r
+# Export data table as a CSV file.\r
+export_data <- function(output, react_values) {\r
+  output$data_export <- downloadHandler(\r
+    filename = function() {\r
+      paste0("Rnaught_data_", format(Sys.time(), "%y-%m-%d_%H-%M-%S"), ".csv")\r
+    },\r
+    content = function(file) {\r
+      write.csv(react_values$data_table, file, row.names = FALSE)\r
+    }\r
+  )\r
+}\r
+\r
+# When new datasets are added, evaluate all existing estimators on them and\r
+# add new rows to the estimates table.\r
+update_estimates_rows <- function(datasets, react_values) {\r
+  new_rows <- data.frame(\r
+    matrix(nrow = nrow(datasets), ncol = ncol(react_values$estimates_table))\r
+  )\r
+  colnames(new_rows) <- colnames(react_values$estimates_table)\r
+  \r
+  for (row in seq_len(nrow(datasets))) {\r
+    new_rows[row, 1] <- datasets[row, 1]\r
+    \r
+    if (length(react_values$estimators) > 0) {\r
+      for (col in 2:ncol(react_values$estimates_table)) {\r
+        new_rows[row, col] <- eval_estimator(\r
+          react_values$estimators[[col - 1]], datasets[row, ]\r
+        )\r
+      }\r
+    }\r
+  }\r
+  \r
+  react_values$estimates_table <- rbind(\r
+    react_values$estimates_table, new_rows\r
+  )\r
+}\r
+#Sample datasets case counts\r
+covid_cases = c("7,1,13,10,6,10,13,28,47,53,62,90,88,130,143,150,186,276,279,350,458,604,570,667,878,883,785,1085,1252",\r
+                "1469,1278,1346,1119,1109,1120,1202,1429,1178,1337,1165,1312,1551,1633,1870,1688,1888,1702,1535,1549,1563,1583,1777,1511,1482,1298,1350,1422,1502,1546",\r
+                "1499,1330,1232,1205,1101,1306,1317,1187,1115,997,953,903,1086,1101,1198,1133,1219,1057,954,1061,1056,1094,922,884,963,660,762,781,1038,763,827",\r
+                "678,656,602,545,557,497,464,411,391,481,402,427,380,322,309,345,358,375,373,300,315,340,288,297,280,330,344,358,242,267",\r
+                "315,291,267,284,244,220,269,313,359,343,348,351,277,362,451,443,517,490,457,472,507,509,573,497,425,408,344,493,405,466,455")\r
+\r

diff --git a/enter-data.html b/enter-data.html
new file mode 100644 (file)
index 0000000..0ff82f2
--- /dev/null
+++ b/enter-data.html
@@ -0,0 +1,20 @@
+<div class="row mb-5">\r
+  <form class="col-md">\r
+    {{ htmlTemplate("templates/content/data/enter-data/single-entry.html") }}\r
+  </form>\r
+  <div class="col-md mt-5 mt-md-0 d-flex flex-column align-items-center">\r
+    <h5>Data plot</h5>\r
+    {{ plotOutput(outputId = "data_plot") }}\r
+  </div>\r
+</div>\r
+<hr>\r
+<form>\r
+  {{ htmlTemplate("templates/content/data/enter-data/bulk-entry.html") }}\r
+</form>\r
+<hr>\r
+<form>\r
+  {{ htmlTemplate("templates/content/data/enter-data/uploadData-entry.html") }}\r
+</form>\r
+<form>\r
+  {{ htmlTemplate("templates/content/data/enter-data/sample-entry.html") }}\r
+</form>
\ No newline at end of file

diff --git a/sample-entry.html b/sample-entry.html
new file mode 100644 (file)
index 0000000..92b9131
--- /dev/null
+++ b/sample-entry.html
@@ -0,0 +1,40 @@
+<h4 class="mb-3">Sample entry</h4>\r
+<!-- Checkboxes -->\r
+\r
+<div>\r
+  \r
+<input type="checkbox" id="march" name="myCheckbox" value="isChecked">\r
+<label for="myCheckbox">Covid-19 March 2020</label>\r
+\r
+</div>\r
+<div>\r
+  \r
+<input type="checkbox" id="april" name="myCheckbox" value="isChecked">\r
+<label for="myCheckbox">Covid-19 April 2020</label>\r
+\r
+</div>\r
+<div>\r
+  \r
+<input type="checkbox" id="may" name="myCheckbox" value="isChecked">\r
+<label for="myCheckbox">Covid-19 May 2020</label>\r
+</div>\r
+\r
+<div>\r
+  \r
+<input type="checkbox" id="june" name="myCheckbox" value="isChecked">\r
+<label for="myCheckbox">Covid-19 June 2020</label></div>\r
+<div><input type="checkbox" id="july" name="myCheckbox" value="isChecked">\r
+<label for="myCheckbox">Covid-19 July 2020</label></div>\r
+\r
+\r
+<div>\r
+\r
+<!-- Submit button -->\r
+<button id="sample_entry" type="button" class="btn btn-outline-primary btn-sm action-button">\r
+  <span class="glyphicon glyphicon-plus"></span> Add\r
+</button>\r
+</div>\r
+<!-- Warning area. -->\r
+<div>\r
+  <small id="sample_area_warn" class="form-text text-primary shiny-html-output"></small>\r
+</div>\r

diff --git a/uploadData-entry.html b/uploadData-entry.html
new file mode 100644 (file)
index 0000000..c1b05c8
--- /dev/null
+++ b/uploadData-entry.html
@@ -0,0 +1,16 @@
+<h4>Upload Data</h4>\r
+<div class="my-3">\r
+  <div id="fileInput" class="col-md mt-5 mt-md-0 d-flex flex-column align-items-left">\r
+    {{ fileInput('upload_csv', 'Choose CSV File', multiple = F, accept= '.csv') }}\r
+  </div>\r
+    <small id="data_load_warn" class="form-text text-primary shiny-html-output"></small>\r
+</div>\r
+<!-- Submit button -->\r
+<button id="data_load" type="button" class="btn btn-outline-primary btn-sm action-button">\r
+  <span class="glyphicon glyphicon-plus"></span> Add\r
+</button>\r
+\r
+<!-- Output message -->\r
+<div class="my-3">\r
+  <p id="output_message"></p>\r
+</div>
\ No newline at end of file