From bd2bfa90dc7bb75cc6cbe8c6b674b7bcf486b519 Mon Sep 17 00:00:00 2001 From: kfiliyork <116465911+kfiliyork@users.noreply.github.com> Date: Fri, 24 May 2024 17:30:01 -0400 Subject: Sample data and Upload data --- data.R | 363 ++++++++++++++++++++++++++++++++++++++++++++++++++ enter-data.html | 20 +++ sample-entry.html | 40 ++++++ uploadData-entry.html | 16 +++ 4 files changed, 439 insertions(+) create mode 100644 data.R create mode 100644 enter-data.html create mode 100644 sample-entry.html create mode 100644 uploadData-entry.html diff --git a/data.R b/data.R new file mode 100644 index 0000000..a07372a --- /dev/null +++ b/data.R @@ -0,0 +1,363 @@ +# Main logic block for data-related interactions. +data_logic <- function(input, output, react_values) { + # Initialize a data frame to hold the datasets. + react_values$data_table <- data.frame( + Name = character(0), + `Time units` = character(0), + `Case counts` = character(0), + check.names = FALSE + ) + + render_plot(input, output) + single_entry(input, output, react_values) + bulk_entry(input, output, react_values) + upload_entry(input, output, react_values) + sample_entry(input, output, react_values) + render_data(output, react_values) + delete_data(input, react_values) + export_data(output, react_values) +} + +warnings <- function(df, df_elems) { + + warning_text <- '' + + # Ensure the dataset names are neither blank nor duplicates. + if (anyNA(df_elems[[1]]) || any(df_elems[[1]] == "")) { + warning_text <- paste0(warning_text, sep = "
", + "Each row must begin with a non-blank dataset name." + ) + } + + if (length(unique(df_elems[[1]])) != length(df_elems[[1]])) { + warning_text <- paste0(warning_text, sep = "
", + "The rows contain duplicate dataset names." + ) + } + + if (any(df_elems[[1]] %in% react_values$data_table[, 1])) { + warning_text <- paste0(warning_text, sep = "
", + "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(df_elems[[2]] %in% c("Days", "Weeks"))) { + warning_text <- paste0(warning_text, sep = "
", + "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(df_elems[[3]] == "")) { + warning_text <- paste0(warning_text, sep = "
", + "Each row must contain at least one non-negative integer." + ) + } + return(warning_text) +} + + +# 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 = "black", + 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]) + } + ) + output$data_area_warn <- renderText("") + warning_text <- warnings(datasets, list(names, units, counts)) + + if (warning_text == "") { + # Add the new datasets to the data table. + new_rows <- data.frame(names, units, counts) + colnames(new_rows) <- c("Name", "Time units", "Case counts") + react_values$data_table <- rbind(react_values$data_table, new_rows) + + # Evaluate all existing estimators on the new dataset and update the + # corresponding row in the estimates table. + update_estimates_rows(new_rows, react_values) + + showNotification("Datasets added successfully.", + duration = 3, id = "notify-success" + ) + } else { + output$data_area_warn <- renderUI(HTML(warning_text)) + } + }, + error = function(e) { + output$data_area_warn <- renderText( + "The input does not match the required format." + ) + } + ) + }) +} + +# Upload datasets to the existing table. +upload_entry <- function(input, output, react_values) { + observeEvent(input$data_load, { + tryCatch( + { + df <- read.csv(file = input$upload_csv$datapath) + names <- trimws(df[, 1]) + units <- trimws(df[, 2]) + counts <- sapply(tokenize_counts(df[, 3:ncol(df)]), + function(row) { + row <- suppressWarnings(as.integer(row)) + toString(row[!is.na(row) & row >= 0]) + } + ) + output$data_load_warn <- renderText("") + warning_text <- '' + warning_text <- warnings(df, list(names, units, counts)) + + if (warning_text == "") { + + # Add the new datasets to the data table. + new_rows <- read.csv(file = input$upload_csv$datapath) + colnames(new_rows) <- c("Name", "Time units", "Case counts") + react_values$data_table <- rbind(react_values$data_table, new_rows) + + # Evaluate all existing estimators on the new dataset and update the + # corresponding row in the estimates table. + update_estimates_rows(new_rows, react_values) + + showNotification("Datasets added successfully.", + duration = 3, id = "notify-success") + + + } else { + output$data_load_warn <- renderUI(HTML(warning_text)) + } + }, + error = function(e) { + output$data_load_warn <- renderText( + "The input does not match the required format." + ) + } + ) + }) +} + +# Add sample datasets to the existing table. +sample_entry <- function(input, output, react_values) { + observeEvent(input$sample_entry, { + tryCatch( + { + # datasets <- read.csv(text = input$sample, header = FALSE, sep = ",") + + names <- c() + units <- c() + counts <-c() + + if (input$march){ + names <- append(names, c("Covid-19 March 2020")) + units<-append(units, c("Daily")) + counts<-append(counts,c(covid_cases[1]))} + if (input$april){ names <- append(names, c("Covid-19 April 2020")) + units<-append(units, c("Daily")) + counts<-append(counts,c(covid_cases[2]))} + if (input$may){ names <- append(names, c("Covid-19 May 2020")) + units<-append(units, c("Daily")) + counts<-append(counts,c(covid_cases[3]))} + + + if (input$june){ names <- append(names, c("Covid-19 June 2020")) + units<-append(units, c("Daily")) + counts<-append(counts,c(covid_cases[4]))} + + if (input$july){ names <- append(names, c("Covid-19 July 2020")) + units<-append(units, c("Daily")) + counts<-append(counts,c(covid_cases[5]))} + + warning_text <- "" + + # Ensure the dataset names are not duplicates. + + + if (any(names %in% react_values$data_table[, 1])) { + warning_text <- paste0(warning_text, sep = "
", + "The rows contain dataset names which already exist." + ) + + } + + + output$sample_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" + ) + } + } + ) + }) +} + +# 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 + ) +} +#Sample datasets case counts +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", + "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", + "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", + "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", + "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") + diff --git a/enter-data.html b/enter-data.html new file mode 100644 index 0000000..0ff82f2 --- /dev/null +++ b/enter-data.html @@ -0,0 +1,20 @@ +
+
+ {{ htmlTemplate("templates/content/data/enter-data/single-entry.html") }} +
+
+
Data plot
+ {{ plotOutput(outputId = "data_plot") }} +
+
+
+
+ {{ htmlTemplate("templates/content/data/enter-data/bulk-entry.html") }} +
+
+
+ {{ htmlTemplate("templates/content/data/enter-data/uploadData-entry.html") }} +
+
+ {{ htmlTemplate("templates/content/data/enter-data/sample-entry.html") }} +
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Sample entry

+ + +
+ + + + +
+
+ + + + +
+
+ + + +
+ +
+ + +
+
+
+ + +
+ + + +
+ +
+ +
diff --git a/uploadData-entry.html b/uploadData-entry.html new file mode 100644 index 0000000..c1b05c8 --- /dev/null +++ b/uploadData-entry.html @@ -0,0 +1,16 @@ +

Upload Data

+
+
+ {{ fileInput('upload_csv', 'Choose CSV File', multiple = F, accept= '.csv') }} +
+ +
+ + + + +
+

+
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