+++ /dev/null
-#' @importFrom methods is
-#' @importFrom utils read.csv write.csv
-server <- function(input, output) {
- reactive <- shiny::reactiveValues(
- data_table = data.frame(Name = character(0),
- `Reporting Frequency` = character(0),
- `Case Counts` = numeric(0), check.names = FALSE),
- est_table = data.frame(Dataset = character(0)),
- estimators = list()
- )
-
- # Validate and add datasets when button is clicked.
- # Also evaluate the new datasets on existing estimators.
- shiny::observeEvent(input$addData, {
- # Option 1: Manual entry.
- if (input$dataInputMethod == 1) {
- checks_passed <- TRUE
-
- # Ensure the dataset name is not blank.
- if (grepl("^\\s*$", input$dataName)) {
- output$dataNameWarn <- shiny::renderText(
- "Error: The dataset name cannot be blank.")
- checks_passed <- FALSE
- }
- # Ensure the dataset name is not a duplicate.
- else if (input$dataName %in% reactive$data_table[,1]) {
- output$dataNameWarn <- shiny::renderText(
- "Error: There is already a dataset with the specified name.")
- checks_passed <- FALSE
- }
- else
- output$dataNameWarn <- shiny::renderText("")
-
- # Ensure the case counts consist only of positive integers, separated by
- # commas.
- counts <- as.numeric(unlist(strsplit(input$dataCounts, split = ",")))
- if (any(is.na(counts)) || any(counts <= 0) || any(counts %% 1 != 0)) {
- output$dataCountsWarn <- shiny::renderText("Error: The list of case
- counts should only contain positive integers, separated by commas.")
- checks_passed <- FALSE
- }
- # Ensure the case counts contain at least two entries.
- else if (length(counts) < 2) {
- output$dataCountsWarn <- shiny::renderText(
- "Error: The list of case counts should contain at least two entries.")
- checks_passed <- FALSE
- }
- else
- output$dataCountsWarn <- shiny::renderText("")
-
- if (checks_passed)
- d <- data.frame(input$dataName, input$dataUnits, t(counts))
- }
-
- else {
- checks_passed <- FALSE
-
- # Option 2: Upload .csv
- if (input$dataInputMethod == 2)
- d <- try(read.csv(input$dataUpload$datapath, header = FALSE))
- # Option 3: Paste .csv
- else
- d <- try(read.csv(text = input$dataPaste, header = FALSE))
-
- if (is(d, "try-error"))
- output$dataCSVWarn <- shiny::renderText("Error reading file.")
- else if (ncol(d) < 4 || anyNA(d[,1]) || anyNA(sapply(d[,3:4], as.numeric))
- || !all(trimws(d[,2]) %in% c("Daily", "Weekly")))
- output$dataCSVWarn <- shiny::renderText(
- "Error: The provided .csv file does not match the required format.")
- else if (length(intersect(reactive$data_table[,1], d[,1])) > 0)
- output$dataCSVWarn <- shiny::renderText("Error: The provided .csv file
- contains dataset names which already exist.")
- else if (length(unique(d[,1])) != length(d[,1]))
- output$dataCSVWarn <- shiny::renderText(
- "Error: The provided .csv file contains duplicate dataset names.")
- else {
- output$dataCSVWarn <- shiny::renderText("")
- checks_passed <- TRUE
- }
- }
-
- if (checks_passed) {
- d[,3:ncol(d)] <- apply(d[,3:ncol(d)], 2, as.numeric)
- d[,3] <- data.frame(I(lapply(split(d[,3:ncol(d)], 1:nrow(d)),
- function(x) x[!is.na(x)])))
- d <- d[,1:3]
- d[,2] <- trimws(d[,2])
- colnames(d) <- c("Name", "Reporting Frequency", "Case Counts")
- reactive$data_table <- rbind(reactive$data_table, d)
- reactive$est_table <- update_est_row(input, output, d,
- reactive$estimators, reactive$est_table)
- }
- })
-
- output$dataTable <- shiny::renderDataTable(reactive$data_table,
- escape = FALSE)
- output$estTable <- shiny::renderDataTable(reactive$est_table,
- escape = FALSE)
-
- # Download table of estimates as a .csv file.
- output$downloadEst <- shiny::downloadHandler(
- filename = function() { paste0("Rnaught-", Sys.Date(), ".csv") },
- content = function(file) { write.csv(reactive$est_table, file) }
- )
-
- shiny::observeEvent(input$addWP, {
- if (input$serialWPKnown == 1) {
- serial <- validate_serial(input, output, "serialWPInput", "serialWPWarn")
- if (!is.na(serial)) {
- reactive$estimators[[length(reactive$estimators) + 1]] <- list(
- method = "WP", mu = serial, mu_units = input$serialWPUnits,
- grid_length = 100, max_shape = 10, max_scale = 10)
- reactive$est_table <- update_est_col(input, output, reactive$data_table,
- reactive$estimators[[length(reactive$estimators)]],
- reactive$est_table)
- }
- }
- else {
- checks_passed <- TRUE
-
- grid_length <- as.numeric(input$gridLengthInput)
- max_shape <- as.numeric(input$gridShapeInput)
- max_scale <- as.numeric(input$gridScaleInput)
-
- if (is.na(grid_length) || grid_length <= 0 || grid_length %% 1 != 0) {
- output$gridLengthWarn <- shiny::renderText(
- "Error: The grid size must be a positive integer.")
- output$gridShapeWarn <- shiny::renderText("")
- output$gridScaleWarn <- shiny::renderText("")
- checks_passed <- FALSE
- }
- else {
- output$gridLengthWarn <- shiny::renderText("")
-
- if (is.na(max_shape) || max_shape < 1 / grid_length) {
- output$gridShapeWarn <- shiny::renderText("Error: The maximum shape
- must be at least the reciprocal of the grid length.")
- checks_passed <- FALSE
- }
- else
- output$gridShapeWarn <- shiny::renderText("")
-
- if (is.na(max_scale) || max_scale < 1 / grid_length) {
- output$gridScaleWarn <- shiny::renderText("Error: The maximum scale
- must be at least the reciprocal of the grid length.")
- checks_passed <- FALSE
- }
- else
- output$gridScaleWarn <- shiny::renderText("")
- }
-
- if (checks_passed) {
- reactive$estimators[[length(reactive$estimators) + 1]] <- list(
- method = "WP", mu = NA, mu_units = input$serialWPUnits,
- grid_length = grid_length, max_shape = max_shape, max_scale = max_scale)
- reactive$est_table <- update_est_col(input, output, reactive$data_table,
- reactive$estimators[[length(reactive$estimators)]],
- reactive$est_table)
- }
- }
- })
-
- shiny::observeEvent(input$addseqB, {
- serial <- validate_serial(input, output, "serialseqBInput",
- "serialseqBWarn")
- checks_passed <- !is.na(serial)
-
- kappa <- as.numeric(input$kappaInput)
- if (is.na(kappa) || kappa <= 0) {
- output$kappaWarn <- shiny::renderText(
- "Error: The maximum value must be a positive number.")
- checks_passed <- FALSE
- }
- else
- output$kappaWarn <- shiny::renderText("")
-
- if (checks_passed) {
- reactive$estimators[[length(reactive$estimators) + 1]] <- list(
- method="seqB", mu = serial, kappa = kappa,
- mu_units = input$serialseqBUnits)
- reactive$est_table <- update_est_col(input, output, reactive$data_table,
- reactive$estimators[[length(reactive$estimators)]], reactive$est_table)
- }
- })
-
- shiny::observeEvent(input$addID, {
- serial <- validate_serial(input, output, "serialIDInput", "serialIDWarn")
- if (!is.na(serial)) {
- reactive$estimators[[length(reactive$estimators) + 1]] <- list(
- method = "ID", mu = serial, mu_units = input$serialIDUnits)
- reactive$est_table <- update_est_col(input, output, reactive$data_table,
- reactive$estimators[[length(reactive$estimators)]], reactive$est_table)
- }
- })
-
- shiny::observeEvent(input$addIDEA, {
- serial <- validate_serial(input, output, "serialIDEAInput",
- "serialIDEAWarn")
- if (!is.na(serial)) {
- reactive$estimators[[length(reactive$estimators) + 1]] <- list(
- method = "IDEA", mu = serial, mu_units = input$serialIDEAUnits)
- reactive$est_table <- update_est_col(input, output, reactive$data_table,
- reactive$estimators[[length(reactive$estimators)]], reactive$est_table)
- }
- })
-}
-
-validate_serial <- function(input, output, serialInputId, serialWarnId) {
- serial <- as.numeric(input[[serialInputId]])
- if (is.na(serial) || serial <= 0) {
- output[[serialWarnId]] <- shiny::renderText(
- "Error: The mean serial interval should be a positive number.")
- serial <- NA
- }
- else
- output[[serialWarnId]] <- shiny::renderText("") # Clear warning text.
-
- return(serial)
-}
-
-# Create a new column in the estimator table when a new estimator is added.
-update_est_col <- function(input, output, datasets, estimator, est_table) {
- if (nrow(datasets) == 0)
- new_est_table <- data.frame(matrix(nrow = 0, ncol = ncol(est_table) + 1))
- else {
- estimates <- rep(NA, nrow(datasets))
-
- for (row in 1:nrow(datasets))
- estimates[row] <- eval_estimator(input, output, estimator, datasets[row,])
-
- if (nrow(est_table) == 0)
- new_est_table <- cbind(datasets[,1], estimates)
- else
- new_est_table <- cbind(est_table, estimates)
- }
-
- colnames(new_est_table) <- c(colnames(est_table), shiny::HTML(
- paste0(estimator$method, "<br/>(μ = ", estimator$mu, " ",
- tolower(estimator$mu_units), ")")))
-
- return(new_est_table)
-}
-
-# Create a new row in the estimator table when new datasets are added.
-update_est_row <- function(input, output, datasets, estimators, est_table) {
- if (length(estimators) == 0) {
- if (nrow(est_table) == 0)
- new_est_table <- data.frame(datasets[,1])
- else
- new_est_table <- data.frame(c(est_table[,1], datasets[,1]))
-
- colnames(new_est_table) <- colnames(est_table)
- }
- else {
- new_est_table <- data.frame(matrix(nrow = nrow(datasets),
- ncol = length(estimators)))
-
- for (row in 1:nrow(datasets))
- for (col in 1:length(estimators))
- new_est_table[row, col] <- eval_estimator(input, output,
- estimators[[col]], datasets[row,])
-
- new_est_table <- cbind(datasets[,1], new_est_table)
- colnames(new_est_table) <- colnames(est_table)
- new_est_table <- rbind(est_table, new_est_table)
- }
-
- return(new_est_table)
-}
-
-# Evaluate an estimator on a given dataset.
-eval_estimator <- function(input, output, estimator, dataset) {
- # Adjust serial interval to match time unit of case counts.
- serial <- estimator$mu
- if (estimator$mu_units == "Days" && dataset[2] == "Weekly")
- serial <- serial / 7
- else if (estimator$mu_units == "Weeks" && dataset[2] == "Daily")
- serial <- serial * 7
-
- # White and Pagano
- if (estimator$method == "WP") {
- estimate <- wp(unlist(dataset[3]), mu = serial, serial = TRUE,
- grid_length = estimator$grid_length,
- max_shape = estimator$max_shape,
- max_scale = estimator$max_scale)
-
- if (!is.na(estimator$mu))
- estimate <- round(estimate$r0, 2)
- # Display the estimated mean of the serial distribution if mu was not
- # specified.
- else {
- if (dataset[2] == "Daily")
- mu_units <- "days"
- else
- mu_units <- "weeks"
- MSI <- sum(estimate$supp * estimate$pmf)
- estimate <- shiny::HTML(paste0(round(estimate$r0, 2), "<br/>(μ = ",
- round(MSI, 2), " ", mu_units, ")"))
- }
- }
- # Sequential Bayes
- else if (estimator$method == "seqB")
- estimate <- round(seq_bayes(unlist(dataset[3]), mu = serial,
- kappa = estimator$kappa), 2)
- # Incidence Decay
- else if (estimator$method == "ID")
- estimate <- round(id(unlist(dataset[3]), mu = serial), 2)
- # Incidence Decay with Exponential Adjustement
- else if (estimator$method == "IDEA")
- estimate <- round(idea(unlist(dataset[3]), mu = serial), 2)
-
- return(estimate)
-}
git.nmode.ca / Rnaught / blobdiff
