Merge pull request #6 from ssi-dk:telkamp7/issue5

Telkamp7/issue5

R/summary.R

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+#' Summary method for aedseo objects
+#'
+#' @description
+#' `r lifecycle::badge("experimental")`
+#'
+#' Summarize the results of an aedseo analysis, including the latest growth rate
+#' estimate, the confidence interval, and information about growth warnings.
+#'
+#' @param object An object of class 'aedseo' containing the results of an aedseo
+#' analysis.
+#' @param ... Additional arguments (not used).
+#'
+#' @return This function is used for its side effect, which is printing a
+#' summary message to the console.
+#'
+#' @examples
+#' # Create a tsibble object from sample data
+#' tsd_data <- tsd(
+#'   observed = c(100, 120, 150, 180, 220, 270),
+#'   time = as.Date(c(
+#'     "2023-01-01",
+#'     "2023-01-02",
+#'     "2023-01-03",
+#'     "2023-01-04",
+#'     "2023-01-05",
+#'     "2023-01-06"
+#'   )),
+#'   time_interval = "day"
+#' )
+#'
+#' # Calculate AEDSEO with a 3-day window and a Poisson family model
+#' aedseo_results <- aedseo(
+#'   tsd = tsd_data,
+#'   k = 3,
+#'   level = 0.95,
+#'   family = "poisson"
+#' )
+#' # Print the summary of the aedseo_results to the console
+#' summary(aedseo_results)
+summary.aedseo <- function(object, ...) {
+  # Extract the last observation
+  last_observation <- dplyr::last(object)
+
+  # Extract the reference time
+  reference_time <- last_observation$reference_time
+
+  # Latest growth warning
+  latest_growth_warning <- object %>%
+    dplyr::filter(.data$growth_warning == TRUE) %>%
+    dplyr::summarise(latest_growth_warning = dplyr::last(reference_time)) %>%
+    dplyr::pull(latest_growth_warning)
+
+  # Calculate the total number of growth warnings
+  sum_of_growth_warnings <- object %>%
+    dplyr::summarise(sum_of_growth_warnings = sum(.data$growth_warning)) %>%
+    dplyr::pull(sum_of_growth_warnings)
+
+  # Generate the summary message
+  summary_message <- sprintf(
+    "Summary of aedseo Object
+
+    Reference time point:
+      %s
+
+    Growth rate estimate:
+      Estimate   Lower   Upper
+         %.3f  %.3f   %.3f
+
+    Total number of growth warnings in the series:
+      %d
+    Latest growth warning:
+      %s",
+    as.character(reference_time),
+    last_observation$growth_rate,
+    last_observation$lower_growth_rate,
+    last_observation$upper_growth_rate,
+    sum_of_growth_warnings,
+    as.character(latest_growth_warning)
+  )
+
+  # Print the summary message
+  cat(summary_message)
+}

tests/testthat/test-summary.R

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+test_that("Summary prints without errors", {
+  # Set start and end dates
+  from_date <- as.Date("2021-01-01")
+  to_date <- as.Date("2021-01-31")
+
+  # Choose some time dates
+  time <- seq.Date(from = from_date, to = to_date, by = "day")
+
+  # Count the number of observations
+  n <- length(time)
+
+  # Data
+  tsd_data_poisson <- tsd(
+    observed = rpois(n = n, lambda = 1:n),
+    time = time,
+    time_interval = "day"
+  )
+  # Calculate AEDSEO with a 3-day window
+  aedseo_poisson <- aedseo(
+    tsd = tsd_data_poisson,
+    k = 3,
+    level = 0.95,
+    family = "poisson"
+  )
+
+  # Capture the output of the summary function
+  tmp <- capture_output(summary.aedseo(aedseo_poisson))
+
+  # Verify that the summary printed without errors
+  expect_true(grepl(pattern = "Summary of aedseo Object", x = tmp))
+})