Pre-Release 0.5.1RC1

Author: ndevln

NEWS.md

@@ -1,6 +1,6 @@
 # ggsurveillance 0.5.1
 
-- Bug fix for corner cases for the `fill_gaps` option in `bin_by_date()`
+-   Bug fix: Fix corner cases for the `fill_gaps` option in `bin_by_date()`
 
 # ggsurveillance 0.5.0
 

R/bin_by_date.R

@@ -143,7 +143,7 @@ bin_by_date <- function(
     df_full_dates <- x |>
       dplyr::select({{ dates_from }}) |>
       .fill_date_gaps(date_resolution = date_resolution)
-    
+
     # Join with data and create observations with weight 0
     suppressMessages(x <- x |>
       dplyr::full_join(df_full_dates) |>
@@ -180,20 +180,21 @@ bin_by_date <- function(
 
 # Internal utility function for filling date gaps
 .fill_date_gaps <- function(dates, date_resolution = "week") {
-
   suppressMessages(group_cols <- dplyr::group_keys(dates))
- 
+
   # Filter out rows with NA dates
   clean_dates <- dates |>
     dplyr::ungroup() |>
     dplyr::select(-colnames(group_cols)) |>
     tidyr::drop_na()
 
-  if (nrow(clean_dates) == 0) return(dates)
-  
+  if (nrow(clean_dates) == 0) {
+    return(dates)
+  }
+
   date_col_name <- colnames(clean_dates)[1]
   date_vector <- clean_dates[[1]]
-  
+
   # Convert lubridate units to seq() compatible units - simple mapping
   seq_by <- dplyr::case_when(
     grepl("sec", date_resolution) & inherits(date_vector, c("POSIXt")) ~ "sec",
@@ -203,19 +204,19 @@ bin_by_date <- function(
     grepl("week", date_resolution) ~ "week",
     # Use week since month can skip February (irregular intervals)
     grepl("month", date_resolution) ~ "week",
-    date_resolution == "bimonth" ~ "month",    # Map to base unit
-    date_resolution == "quarter" ~ "month",    # Map to base unit
-    date_resolution == "season" ~ "month",     # Map to base unit
-    date_resolution == "halfyear" ~ "month",   # Map to base unit
+    date_resolution == "bimonth" ~ "month", # Map to base unit
+    date_resolution == "quarter" ~ "month", # Map to base unit
+    date_resolution == "season" ~ "month", # Map to base unit
+    date_resolution == "halfyear" ~ "month", # Map to base unit
     # Use month since epi/isoyear often has only 364 days (52*7)
-    grepl("year", date_resolution) ~ "month", 
-    TRUE ~ "day"  # default
+    grepl("year", date_resolution) ~ "month",
+    TRUE ~ "day" # default
   )
-  
+
   # Get date range
   min_date <- min(date_vector, na.rm = TRUE)
   max_date <- max(date_vector, na.rm = TRUE)
-  
+
   # Generate complete sequence based on date type
   # TODO: Is this needed?
   if (inherits(date_vector, "Date")) {
@@ -227,7 +228,9 @@ bin_by_date <- function(
   }
 
   # Create result data frame
-  result <- group_cols |> dplyr::group_by_all() |> dplyr::reframe(!!date_col_name := full_sequence)
-  
+  result <- group_cols |>
+    dplyr::group_by_all() |>
+    dplyr::reframe(!!date_col_name := full_sequence)
+
   return(result)
-}
+}

R/geom_epicurve.R

@@ -76,7 +76,7 @@
 #'   labs(title = "Epicurve Example") +
 #'   scale_y_cases_5er() +
 #'   # Correct ISOWeek labels for week-year
-#'   scale_x_date(date_breaks = "4 weeks", date_labels = "W%V'%g") + 
+#'   scale_x_date(date_breaks = "4 weeks", date_labels = "W%V'%g") +
 #'   coord_equal(ratio = 7) + # Use coord_equal for square boxes. 'ratio' are the days per week.
 #'   theme_bw()
 #'

man/geom_epicurve.Rd

@@ -227,64 +227,68 @@ test_that("bin_by_date fill_gaps parameter works", {
   # Check that gaps are filled with zeros
   zero_rows <- result_fill[result_fill$n == 0, ]
   expect_identical(nrow(zero_rows), 2L)
-  
+
   df2 <- data.frame(
-    date = as.Date(c("2024-01-01", "2024-01-15", "2024-01-29")), 
+    date = as.Date(c("2024-01-01", "2024-01-15", "2024-01-29")),
     cases = c(1, 2, 3)
   )
-  
+
   result_fill2 <- bin_by_date(df,
-                             dates_from = date, n = cases,
-                             date_resolution = "week", fill_gaps = TRUE
+    dates_from = date, n = cases,
+    date_resolution = "week", fill_gaps = TRUE
   )
-  
+
   expect_identical(nrow(result_fill2), 5L)
-  
+
   # Check that gaps are filled with zeros
   zero_rows <- result_fill[result_fill2$n == 0, ]
   expect_identical(nrow(zero_rows), 2L)
-  
+
   # Check corner cases, isoyear has often 364 days
   res1 <- data.frame(date = c(as_date("2001-01-01"), as_date("2025-11-05"))) |>
     bin_by_date(dates_from = date, date_resolution = "isoyear", fill_gaps = TRUE)
-  
-  expect_identical(res1$date, 2001:2025*1.0)
-  
+
+  expect_identical(res1$date, 2001:2025 * 1.0)
+
   # Check corner cases, shorter months should not be skipped (February, April)
   res2 <- data.frame(date = c(as_date("2023-01-31"), as_date("2023-06-05"))) |>
     bin_by_date(dates_from = date, date_resolution = "month", fill_gaps = TRUE)
-  
-  expect_identical(month(res2$date), 1:6*1.0)
+
+  expect_identical(month(res2$date), 1:6 * 1.0)
 })
 
 test_that("bin_by_date fill_gaps works with grouped data", {
   # Create data with gaps within groups
   df <- data.frame(
-    date = as.Date(c("2024-01-01", "2024-01-15", "2024-01-29", # Group A with gaps
-                     "2024-01-08", "2024-01-22")),               # Group B with gaps
+    date = as.Date(c(
+      "2024-01-01", "2024-01-15", "2024-01-29", # Group A with gaps
+      "2024-01-08", "2024-01-22"
+    )), # Group B with gaps
     group = c("A", "A", "A", "B", "B"),
     cases = c(1, 2, 3, 4, 5)
   )
-  
+
   # Test with grouping and fill_gaps = TRUE
   result_grouped_fill <- df |>
     dplyr::group_by(group) |>
-    bin_by_date(dates_from = date, n = cases,
-                date_resolution = "week", fill_gaps = TRUE, .groups = "drop_last")
-  
+    bin_by_date(
+      dates_from = date, n = cases,
+      date_resolution = "week", fill_gaps = TRUE, .groups = "drop_last"
+    )
+
   # Should preserve grouping
   expect_true(dplyr::is_grouped_df(result_grouped_fill))
   expect_identical(dplyr::group_vars(result_grouped_fill), "group")
-  expect_identical(nrow(result_grouped_fill), 2L*5L) # Both have same length
-  
+  expect_identical(nrow(result_grouped_fill), 2L * 5L) # Both have same length
+
   # Check that gaps are filled with zeros within groups
   zero_rows <- result_grouped_fill[result_grouped_fill$n == 0, ]
   expect_identical(nrow(zero_rows), 5L) # 2 gaps in A + 3 gaps in B
-  
+
   # Test without fill_gaps for comparison
   result_grouped_no_fill <- df |>
     dplyr::group_by(group) |>
     bin_by_date(dates_from = date, n = cases, date_resolution = "week")
-    
+
   expect_identical(nrow(result_grouped_no_fill), 5L) # Original data only
 })