From 8319934ee7b70ced8cb429d69055d8c6f2ad1a0a Mon Sep 17 00:00:00 2001
From: scarlettlee9 <tqz9@cdc.gov>
Date: Fri, 7 Aug 2026 11:48:16 -0400
Subject: [PATCH 1/2] Update dr.figure.functions.R

---
 R/dr.figure.functions.R | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/R/dr.figure.functions.R b/R/dr.figure.functions.R
index 053bde90..12fc5ab8 100644
--- a/R/dr.figure.functions.R
+++ b/R/dr.figure.functions.R
@@ -230,10 +230,18 @@ generate_afp_epicurve <- function(ctry.data,
     dplyr::filter(
       dplyr::between(date, start_date, end_date)
     ) |>
-    dplyr::mutate(epi.week = epiweek(date),
-                  epiweek.year = paste0(year, "-", epi.week)) |>
-    dplyr::select(place.admin.0 = ctry, epi.week,
-                  yronset = year, cdc.classification.all2, epiweek.year) |>
+    dplyr::mutate(
+      epi.week = lubridate::epiweek(date),
+      epi.year = lubridate::epiyear(date),
+      epiweek.year = paste0(epi.year, "-", epi.week)
+    ) |>
+    dplyr::select(
+      place.admin.0 = ctry,
+      epi.week,
+      yronset = epi.year,
+      cdc.classification.all2,
+      epiweek.year
+    ) |>
     dplyr::group_by(place.admin.0, epi.week, yronset,
                     cdc.classification.all2, epiweek.year) |>
     dplyr::summarize(afp.cases = dplyr::n())

From fc86d11b4e1bcb71b086dce8b9aa80612ac9935a Mon Sep 17 00:00:00 2001
From: Andrea Stewart <55840298+als329@users.noreply.github.com>
Date: Wed, 12 Aug 2026 09:06:48 -0400
Subject: [PATCH 2/2] Update dr.figure.functions.R

change to isoweek() and isoyear(), filter out cases from outside the iso year window, display calendar year totals above graphs, footnote.
---
 R/dr.figure.functions.R | 30 +++++++++++++++++++++---------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/R/dr.figure.functions.R b/R/dr.figure.functions.R
index 12fc5ab8..d5d9c6fb 100644
--- a/R/dr.figure.functions.R
+++ b/R/dr.figure.functions.R
@@ -226,35 +226,41 @@ generate_afp_epicurve <- function(ctry.data,
   start_date <- lubridate::as_date(start_date)
   end_date <- lubridate::as_date(end_date)
 
-  afp.epi.date.filter <- ctry.data$afp.all.2 %>%
+  afp.epi.date.filter <- ctry.data$afp.all.2 |>
     dplyr::filter(
       dplyr::between(date, start_date, end_date)
     ) |>
     dplyr::mutate(
-      epi.week = lubridate::epiweek(date),
-      epi.year = lubridate::epiyear(date),
+      epi.week = lubridate::isoweek(date),
+      epi.year = lubridate::isoyear(date),
       epiweek.year = paste0(epi.year, "-", epi.week)
     ) |>
+    # need to remove cases with isoyears that fall outside the report window
+    dplyr::filter(
+      dplyr::between(epi.year, lubridate::year(start_date), lubridate::year(end_date))
+    ) |>
     dplyr::select(
       place.admin.0 = ctry,
       epi.week,
-      yronset = epi.year,
+      year = epi.year,
       cdc.classification.all2,
       epiweek.year
     ) |>
-    dplyr::group_by(place.admin.0, epi.week, yronset,
+    dplyr::group_by(place.admin.0, epi.week, year,
                     cdc.classification.all2, epiweek.year) |>
     dplyr::summarize(afp.cases = dplyr::n())
 
+  # get total case counts by calendar year
   case.num.labs <- dplyr::reframe(
-    dplyr::group_by(afp.epi.date.filter, yronset),
-    labs = paste0(yronset, " (N = ", sum(afp.cases), ")")
+    dplyr::group_by(ctry.data$afp.all.2, year),
+    labs = paste0(year, " (N = ", n(), ")")
   ) %>%
     dplyr::distinct(.)
 
+
   afp.epi.date.filter1 <- dplyr::left_join(afp.epi.date.filter,
     case.num.labs,
-    by = c("yronset" = "yronset")
+    by = c("year" = "year")
   )
 
   if (nrow(afp.epi.date.filter1) == 0) {
@@ -272,7 +278,13 @@ generate_afp_epicurve <- function(ctry.data,
       drop = T
     ) +
     sirfunctions::f.plot.looks(type = "epicurve") +
-    ggplot2::facet_wrap(~labs, ncol = 3, drop = F)
+    ggplot2::facet_wrap(~labs, ncol = 3, drop = F) +
+    ggplot2::labs(
+      caption = paste(
+        "Note: Bars represent total cases by ISO weeks (starts on Monday).",
+        "Ns displayed above represent calendar year totals."
+      )
+    )
 
   ggplot2::ggsave(
     "afp.epi.curve.png",