From 190cbed757b62c8f1a52e61e7df65b280090467a Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 15 Dec 2025 11:11:04 -0500
Subject: [PATCH 01/29] Write function to read a pins board from EDAV

---
 R/get_edav_pins_board.R | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 R/get_edav_pins_board.R

diff --git a/R/get_edav_pins_board.R b/R/get_edav_pins_board.R
new file mode 100644
index 00000000..bc0b476f
--- /dev/null
+++ b/R/get_edav_pins_board.R
@@ -0,0 +1,24 @@
+#' Obtain a pins board from EDAV
+#'
+#' @description
+#' This is a convenience function to obtain a pins board in EDAV. After the pins
+#' board is loaded, several functions from the pins package are available to explore
+#' the board. Please see the pins package [get started](https://pins.rstudio.com/articles/pins.html) page.
+#'
+#' @param board_loc `str` Location of the pins board in Azure.
+#' @param azcontainer `azcontainer` An Azure container.
+#'
+#' @returns `pins board` An Azure pins board.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' edav_board <- get_edav_pins_board()
+#' }
+get_edav_pins_board <- function(board_loc = "GID/PEB/SIR/pins_board",
+                                azcontainer = get_azure_storage_connection()) {
+
+  azboard <- pins::board_azure(azcontainer, board_loc)
+
+  return(azboard)
+}

From 860ccce85114b3c291ae47c856914641371caf71 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 15 Dec 2025 11:11:43 -0500
Subject: [PATCH 02/29] Ensure pins dependency is reflected on the description
 and package level import from

---
 DESCRIPTION              | 3 ++-
 R/sirfunctions-package.R | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0357100a..2f11ddda 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -47,7 +47,8 @@ Imports:
     stats,
     rappdirs,
     rmarkdown,
-    grDevices
+    grDevices,
+    pins
 Suggests:
     arrow,
     qs2,
diff --git a/R/sirfunctions-package.R b/R/sirfunctions-package.R
index 41c0aa3b..f44b942c 100644
--- a/R/sirfunctions-package.R
+++ b/R/sirfunctions-package.R
@@ -44,6 +44,7 @@
 #' @importFrom lifecycle deprecate_warn
 #' @importFrom lifecycle deprecated
 #' @importFrom lifecycle is_present
+#' @importFrom pins board_azure
 #' @importFrom purrr map
 #' @importFrom rappdirs user_data_dir
 #' @importFrom readr read_csv

From f2f41c95f3ea9528f8599c6b428718736cfb4086 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 15 Dec 2025 11:11:58 -0500
Subject: [PATCH 03/29] Generate documentation for the new function

---
 NAMESPACE                   |  2 ++
 man/get_edav_pins_board.Rd  | 29 +++++++++++++++++++++++++++++
 man/sirfunctions-package.Rd |  5 ++---
 3 files changed, 33 insertions(+), 3 deletions(-)
 create mode 100644 man/get_edav_pins_board.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 8dff4417..50753d80 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -104,6 +104,7 @@ export(get_cdc_childvaxview_data)
 export(get_constant)
 export(get_ctry_abbrev)
 export(get_diff_cols)
+export(get_edav_pins_board)
 export(get_lab_date_col_missingness)
 export(get_lab_locs)
 export(get_ppt_template)
@@ -171,6 +172,7 @@ importFrom(lifecycle,badge)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
 importFrom(lifecycle,is_present)
+importFrom(pins,board_azure)
 importFrom(purrr,map)
 importFrom(rappdirs,user_data_dir)
 importFrom(readr,read_csv)
diff --git a/man/get_edav_pins_board.Rd b/man/get_edav_pins_board.Rd
new file mode 100644
index 00000000..f41c080e
--- /dev/null
+++ b/man/get_edav_pins_board.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_edav_pins_board.R
+\name{get_edav_pins_board}
+\alias{get_edav_pins_board}
+\title{Obtain a pins board from EDAV}
+\usage{
+get_edav_pins_board(
+  board_loc = "GID/PEB/SIR/pins_board",
+  azcontainer = get_azure_storage_connection()
+)
+}
+\arguments{
+\item{board_loc}{\code{str} Location of the pins board in Azure.}
+
+\item{azcontainer}{\code{azcontainer} An Azure container.}
+}
+\value{
+\verb{pins board} An Azure pins board.
+}
+\description{
+This is a convenience function to obtain a pins board in EDAV. After the pins
+board is loaded, several functions from the pins package are available to explore
+the board. Please see the pins package \href{https://pins.rstudio.com/articles/pins.html}{get started} page.
+}
+\examples{
+\dontrun{
+edav_board <- get_edav_pins_board()
+}
+}
diff --git a/man/sirfunctions-package.Rd b/man/sirfunctions-package.Rd
index 8201e132..5bbb787d 100644
--- a/man/sirfunctions-package.Rd
+++ b/man/sirfunctions-package.Rd
@@ -13,17 +13,16 @@ The sirfunctions package contains key functions used by the Surveillance, Innova
 \seealso{
 Useful links:
 \itemize{
-  \item \url{https://github.com/nish-kishore/sirfunctions}
   \item \url{https://cdcgov.github.io/sirfunctions/}
 }
 
 }
 \author{
-\strong{Maintainer}: Nishant Kishore \email{ynm2@cdc.gov} (\href{https://orcid.org/0000-0003-0408-2747}{ORCID})
+\strong{Maintainer}: Mervin Keith Cuadera \email{xrg9@cdc.gov} (\href{https://orcid.org/0000-0003-4898-2659}{ORCID})
 
 Authors:
 \itemize{
-  \item Mervin Keith Cuadera \email{xrg9@cdc.gov} (\href{https://orcid.org/0000-0003-4898-2659}{ORCID})
+  \item Nishant Kishore \email{ynm2@cdc.gov} (\href{https://orcid.org/0000-0003-0408-2747}{ORCID})
   \item Nicholas Heaghney \email{uic3@cdc.gov}
   \item Elizabeth Krow-Lucal \email{yxn9@cdc.gov}
   \item Smita Chavan \email{wsy2@cdc.gov}

From 94edab7f5b05b77b5e7fbc8ef0ab6d246453e2a4 Mon Sep 17 00:00:00 2001
From: chadhunt2 <chaddrick.hunter@gmail.com>
Date: Fri, 16 Jan 2026 13:42:42 -0500
Subject: [PATCH 04/29] Update dr.main.functions.R

Updated to allow countries with commas in the name to pass as one country.
---
 R/dr.main.functions.R | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/R/dr.main.functions.R b/R/dr.main.functions.R
index a29f74ca..dfd521f6 100644
--- a/R/dr.main.functions.R
+++ b/R/dr.main.functions.R
@@ -251,9 +251,14 @@ update_data <-
                                        polis_folder = .polis_folder,
                                        use_edav = .use_edav
                                        )
-    country_name <- stringr::str_replace_all(country_name, ", ", ",") |>
-      stringr::str_split(",") |>
-      unlist()
+    country_name <- stringr::str_squish(country_name)
+
+    if (length(country_name) == 1) {
+
+      if (stringr::str_detect(country_name, "\\|")) {
+        country_name <- stringr::str_split(country_name, "\\s*\\|\\s*") |> unlist()
+      }
+    }
     country_data <- sirfunctions::extract_country_data(country_name, raw_data)
     readr::write_rds(country_data, path_to_save)
     message(paste0("Data saved at:\n", dr_data_path))
@@ -521,19 +526,19 @@ init_dr <-
 
     if (is.null(end_date)) {
       end_date <- Sys.Date() - lubridate::weeks(6)
-      assign("end_date", end_date, envir = .GlobalEnv)
+      end_date <<- end_date
     } else {
       end_date <- lubridate::as_date(end_date)
-      assign("end_date", end_date, envir = .GlobalEnv)
+      end_date <<- end_date
     }
 
     if (is.null(start_date)) {
       start_date <- (end_date - lubridate::years(3)) |>
         lubridate::floor_date("year")
-      assign("start_date", start_date, envir = .GlobalEnv)
+      start_date <<- start_date
     } else {
       start_date <- lubridate::as_date(start_date)
-      assign("start_date", start_date, envir = .GlobalEnv)
+      start_date <<- start_date
     }
 
     year <- lubridate::year(end_date)
@@ -641,8 +646,7 @@ init_dr <-
                   (stringr::str_detect(data_folder_files, "_lab_data_") |> sum() != 0)) {
           cli::cli_alert_info("Loading cached lab data")
           lab_files <- data_folder_files[stringr::str_detect(data_folder_files, "lab_data")]
-          lab_data <- readRDS(file.path(data_path, lab_files[1]))
-          assign("lab_data", lab_data, envir = .GlobalEnv)
+          lab_data <<- readRDS(file.path(data_path, lab_files[1]))
           Sys.setenv(DR_LAB_PATH = file.path(data_path, lab_files[1]))
           }
 
@@ -670,12 +674,8 @@ init_dr <-
       start_date, end_date, country_name
     )
 
-    end_date <- lubridate::as_date(end_date)
-    assign("end_date", end_date, envir = .GlobalEnv)
-
-    start_date <- lubridate::as_date(start_date)
-    assign("start_date", start_date, envir = .GlobalEnv)
-
+    end_date <<- lubridate::as_date(end_date)
+    start_date <<- lubridate::as_date(start_date)
     # Setting environmental variables
     Sys.setenv(DR_PATH = file.path(country_dir_path))
     Sys.setenv(DR_DATA_PATH = file.path(country_dir_path, "data"))
@@ -705,7 +705,7 @@ init_dr <-
       cli::cli_process_done()
     }
 
-    assign("ctry.data", country_data, envir = .GlobalEnv)
+    ctry.data <<- country_data
     cli::cli_alert_success("ctry.data loaded to the global environment")
     cli::cli_alert_success("Desk review analysis set up complete.")
     cli::cli_text(paste0("Click here to access the template file: ",

From 73c3c151d5aa5624fa532be45e89cf7f825e8a01 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Fri, 16 Jan 2026 15:30:21 -0500
Subject: [PATCH 05/29] get rid of <<- assignments

<<- will be a warning when devtools::check() runs. assign() is a way to circumvent that
---
 R/dr.main.functions.R | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/R/dr.main.functions.R b/R/dr.main.functions.R
index dfd521f6..88d1007d 100644
--- a/R/dr.main.functions.R
+++ b/R/dr.main.functions.R
@@ -526,19 +526,19 @@ init_dr <-
 
     if (is.null(end_date)) {
       end_date <- Sys.Date() - lubridate::weeks(6)
-      end_date <<- end_date
+      assign("end_date", end_date, envir = .GlobalEnv)
     } else {
       end_date <- lubridate::as_date(end_date)
-      end_date <<- end_date
+      assign("end_date", end_date, envir = .GlobalEnv)
     }
 
     if (is.null(start_date)) {
       start_date <- (end_date - lubridate::years(3)) |>
         lubridate::floor_date("year")
-      start_date <<- start_date
+      assign("start_date", start_date, envir = .GlobalEnv)
     } else {
       start_date <- lubridate::as_date(start_date)
-      start_date <<- start_date
+      assign("start_date", start_date, envir = .GlobalEnv)
     }
 
     year <- lubridate::year(end_date)
@@ -646,7 +646,8 @@ init_dr <-
                   (stringr::str_detect(data_folder_files, "_lab_data_") |> sum() != 0)) {
           cli::cli_alert_info("Loading cached lab data")
           lab_files <- data_folder_files[stringr::str_detect(data_folder_files, "lab_data")]
-          lab_data <<- readRDS(file.path(data_path, lab_files[1]))
+          lab_data <- readRDS(file.path(data_path, lab_files[1]))
+          assign("lab_data", lab_data, envir = .GlobalEnv)
           Sys.setenv(DR_LAB_PATH = file.path(data_path, lab_files[1]))
           }
 
@@ -674,8 +675,12 @@ init_dr <-
       start_date, end_date, country_name
     )
 
-    end_date <<- lubridate::as_date(end_date)
-    start_date <<- lubridate::as_date(start_date)
+    end_date <- lubridate::as_date(end_date)
+    assign("end_date", end_date, envir = .GlobalEnv)
+
+    start_date <- lubridate::as_date(start_date)
+    assign("start_date", start_date, envir = .GlobalEnv)
+
     # Setting environmental variables
     Sys.setenv(DR_PATH = file.path(country_dir_path))
     Sys.setenv(DR_DATA_PATH = file.path(country_dir_path, "data"))
@@ -705,7 +710,7 @@ init_dr <-
       cli::cli_process_done()
     }
 
-    ctry.data <<- country_data
+    assign("ctry.data", country_data, envir = .GlobalEnv)
     cli::cli_alert_success("ctry.data loaded to the global environment")
     cli::cli_alert_success("Desk review analysis set up complete.")
     cli::cli_text(paste0("Click here to access the template file: ",

From 7efac946ee62a043a4feb413df5a3980520e6e33 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Fri, 16 Jan 2026 15:41:23 -0500
Subject: [PATCH 06/29] add doc for init_dr

---
 R/dr.main.functions.R | 3 ++-
 man/init_dr.Rd        | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/dr.main.functions.R b/R/dr.main.functions.R
index 88d1007d..420bc1bb 100644
--- a/R/dr.main.functions.R
+++ b/R/dr.main.functions.R
@@ -484,7 +484,7 @@ fetch_dr_data <- function(country, year, local_dr_repo) {
 #' environmental variables (i.e., [Sys.getenv()], where values for `x` related to
 #' the desk review is prefixed with `"DR"`) . The function only supports running one country at a time.
 #'
-#' @param country_name `str` Name of the country.
+#' @param country_name `str` Name of the country. You may pass multiple countries as a vector of strings.
 #' @param start_date `str` Start date of the desk review. If `NULL`, defaults to four years
 #' from when the function was ran on January 1st.
 #' @param end_date `str` End date of the desk review. If `NULL`, defaults to six weeks from when
@@ -505,6 +505,7 @@ fetch_dr_data <- function(country, year, local_dr_repo) {
 #' \dontrun{
 #' ctry.data <- init_dr("algeria", source = F) # Sets up folder in the current working directory
 #' ctry.data <- init_dr("algeria", branch = "dev") # Use functions from the dev branch
+#' ctry.data <- init_dr(c("algeria", "nigeria"), source = F) # Multiple countries.
 #' }
 #'
 #' @export
diff --git a/man/init_dr.Rd b/man/init_dr.Rd
index 14ebb26e..b411f3a7 100644
--- a/man/init_dr.Rd
+++ b/man/init_dr.Rd
@@ -20,7 +20,7 @@ init_dr(
 )
 }
 \arguments{
-\item{country_name}{\code{str} Name of the country.}
+\item{country_name}{\code{str} Name of the country. You may pass multiple countries as a vector of strings.}
 
 \item{start_date}{\code{str} Start date of the desk review. If \code{NULL}, defaults to four years
 from when the function was ran on January 1st.}
@@ -63,6 +63,7 @@ the desk review is prefixed with \code{"DR"}) . The function only supports runni
 \dontrun{
 ctry.data <- init_dr("algeria", source = F) # Sets up folder in the current working directory
 ctry.data <- init_dr("algeria", branch = "dev") # Use functions from the dev branch
+ctry.data <- init_dr(c("algeria", "nigeria"), source = F) # Multiple countries.
 }
 
 }

From fc270c569704be248532e4c0c07c5eed701ea905 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Fri, 16 Jan 2026 15:45:18 -0500
Subject: [PATCH 07/29] fix spatial_data to spatial.data

---
 R/dal.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/dal.R b/R/dal.R
index 1016c22f..e254a9f4 100644
--- a/R/dal.R
+++ b/R/dal.R
@@ -3655,7 +3655,7 @@ force_load_polio_data_cache <- function(attach.spatial.data, output_format = ".r
     # Check if spatial data exists in the cache
     if (sirfunctions_io("exists.file", NULL, spatial_data_path, edav = FALSE)) {
       cli::cli_alert_info("Loading spatial data from cache")
-      spatial_data <- sirfunctions_io("read", NULL, spatial_data_path, edav = FALSE)
+      spatial.data <- sirfunctions_io("read", NULL, spatial_data_path, edav = FALSE)
 
       raw.data$global.ctry <- spatial.data$global.ctry
       raw.data$global.prov <- spatial.data$global.prov

From 312191d9d6f445b486c10a799e355f7a4afa5914 Mon Sep 17 00:00:00 2001
From: chadhunt2 <chaddrick.hunter@gmail.com>
Date: Tue, 10 Feb 2026 16:00:28 -0500
Subject: [PATCH 08/29] Update dr.main.functions.R

---
 R/dr.main.functions.R | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/R/dr.main.functions.R b/R/dr.main.functions.R
index 420bc1bb..3be9875a 100644
--- a/R/dr.main.functions.R
+++ b/R/dr.main.functions.R
@@ -251,14 +251,8 @@ update_data <-
                                        polis_folder = .polis_folder,
                                        use_edav = .use_edav
                                        )
-    country_name <- stringr::str_squish(country_name)
 
-    if (length(country_name) == 1) {
 
-      if (stringr::str_detect(country_name, "\\|")) {
-        country_name <- stringr::str_split(country_name, "\\s*\\|\\s*") |> unlist()
-      }
-    }
     country_data <- sirfunctions::extract_country_data(country_name, raw_data)
     readr::write_rds(country_data, path_to_save)
     message(paste0("Data saved at:\n", dr_data_path))
@@ -546,13 +540,14 @@ init_dr <-
 
     # Set up local directory for storing for data and metadata
     df_name <-
-      stringr::str_c(stringr::str_to_lower(country_name))
+      stringr::str_c(stringr::str_to_lower(country_name)) |>
+      paste(collapse = ", ")
 
     # Relative path of where data and metadata is stored
     dr_path <-
       file.path(
         local_dr_folder,
-        stringr::str_to_lower(country_name),
+        stringr::str_to_lower(df_name),
         year
       )
 

From 9f0f212500f8a72e225a1f89296090894501601c Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 09:42:38 -0400
Subject: [PATCH 09/29] update geo names to reflect new pop file names

---
 R/kpi.table.functions.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/kpi.table.functions.R b/R/kpi.table.functions.R
index 4c1b311c..535dbd09 100644
--- a/R/kpi.table.functions.R
+++ b/R/kpi.table.functions.R
@@ -718,7 +718,7 @@ generate_c1_table <- function(raw_data, start_date, end_date,
 
   # Calculate meeting indicators
   dist_lookup_table <- raw_data$dist.pop |>
-    dplyr::select(ctry = ADM0_NAME, prov = ADM1_NAME, dist = ADM2_NAME, adm2guid) |>
+    dplyr::select(ctry, prov, dist, adm2guid) |>
     dplyr::distinct()
 
   # Flag any inconsistent GUIDs to say any calculations are invalid
@@ -1012,9 +1012,6 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
     cdc.classification.all = "cdc.class"
   )
   pop_data <- dplyr::rename_with(pop_data, recode,
-    ADM0_NAME = "ctry",
-    ADM1_NAME = "prov",
-    ADM2_NAME = "dist",
     ADM0_GUID = "adm0guid",
     u15pop.prov = "u15pop",
     WHO_REGION = "who_region"

From b4d76f8d6383eb8fb1532fb3c445cec80421e30c Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 09:45:20 -0400
Subject: [PATCH 10/29] update who region col name to reflect name in the pop
 data

---
 R/kpi.table.functions.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/kpi.table.functions.R b/R/kpi.table.functions.R
index 535dbd09..b3c33bb1 100644
--- a/R/kpi.table.functions.R
+++ b/R/kpi.table.functions.R
@@ -1014,7 +1014,7 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
   pop_data <- dplyr::rename_with(pop_data, recode,
     ADM0_GUID = "adm0guid",
     u15pop.prov = "u15pop",
-    WHO_REGION = "who_region"
+    WHO_REGION = "who.region"
   )
   cli::cli_progress_update()
 
@@ -1375,13 +1375,13 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
 
   # Add region and risk levels
   region_lookup_table <- pop_data |>
-    dplyr::select(dplyr::any_of(c("ctry", "prov", "dist", "who_region"))) |>
+    dplyr::select(dplyr::any_of(c("ctry", "prov", "dist", "who.region"))) |>
     dplyr::distinct()
 
   results <- add_risk_category(results, risk_table) |>
     dplyr::left_join(region_lookup_table) |>
     dplyr::select(-Region) |>
-    dplyr::rename(Region = who_region) |>
+    dplyr::rename(Region = who.region) |>
     tidyr::replace_na(list(`SG Priority Level` = "LOW"))
 
   cli::cli_progress_done()

From 8bd6fe2560c8cb95aded7f9bc5f5512d1f2c99f1 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 10:16:22 -0400
Subject: [PATCH 11/29] manual edit to reflect indonesia region change in 2025

---
 R/kpi.table.functions.R | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/R/kpi.table.functions.R b/R/kpi.table.functions.R
index b3c33bb1..e0b4de35 100644
--- a/R/kpi.table.functions.R
+++ b/R/kpi.table.functions.R
@@ -886,6 +886,11 @@ generate_c1_table <- function(raw_data, start_date, end_date,
     dplyr::mutate(dplyr::across(dplyr::ends_with("label"), \(x) tidyr::replace_na(x, "0/0"))) |>
     dplyr::rename(Region = whoregion)
 
+  # Manual edit to reflect Indonesia WPRO change in May 23, 2025
+  combine <- combine |>
+    dplyr::mutate(Region = ifelse(ctry == "INDONESIA" & 
+      analysis_year_start >= lubridate::as_date("2025-05-23"), "WPRO", Region))
+
   cli::cli_progress_update()
   cli::cli_progress_done()
 
@@ -1384,6 +1389,11 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
     dplyr::rename(Region = who.region) |>
     tidyr::replace_na(list(`SG Priority Level` = "LOW"))
 
+  # Manual edit to reflect Indonesia WPRO change in May 23, 2025
+  results <- results |>
+    dplyr::mutate(Region = ifelse(ctry == "INDONESIA" & 
+      analysis_year_start >= lubridate::as_date("2025-05-23"), "WPRO", Region))
+
   cli::cli_progress_done()
 
   return(results)

From 06d497008c3a4c0c10cdedbdb28c7bebde1a0d0c Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 10:27:29 -0400
Subject: [PATCH 12/29] reflect seq lab changes in 2025

when generating the positives timeliness data
---
 R/kpi.table.functions.R | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/R/kpi.table.functions.R b/R/kpi.table.functions.R
index e0b4de35..c1127b82 100644
--- a/R/kpi.table.functions.R
+++ b/R/kpi.table.functions.R
@@ -158,6 +158,26 @@ generate_pos_timeliness <- function(raw_data, start_date, end_date,
   pos <- add_rolling_years(pos, start_date, end_date, "dateonset")
   pos <- add_seq_capacity(pos, ctry_col = "place.admin.0", lab_locs)
 
+  # Manual edit based on changes to the sequencing lab list in Feb 2025
+  # There is no collection date, so will use dateonset to classify
+  pos <- pos |>
+    mutate(seq.lab = case_when(
+    seq.lab == "CDC-Atlanta" & dateonset >= as_date("2025-02-01") & culture.itd.lab == "Cameroon" ~ "NICD-South Africa",
+    seq.lab == "CDC-Atlanta" & dateonset >= as_date("2025-02-01") & culture.itd.lab == "ETHIOPIA/ KEMRI-Kenya" ~ "UVRI-Uganda",
+    seq.lab == "CDC-Atlanta" & dateonset >= as_date("2025-02-01") & culture.itd.lab %in% c("Ibadan-Nigeria, Maiduguri-Nigeria", "Nigeria") ~ "Ibadan-Nigeria",
+    seq.lab == "CDC-Atlanta" & dateonset >= as_date("2025-02-01") & culture.itd.lab == "KEMRI-Kenya" ~ "UVRI-Uganda",
+    place.admin.0 == "UGANDA" & dateonset >= as_date("2025-02-01") ~ "UVRI-Uganda",
+    seq.lab == "CDC-Atlanta" & dateonset >= as_date("2025-02-01") & culture.itd.lab == "Senegal" ~ "NICD-South Africa",
+    seq.lab == "CDC-Atlanta" & dateonset >= as_date("2025-02-01") & culture.itd.lab == "Varied (KEMRI-Kenya/ Oman/ Jordan)" ~ "Varied (UVRI/ Oman/ Jordan)",
+    .default = seq.lab
+  )) |>
+  mutate(seq.cat = case_when(
+    dateonset >= as_date("2025-02-01") & culture.itd.lab %in% c("Ibadan-Nigeria, Maiduguri-Nigeria", "Nigeria") & seq.lab == "Ibadan-Nigeria" ~ "Not shipped for sequencing",
+    place.admin.0 == "UGANDA" & dateonset >= as_date("2025-02-01") ~ "Not shipped for sequencing",
+    .default = seq.cat
+  )) |>
+  mutate(seq.capacity = if_else(place.admin.0 %in% c("NIGERIA", "UGANDA") & dateonset >= as_date("2025-02-01"), "yes", seq.capacity))
+
   pos_summary <- pos |>
     dplyr::mutate(
       ontonothq = as.numeric(lubridate::as_date(.data$datenotificationtohq) -

From 4009622dc2b78154044f557d5a36c1d353522663 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 10:30:37 -0400
Subject: [PATCH 13/29] add missing param for timely det violin

---
 R/kpi.figure.functions.R          | 9 ++++++++-
 man/generate_timely_det_violin.Rd | 9 +++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index 4e82d4e3..624816eb 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -736,6 +736,11 @@ generate_kpi_violin <- function(
 #' @param rolling `logical` Using rolling periods or year-to-year? Defaults to `TRUE`.
 #' @param who_region `list` Regions to display. Defaults to `NULL`, which shows
 #' all of the regions.
+#' @param risk_table `tibble` Priority level of each country. Defaults to `NULL`,
+#' which will download the information directly from EDAV.
+#' @param lab_locs `tibble` Summary of the sequencing capacities of labs.
+#' Output of [get_lab_locs()]. Defaults to `NULL`, which will download the information
+#' directly from EDAV.
 #' @param output_path `str` Where to output the figure to.
 #' @param y_max `num` The maximum y-axis value.
 #'
@@ -752,12 +757,14 @@ generate_timely_det_violin <- function(raw_data,
                                        priority_level = c("HIGH", "MEDIUM", "LOW (WATCHLIST)", "LOW"),
                                        who_region = NULL,
                                        rolling = TRUE,
+                                       risk_table = NULL, 
+                                       lab_locs = NULL,
                                        output_path = Sys.getenv("KPI_FIGURES"),
                                        y_max = 250) {
 
   start_date <- lubridate::as_date(start_date)
   end_date <- lubridate::as_date(end_date)
-  pos <- generate_pos_timeliness(raw_data, start_date, end_date)
+  pos <- generate_pos_timeliness(raw_data, start_date, end_date, risk_table, lab_locs)
   ctry_abbrev <- get_ctry_abbrev(raw_data$afp)
   color.risk.cat <- c(
     "HIGH" = "#d73027",
diff --git a/man/generate_timely_det_violin.Rd b/man/generate_timely_det_violin.Rd
index 69eba8ba..a78d0cf5 100644
--- a/man/generate_timely_det_violin.Rd
+++ b/man/generate_timely_det_violin.Rd
@@ -11,6 +11,8 @@ generate_timely_det_violin(
   priority_level = c("HIGH", "MEDIUM", "LOW (WATCHLIST)", "LOW"),
   who_region = NULL,
   rolling = TRUE,
+  risk_table = NULL,
+  lab_locs = NULL,
   output_path = Sys.getenv("KPI_FIGURES"),
   y_max = 250
 )
@@ -30,6 +32,13 @@ all of the regions.}
 
 \item{rolling}{\code{logical} Using rolling periods or year-to-year? Defaults to \code{TRUE}.}
 
+\item{risk_table}{\code{tibble} Priority level of each country. Defaults to \code{NULL},
+which will download the information directly from EDAV.}
+
+\item{lab_locs}{\code{tibble} Summary of the sequencing capacities of labs.
+Output of \code{\link[=get_lab_locs]{get_lab_locs()}}. Defaults to \code{NULL}, which will download the information
+directly from EDAV.}
+
 \item{output_path}{\code{str} Where to output the figure to.}
 
 \item{y_max}{\code{num} The maximum y-axis value.}

From 0585544d31e12f279ff3acc5d7ba83f74fa66686 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 11:40:29 -0400
Subject: [PATCH 14/29] use get_region inside get_ctry_abbrev for consistency

---
 R/kpi.main.functions.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/kpi.main.functions.R b/R/kpi.main.functions.R
index 63b638e3..156579a4 100644
--- a/R/kpi.main.functions.R
+++ b/R/kpi.main.functions.R
@@ -196,7 +196,7 @@ get_ctry_abbrev <- function(afp_data) {
         .data$whoregion != "AFRO" ~ .data$country.iso3
       )
     ) |>
-    dplyr::select("ctry.short", "place.admin.0", "whoregion") |>
+    dplyr::select("ctry.short", "place.admin.0") |>
     # fixing bad abbreviation in Gabon and turning all to upper case to eliminate dupes
     dplyr::mutate(
       ctry.short = ifelse(.data$place.admin.0 == "GABON" & .data$ctry.short == "BUU",
@@ -224,6 +224,9 @@ get_ctry_abbrev <- function(afp_data) {
       ctry.short == "IND" & place.admin.0 == "INDONESIA" ~ "IDN",
       .default = ctry.short
     ))
+  
+  ctry_abbrev <- ctry_abbrev |>
+    dplyr::mutate(whoregion = get_region(place.admin.0))
 
   summarize_ctry_abbrev <- ctry_abbrev |>
     dplyr::group_by(place.admin.0) |>

From 559416b1690daed35c110c8efe835e82d0ae5cea Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 11:40:52 -0400
Subject: [PATCH 15/29] manually correct regions

---
 R/kpi.figure.functions.R | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index 624816eb..a0846565 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -781,10 +781,18 @@ generate_timely_det_violin <- function(raw_data,
   }
 
   pos_filtered <- pos |>
+    dplyr::mutate(whoregion = get_region(place.admin.0)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     dplyr::filter(.data$`SG Priority Level` %in% priority_level,
                   .data$whoregion %in% who_region) |>
     dplyr::left_join(ctry_abbrev,
                      by = c("place.admin.0", "whoregion")) |>
+    # Manually change the region of Indonesia based on change
+    # since get_region() defaults to WPRO now, we have to do the opposite
+    # to assign Indonesia samples to SEARO prior to May 23, 2025
+    dplyr::mutate(whoregion = ifelse(place.admin.0 == "INDONESIA" & 
+      analysis_year_start < lubridate::as_date("2025-05-23"), "SEARO", whoregion)) |>
     dplyr::mutate(seq_lab = case_when(
       .data$seq.capacity == "no" ~ "No sequencing capacity",
       .data$seq.capacity == "yes" ~ "Sequencing capacity"
@@ -796,12 +804,12 @@ generate_timely_det_violin <- function(raw_data,
     )
 
   if (rolling) {
-    facets <- ggh4x::facet_nested(rolling_period~seq_lab+who.region,
+    facets <- ggh4x::facet_nested(rolling_period~seq_lab+whoregion,
                                     scales = "free", space = "free",
                                     labeller = ggplot2::label_wrap_gen(13),
                                     switch = "y")
   } else {
-    facets <- ggh4x::facet_nested(year~seq_lab+who.region,
+    facets <- ggh4x::facet_nested(year~seq_lab+whoregion,
                                     scales = "free", space = "free",
                                     labeller = ggplot2::label_wrap_gen(13),
                                     switch = "y")

From 71d2280a332e4a8eac0073a95acb8dc41cedf2ea Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 12:13:26 -0400
Subject: [PATCH 16/29] fix regions for the lab violin plots

---
 R/kpi.figure.functions.R | 33 ++++++++++++++++++++++++++++++---
 1 file changed, 30 insertions(+), 3 deletions(-)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index a0846565..70fbd20b 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -529,8 +529,11 @@ generate_kpi_npafp_bar <- function(c1, afp_data,
   ctry_abbrev <- get_ctry_abbrev(afp_data)
   priority_ctry <- c1 |>
     dplyr::left_join(ctry_abbrev,
-                     by = c("ctry" = "place.admin.0", "Region" = "whoregion")) |>
+                     by = c("ctry" = "place.admin.0")) |>
     dplyr::filter(.data$`SG Priority Level` == "HIGH") |>
+    # Remove whoregion from ctry_abbrev and use Region since 
+    # c1 already accounts for Indonesia change and it's not used here
+    dplyr::select(-whoregion) |>
     dplyr::mutate(prop_met_npafp = .data$prop_met_npafp)
 
   bar_plot <- generate_kpi_barchart(priority_ctry,
@@ -587,7 +590,10 @@ generate_kpi_evdetect_bar <- function(c1, afp_data,
   ctry_abbrev <- get_ctry_abbrev(afp_data)
   priority_ctry <- c1 |>
     dplyr::left_join(ctry_abbrev,
-                     by = c("ctry" = "place.admin.0", "Region" = "whoregion")) |>
+                     by = c("ctry" = "place.admin.0")) |>
+    # Remove whoregion from ctry_abbrev and use Region since 
+    # c1 already accounts for Indonesia change and it's not used here
+    dplyr::select(-whoregion) |>
     dplyr::mutate(prop_met_ev = .data$prop_met_ev)
 
   if (!is.null(who_region)) {
@@ -635,7 +641,10 @@ generate_kpi_stoolad_bar <- function(c1, afp_data,
   ctry_abbrev <- get_ctry_abbrev(afp_data)
   priority_ctry <- c1 |>
     dplyr::left_join(ctry_abbrev,
-                     by = c("ctry" = "place.admin.0", "Region" = "whoregion")) |>
+                     by = c("ctry" = "place.admin.0")) |>
+    # Remove whoregion from ctry_abbrev and use Region since 
+    # c1 already accounts for Indonesia change and it's not used here
+    dplyr::select(-whoregion) |>
     dplyr::filter(.data$`SG Priority Level` == "HIGH") |>
     dplyr::mutate(prop_met_stool = .data$prop_met_stool)
 
@@ -932,6 +941,9 @@ generate_timely_ship_violin <- function(afp_data,
   afp_filtered <- afp_data |>
     dplyr::filter(.data$`SG Priority Level` %in% priority_level,
                   .data$whoregion %in% who_region) |>
+    dplyr::mutate(whoregion = get_region(place.admin.0)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     dplyr::left_join(ctry_abbrev,
                      by = c("ctry" = "place.admin.0", "whoregion")) |>
     dplyr::mutate(
@@ -1053,6 +1065,9 @@ generate_lab_culture_violin <- function(lab_data, afp_data,
   lab_filtered <- lab_data |> dplyr::left_join(ctry_abbrev,
                                            by = c("country" = "place.admin.0",
                                                   "whoregion")) |>
+    dplyr::mutate(whoregion = get_region(country)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
@@ -1139,6 +1154,9 @@ generate_lab_itd_violin <- function(lab_data, afp_data,
   lab_filtered <- lab_data |> dplyr::left_join(ctry_abbrev,
                                                by = c("country" = "place.admin.0",
                                                       "whoregion")) |>
+    dplyr::mutate(whoregion = get_region(country)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
@@ -1225,6 +1243,9 @@ generate_lab_seqship_violin <- function(lab_data, afp_data,
   lab_filtered <- lab_data |> dplyr::left_join(ctry_abbrev,
                                                by = c("country" = "place.admin.0",
                                                       "whoregion")) |>
+    dplyr::mutate(whoregion = get_region(country)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
@@ -1312,6 +1333,9 @@ generate_lab_seqres_violin <- function(lab_data, afp_data,
   lab_filtered <- lab_data |> dplyr::left_join(ctry_abbrev,
                                                by = c("country" = "place.admin.0",
                                                       "whoregion")) |>
+    dplyr::mutate(whoregion = get_region(country)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
@@ -1425,6 +1449,9 @@ generate_lab_itdres_seqres_violin <- function(lab_data, afp_data,
   lab_filtered <- lab_data |> dplyr::left_join(ctry_abbrev,
                                                by = c("country" = "place.admin.0",
                                                       "whoregion")) |>
+    dplyr::mutate(whoregion = get_region(country)) |>
+    # Remove other who region columns because it's confusing
+    dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)

From 6b9accc99ac437483e0a33ea4791d852d06c4392 Mon Sep 17 00:00:00 2001
From: Mervin Keith Cuadera <40894971+mcuadera@users.noreply.github.com>
Date: Mon, 23 Mar 2026 12:31:44 -0400
Subject: [PATCH 17/29] get rid of incorrectly assigned dates

some date collections are more than a year ahead of the date onset
---
 R/kpi.figure.functions.R | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index 70fbd20b..1e8fb7ba 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -1072,6 +1072,9 @@ generate_lab_culture_violin <- function(lab_data, afp_data,
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
     ) |>
+    # Filter out "incorrect" lab data where the date onset doesn't match
+    # the stool collection date
+    dplyr::filter(dplyr::between(DateStoolCollected, analysis_year_start, analysis_year_end)) |>
     dplyr::filter(.data$`SG Priority Level` %in% priority_level,
                   !is.na(.data$culture.itd.cat),
                   dplyr::between(DateStoolCollected, start_date, end_date)) |>
@@ -1158,6 +1161,9 @@ generate_lab_itd_violin <- function(lab_data, afp_data,
     # Remove other who region columns because it's confusing
     dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
+    # Filter out "incorrect" lab data where the date onset doesn't match
+    # the stool collection date
+    dplyr::filter(dplyr::between(DateStoolCollected, analysis_year_start, analysis_year_end)) |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
     ) |>
@@ -1247,6 +1253,9 @@ generate_lab_seqship_violin <- function(lab_data, afp_data,
     # Remove other who region columns because it's confusing
     dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
+    # Filter out "incorrect" lab data where the date onset doesn't match
+    # the stool collection date
+    dplyr::filter(dplyr::between(DateStoolCollected, analysis_year_start, analysis_year_end)) |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
     ) |>
@@ -1337,6 +1346,9 @@ generate_lab_seqres_violin <- function(lab_data, afp_data,
     # Remove other who region columns because it's confusing
     dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
+    # Filter out "incorrect" lab data where the date onset doesn't match
+    # the stool collection date
+    dplyr::filter(dplyr::between(DateStoolCollected, analysis_year_start, analysis_year_end)) |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
     ) |>
@@ -1453,6 +1465,9 @@ generate_lab_itdres_seqres_violin <- function(lab_data, afp_data,
     # Remove other who region columns because it's confusing
     dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
+    # Filter out "incorrect" lab data where the date onset doesn't match
+    # the stool collection date
+    dplyr::filter(dplyr::between(DateStoolCollected, analysis_year_start, analysis_year_end)) |>
     dplyr::mutate(
       year = lubridate::year(.data$DateStoolCollected)
     ) |>

From 6a6499941e574da13b80f84e7a92c76025f8768a Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Mon, 13 Apr 2026 12:27:00 -0400
Subject: [PATCH 18/29] Update kpi.table.functions.R

Removed the pop data renaming code because it was not doing anything with the new names in pop dataset.
---
 R/kpi.table.functions.R | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/R/kpi.table.functions.R b/R/kpi.table.functions.R
index c1127b82..6bf768b5 100644
--- a/R/kpi.table.functions.R
+++ b/R/kpi.table.functions.R
@@ -908,7 +908,7 @@ generate_c1_table <- function(raw_data, start_date, end_date,
 
   # Manual edit to reflect Indonesia WPRO change in May 23, 2025
   combine <- combine |>
-    dplyr::mutate(Region = ifelse(ctry == "INDONESIA" & 
+    dplyr::mutate(Region = ifelse(ctry == "INDONESIA" &
       analysis_year_start >= lubridate::as_date("2025-05-23"), "WPRO", Region))
 
   cli::cli_progress_update()
@@ -1036,11 +1036,7 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
     dateinvest = "date.invest",
     cdc.classification.all = "cdc.class"
   )
-  pop_data <- dplyr::rename_with(pop_data, recode,
-    ADM0_GUID = "adm0guid",
-    u15pop.prov = "u15pop",
-    WHO_REGION = "who.region"
-  )
+
   cli::cli_progress_update()
 
   # Add required columns
@@ -1411,7 +1407,7 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
 
   # Manual edit to reflect Indonesia WPRO change in May 23, 2025
   results <- results |>
-    dplyr::mutate(Region = ifelse(ctry == "INDONESIA" & 
+    dplyr::mutate(Region = ifelse(ctry == "INDONESIA" &
       analysis_year_start >= lubridate::as_date("2025-05-23"), "WPRO", Region))
 
   cli::cli_progress_done()

From 657ae513b3fc50c8da932f347c687bda33b432a8 Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Mon, 13 Apr 2026 14:33:23 -0400
Subject: [PATCH 19/29] corrections for PR 430

- correct region lookup to ensure WPRO for Indonesia
- correctly get_ctry_abbrev function to address Paraguay
---
 R/kpi.main.functions.R  | 7 ++++---
 R/kpi.table.functions.R | 9 ++-------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/R/kpi.main.functions.R b/R/kpi.main.functions.R
index 156579a4..aaf68d2b 100644
--- a/R/kpi.main.functions.R
+++ b/R/kpi.main.functions.R
@@ -218,13 +218,14 @@ get_ctry_abbrev <- function(afp_data) {
       !(place.admin.0 == "GHANA" & ctry.short == "TOG"),
       !(place.admin.0 == "INDIA" & ctry.short == "PAK"),
       !(place.admin.0 == "PAKISTAN" & ctry.short == "IND"),
-      !(place.admin.0 == "ZAMBIA" & ctry.short == "TAN")
+      !(place.admin.0 == "ZAMBIA" & ctry.short == "TAN"),
+      !(place.admin.0 == "PARAGUAY" & ctry.short == "TTO")
     ) |>
     dplyr::mutate(ctry.short = dplyr::case_when(
       ctry.short == "IND" & place.admin.0 == "INDONESIA" ~ "IDN",
       .default = ctry.short
     ))
-  
+
   ctry_abbrev <- ctry_abbrev |>
     dplyr::mutate(whoregion = get_region(place.admin.0))
 
@@ -235,7 +236,7 @@ get_ctry_abbrev <- function(afp_data) {
     dplyr::ungroup()
 
   if (nrow(summarize_ctry_abbrev) > 0) {
-    cli::cli_alert_warning("Some values in the country lookup table are not unique for the following countries: ")
+    cli::cli_alert_warning("Some values in the country lookup table are not unique for the following countries, please updated code in get_ctry_abbrev: ")
     non_unique <- ctry_abbrev |>
       dplyr::filter(place.admin.0 %in% summarize_ctry_abbrev$place.admin.0)
 
diff --git a/R/kpi.table.functions.R b/R/kpi.table.functions.R
index 6bf768b5..5c4a882c 100644
--- a/R/kpi.table.functions.R
+++ b/R/kpi.table.functions.R
@@ -1394,15 +1394,10 @@ generate_c2_table <- function(afp_data, pop_data, start_date, end_date,
     # NPAFP is only NA if it's missing population
     dplyr::mutate(npafp_rate = dplyr::if_else(npafp_cat != "Missing Pop" & is.nan(npafp_rate), 0, npafp_rate))
 
-  # Add region and risk levels
-  region_lookup_table <- pop_data |>
-    dplyr::select(dplyr::any_of(c("ctry", "prov", "dist", "who.region"))) |>
-    dplyr::distinct()
-
   results <- add_risk_category(results, risk_table) |>
-    dplyr::left_join(region_lookup_table) |>
+    dplyr::mutate(whoregion = get_region(ctry)) |>
     dplyr::select(-Region) |>
-    dplyr::rename(Region = who.region) |>
+    dplyr::rename(Region = whoregion) |>
     tidyr::replace_na(list(`SG Priority Level` = "LOW"))
 
   # Manual edit to reflect Indonesia WPRO change in May 23, 2025

From 61c38bd3432e3a40650d7e500f9f4a3fdb16e9d6 Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Mon, 13 Apr 2026 17:14:14 -0400
Subject: [PATCH 20/29] Update kpi.figure.functions.R

-add filter to the image to only show High Priority countries
---
 R/kpi.figure.functions.R | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index 1e8fb7ba..52c401e1 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -531,7 +531,7 @@ generate_kpi_npafp_bar <- function(c1, afp_data,
     dplyr::left_join(ctry_abbrev,
                      by = c("ctry" = "place.admin.0")) |>
     dplyr::filter(.data$`SG Priority Level` == "HIGH") |>
-    # Remove whoregion from ctry_abbrev and use Region since 
+    # Remove whoregion from ctry_abbrev and use Region since
     # c1 already accounts for Indonesia change and it's not used here
     dplyr::select(-whoregion) |>
     dplyr::mutate(prop_met_npafp = .data$prop_met_npafp)
@@ -591,10 +591,11 @@ generate_kpi_evdetect_bar <- function(c1, afp_data,
   priority_ctry <- c1 |>
     dplyr::left_join(ctry_abbrev,
                      by = c("ctry" = "place.admin.0")) |>
-    # Remove whoregion from ctry_abbrev and use Region since 
+    # Remove whoregion from ctry_abbrev and use Region since
     # c1 already accounts for Indonesia change and it's not used here
     dplyr::select(-whoregion) |>
-    dplyr::mutate(prop_met_ev = .data$prop_met_ev)
+    dplyr::mutate(prop_met_ev = .data$prop_met_ev) |>
+    dplyr::filter(`SG Priority Level` == "HIGH")
 
   if (!is.null(who_region)) {
     priority_ctry <- priority_ctry |> dplyr::filter(Region %in% who_region)
@@ -642,7 +643,7 @@ generate_kpi_stoolad_bar <- function(c1, afp_data,
   priority_ctry <- c1 |>
     dplyr::left_join(ctry_abbrev,
                      by = c("ctry" = "place.admin.0")) |>
-    # Remove whoregion from ctry_abbrev and use Region since 
+    # Remove whoregion from ctry_abbrev and use Region since
     # c1 already accounts for Indonesia change and it's not used here
     dplyr::select(-whoregion) |>
     dplyr::filter(.data$`SG Priority Level` == "HIGH") |>
@@ -766,7 +767,7 @@ generate_timely_det_violin <- function(raw_data,
                                        priority_level = c("HIGH", "MEDIUM", "LOW (WATCHLIST)", "LOW"),
                                        who_region = NULL,
                                        rolling = TRUE,
-                                       risk_table = NULL, 
+                                       risk_table = NULL,
                                        lab_locs = NULL,
                                        output_path = Sys.getenv("KPI_FIGURES"),
                                        y_max = 250) {
@@ -800,7 +801,7 @@ generate_timely_det_violin <- function(raw_data,
     # Manually change the region of Indonesia based on change
     # since get_region() defaults to WPRO now, we have to do the opposite
     # to assign Indonesia samples to SEARO prior to May 23, 2025
-    dplyr::mutate(whoregion = ifelse(place.admin.0 == "INDONESIA" & 
+    dplyr::mutate(whoregion = ifelse(place.admin.0 == "INDONESIA" &
       analysis_year_start < lubridate::as_date("2025-05-23"), "SEARO", whoregion)) |>
     dplyr::mutate(seq_lab = case_when(
       .data$seq.capacity == "no" ~ "No sequencing capacity",

From 0a33bb6e76553f342e9ac1652282b1c5dc37fea0 Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Tue, 14 Apr 2026 13:02:55 -0400
Subject: [PATCH 21/29] Update kpi.figure.functions.R

various updates to correct violin plot outputs:
- some cleanup of unnecessary code
- change y_max for two violin plots to be max of indicator
- correct a lab indicator to ensure all seq.capcity are considered
---
 R/kpi.figure.functions.R | 32 +++++++++++++++++---------------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index 52c401e1..f7e19ee5 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -533,8 +533,7 @@ generate_kpi_npafp_bar <- function(c1, afp_data,
     dplyr::filter(.data$`SG Priority Level` == "HIGH") |>
     # Remove whoregion from ctry_abbrev and use Region since
     # c1 already accounts for Indonesia change and it's not used here
-    dplyr::select(-whoregion) |>
-    dplyr::mutate(prop_met_npafp = .data$prop_met_npafp)
+    dplyr::select(-whoregion)
 
   bar_plot <- generate_kpi_barchart(priority_ctry,
                         "prop_met_npafp",
@@ -594,7 +593,6 @@ generate_kpi_evdetect_bar <- function(c1, afp_data,
     # Remove whoregion from ctry_abbrev and use Region since
     # c1 already accounts for Indonesia change and it's not used here
     dplyr::select(-whoregion) |>
-    dplyr::mutate(prop_met_ev = .data$prop_met_ev) |>
     dplyr::filter(`SG Priority Level` == "HIGH")
 
   if (!is.null(who_region)) {
@@ -646,8 +644,7 @@ generate_kpi_stoolad_bar <- function(c1, afp_data,
     # Remove whoregion from ctry_abbrev and use Region since
     # c1 already accounts for Indonesia change and it's not used here
     dplyr::select(-whoregion) |>
-    dplyr::filter(.data$`SG Priority Level` == "HIGH") |>
-    dplyr::mutate(prop_met_stool = .data$prop_met_stool)
+    dplyr::filter(.data$`SG Priority Level` == "HIGH")
 
   bar_plot <- generate_kpi_barchart(priority_ctry,
                                     "prop_met_stool",
@@ -770,7 +767,7 @@ generate_timely_det_violin <- function(raw_data,
                                        risk_table = NULL,
                                        lab_locs = NULL,
                                        output_path = Sys.getenv("KPI_FIGURES"),
-                                       y_max = 250) {
+                                       y_max = NULL) {
 
   start_date <- lubridate::as_date(start_date)
   end_date <- lubridate::as_date(end_date)
@@ -801,18 +798,21 @@ generate_timely_det_violin <- function(raw_data,
     # Manually change the region of Indonesia based on change
     # since get_region() defaults to WPRO now, we have to do the opposite
     # to assign Indonesia samples to SEARO prior to May 23, 2025
-    dplyr::mutate(whoregion = ifelse(place.admin.0 == "INDONESIA" &
-      analysis_year_start < lubridate::as_date("2025-05-23"), "SEARO", whoregion)) |>
-    dplyr::mutate(seq_lab = case_when(
-      .data$seq.capacity == "no" ~ "No sequencing capacity",
-      .data$seq.capacity == "yes" ~ "Sequencing capacity"
-    )) |>
+    # dplyr::mutate(whoregion = ifelse(place.admin.0 == "INDONESIA" &
+    #   analysis_year_start < lubridate::as_date("2025-05-23"), "SEARO", whoregion)) |>
+    dplyr::mutate(seq_lab = stringr::str_to_lower(seq.capacity),
+                  seq_lab = ifelse(seq_lab == "yes",
+                                   "Sequencing capacity",
+                                   "No sequencing capacity"
+                  ))  |>
     dplyr::filter(!is.na(.data$seq_lab)) |>
     dplyr::mutate(
       sg_priority_level = factor(.data$`SG Priority Level`, levels = c(
         "LOW", "LOW (WATCHLIST)", "MEDIUM", "HIGH"))
     )
 
+  y_max <- max(pos_filtered$ontonothq, na.rm = T)
+
   if (rolling) {
     facets <- ggh4x::facet_nested(rolling_period~seq_lab+whoregion,
                                     scales = "free", space = "free",
@@ -836,7 +836,7 @@ generate_timely_det_violin <- function(raw_data,
   plot_mock_legend <- ggpubr::get_legend(plot_mock)
 
   plot_1 <- generate_kpi_violin(pos_filtered |>
-                                  filter(seq.capacity == "no"), "ctry.short", "ontonothq",
+                                  filter(seq_lab == "No sequencing capacity"), "ctry.short", "ontonothq",
                               "sg_priority_level",
                               facets,
                               46, y.max = y_max)
@@ -845,7 +845,7 @@ generate_timely_det_violin <- function(raw_data,
                                name = "Priority Level",
                                na.value = "white")
 
-  plot_2 <- generate_kpi_violin(pos_filtered |> filter(seq.capacity == "yes"), "ctry.short", "ontonothq",
+  plot_2 <- generate_kpi_violin(pos_filtered |> filter(seq_lab == "Sequencing capacity"), "ctry.short", "ontonothq",
                                 "sg_priority_level",
                                 facets,
                                 35, y.max = y_max)
@@ -1326,7 +1326,7 @@ generate_lab_seqres_violin <- function(lab_data, afp_data,
                                               who_region = NULL,
                                               rolling = TRUE,
                                               output_path = Sys.getenv("KPI_FIGURES"),
-                                              y_max = 60) {
+                                              y_max = NULL) {
 
   start_date <- lubridate::as_date(start_date)
   end_date <- lubridate::as_date(end_date)
@@ -1361,6 +1361,8 @@ generate_lab_seqres_violin <- function(lab_data, afp_data,
         "LOW", "LOW (WATCHLIST)", "MEDIUM", "HIGH"))
     )
 
+  y_max <- as.numeric(max(lab_filtered$days.seq.rec.res, na.rm = T))
+
   if (!is.null(who_region)) {
     lab_filtered <- lab_filtered |>
       dplyr::filter(.data$whoregion %in% who_region)

From 42838c8275b495bc62a5c0d304bd6959b9157cf0 Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Tue, 14 Apr 2026 15:02:30 -0400
Subject: [PATCH 22/29] Update dr.lab.functions.R

correct issue with return df
---
 R/dr.lab.functions.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/dr.lab.functions.R b/R/dr.lab.functions.R
index 14d6bf9d..36df2c88 100644
--- a/R/dr.lab.functions.R
+++ b/R/dr.lab.functions.R
@@ -1232,7 +1232,7 @@ clean_lab_data <- function(lab_data, start_date, end_date,
   )) |>
   mutate(seq.capacity = if_else(country %in% c("NIGERIA", "UGANDA") & DateStoolCollected >= as_date("2025-02-01"), "Sequencing capacity", seq.capacity))
 
-  return(lab_data)
+  return(lab_data_man)
 }
 
 

From 2803f5580e433bb5d6892fb2422e66174632826f Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 15:13:29 -0400
Subject: [PATCH 23/29] Update kpi.figure.functions.R

correction to added y_max to allow user to enter a number as a function argument
---
 R/kpi.figure.functions.R | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/R/kpi.figure.functions.R b/R/kpi.figure.functions.R
index f7e19ee5..23212f87 100644
--- a/R/kpi.figure.functions.R
+++ b/R/kpi.figure.functions.R
@@ -749,7 +749,8 @@ generate_kpi_violin <- function(
 #' Output of [get_lab_locs()]. Defaults to `NULL`, which will download the information
 #' directly from EDAV.
 #' @param output_path `str` Where to output the figure to.
-#' @param y_max `num` The maximum y-axis value.
+#' @param y_max `num` The maximum y-axis value. Defaults to `NULL`, which will compute the
+#' y_max as the max value of days to notify hq.
 #'
 #' @returns `ggplot` A violin plot showing timeliness of detection.
 #' @export
@@ -811,7 +812,9 @@ generate_timely_det_violin <- function(raw_data,
         "LOW", "LOW (WATCHLIST)", "MEDIUM", "HIGH"))
     )
 
-  y_max <- max(pos_filtered$ontonothq, na.rm = T)
+  if (is.null(y_max)) {
+  y_max <- max(pos_filtered$ontonothq, na.rm = TRUE)
+  }
 
   if (rolling) {
     facets <- ggh4x::facet_nested(rolling_period~seq_lab+whoregion,
@@ -1343,7 +1346,6 @@ generate_lab_seqres_violin <- function(lab_data, afp_data,
   lab_filtered <- lab_data |> dplyr::left_join(ctry_abbrev,
                                                by = c("country" = "place.admin.0",
                                                       "whoregion")) |>
-    dplyr::mutate(whoregion = get_region(country)) |>
     # Remove other who region columns because it's confusing
     dplyr::select(-dplyr::any_of(c("who.region", "Region"))) |>
     add_risk_category(ctry_col = "country") |>
@@ -1361,13 +1363,16 @@ generate_lab_seqres_violin <- function(lab_data, afp_data,
         "LOW", "LOW (WATCHLIST)", "MEDIUM", "HIGH"))
     )
 
-  y_max <- as.numeric(max(lab_filtered$days.seq.rec.res, na.rm = T))
 
   if (!is.null(who_region)) {
     lab_filtered <- lab_filtered |>
       dplyr::filter(.data$whoregion %in% who_region)
   }
 
+  if (is.null(y_max)) {
+    y_max <- as.numeric(max(lab_filtered$days.seq.rec.res, na.rm = TRUE))
+  }
+
   if (rolling) {
     facets <- ggh4x::facet_nested(rolling_period ~ seq.cat + seq.lab,
                                   scales = "free", space = "free",

From 8a9d986b8c2fb36b8b7ea46e1812614d7b4efeba Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 15:13:54 -0400
Subject: [PATCH 24/29] Update kpi.main.functions.R

update to kpi template to add code for users to check violin ranges
---
 R/kpi.main.functions.R | 45 ++++++++++++++++++++++++++++++++++++++----
 1 file changed, 41 insertions(+), 4 deletions(-)

diff --git a/R/kpi.main.functions.R b/R/kpi.main.functions.R
index aaf68d2b..20721e66 100644
--- a/R/kpi.main.functions.R
+++ b/R/kpi.main.functions.R
@@ -305,11 +305,12 @@ generate_kpi_template <- function(output_path, name, edav) {
   stool_bar <- "generate_kpi_stoolad_bar(c1, raw_data$afp)"
   ev_bar <- "generate_kpi_evdetect_bar(c1, raw_data$afp)"
 
-  timely_violin <- 'generate_timely_det_violin(raw_data, start_date, end_date)'
+
   culture_violin <- 'generate_lab_culture_violin(lab_data, raw_data$afp, start_date, end_date)'
   itd_violin <- 'generate_lab_itd_violin(lab_data, raw_data$afp, start_date, end_date)'
   seqship_violin <- 'generate_lab_seqship_violin(lab_data, raw_data$afp, start_date, end_date)'
   seqres_violin <- 'generate_lab_seqres_violin(lab_data, raw_data$afp, start_date, end_date)'
+  timely_violin <- 'generate_timely_det_violin(raw_data, start_date, end_date)'
 
   kpi_tile <- 'generate_kpi_tile(c1)'
 
@@ -341,9 +342,44 @@ generate_kpi_template <- function(output_path, name, edav) {
     "# and may take a while to complete.",
     sg_priority_map, npafp_kpi_loop, stool_kpi_loop, ev_kpi_loop, "\n",
     npafp_bar, stool_bar, ev_bar, "\n",
-    "# Adjust the y_max as needed via the 'y_max' parameter",
-    timely_violin, culture_violin, itd_violin, seqship_violin,
-    seqres_violin, "\n",
+    "# Violin plots ----",
+    "# Check the indicator ranges below before setting y_max manually.",
+    "# Note these are approximations; ranges reflect the full dataset before additional filtering in plots.",
+    "# Examine plots carefully to finalize y_max.",
+    "# Example to change y_max: generate_lab_seqres_violin(lab_data, raw_data$afp, start_date, end_date, y_max = 250)",
+    "",
+    "# Build base dataset for lab violin date checks",
+    'lab_kpi_check <- generate_kpi_lab_timeliness(lab_data, start_date, end_date, raw_data$afp)',
+    "",
+    "# For generate_lab_culture_violin()",
+    "# Default y_max is 60",
+    'range(lab_kpi_check$days.lab.culture, na.rm = TRUE)',
+    'summary(lab_kpi_check$days.lab.culture)',
+    "",
+    "# For generate_lab_itd_violin()",
+    "# Default y_max is 30",
+    'range(lab_kpi_check$days.culture.itd, na.rm = TRUE)',
+    'summary(lab_kpi_check$days.culture.itd)',
+    "",
+    "# For generate_lab_seqship_violin()",
+    "# Default y_max is 50",
+    'range(lab_kpi_check$days.seq.ship, na.rm = TRUE)',
+    'summary(lab_kpi_check$days.seq.ship)',
+    "",
+    "# For generate_lab_seqres_violin()",
+    "# Default y_max is dynamic to the max of days.seq.rec.res",
+    'range(as.numeric(lab_kpi_check$days.seq.rec.res), na.rm = TRUE)',
+    'summary(as.numeric(lab_kpi_check$days.seq.rec.res))',
+    "",
+    "# For generate_timely_det_violin()",
+    "# Default y_max is dynamic to the max of ontonothq",
+    "# Uses internal processing; this check approximates the plotted data.",
+    'pos_timeliness_check <- sirfunctions:::generate_pos_timeliness(raw_data, start_date, end_date)',
+    'range(pos_timeliness_check$ontonothq, na.rm = TRUE)',
+    'summary(pos_timeliness_check$ontonothq)',
+    "",
+    "",
+    culture_violin, itd_violin, seqship_violin, seqres_violin, timely_violin, "\n",
     "# Generate C1 KPI tile ----",
     kpi_tile, "\n",
     "# Export GPSAP tables ----",
@@ -351,4 +387,5 @@ generate_kpi_template <- function(output_path, name, edav) {
   )
 
   writeLines(output_string, conn)
+  close(conn)
 }

From 9ea11675f727acaf79f317f4d29f5c9033370dcc Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 15:27:12 -0400
Subject: [PATCH 25/29] documentation update

update documentation with document()
---
 man/generate_lab_seqres_violin.Rd | 2 +-
 man/generate_timely_det_violin.Rd | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/man/generate_lab_seqres_violin.Rd b/man/generate_lab_seqres_violin.Rd
index 3f0d5d40..b17efe67 100644
--- a/man/generate_lab_seqres_violin.Rd
+++ b/man/generate_lab_seqres_violin.Rd
@@ -13,7 +13,7 @@ generate_lab_seqres_violin(
   who_region = NULL,
   rolling = TRUE,
   output_path = Sys.getenv("KPI_FIGURES"),
-  y_max = 60
+  y_max = NULL
 )
 }
 \arguments{
diff --git a/man/generate_timely_det_violin.Rd b/man/generate_timely_det_violin.Rd
index a78d0cf5..72ae188a 100644
--- a/man/generate_timely_det_violin.Rd
+++ b/man/generate_timely_det_violin.Rd
@@ -14,7 +14,7 @@ generate_timely_det_violin(
   risk_table = NULL,
   lab_locs = NULL,
   output_path = Sys.getenv("KPI_FIGURES"),
-  y_max = 250
+  y_max = NULL
 )
 }
 \arguments{
@@ -41,7 +41,8 @@ directly from EDAV.}
 
 \item{output_path}{\code{str} Where to output the figure to.}
 
-\item{y_max}{\code{num} The maximum y-axis value.}
+\item{y_max}{\code{num} The maximum y-axis value. Defaults to \code{NULL}, which will compute the
+y_max as the max value of days to notify hq.}
 }
 \value{
 \code{ggplot} A violin plot showing timeliness of detection.

From 74c3b3c8e9ad9ef9a2f568f39abb2851cafb8434 Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 15:52:47 -0400
Subject: [PATCH 26/29] Update kpi.main.functions.R

additional changes to kpi template
---
 R/kpi.main.functions.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/kpi.main.functions.R b/R/kpi.main.functions.R
index 20721e66..2557b0ab 100644
--- a/R/kpi.main.functions.R
+++ b/R/kpi.main.functions.R
@@ -343,8 +343,9 @@ generate_kpi_template <- function(output_path, name, edav) {
     sg_priority_map, npafp_kpi_loop, stool_kpi_loop, ev_kpi_loop, "\n",
     npafp_bar, stool_bar, ev_bar, "\n",
     "# Violin plots ----",
-    "# Check the indicator ranges below before setting y_max manually.",
-    "# Note these are approximations; ranges reflect the full dataset before additional filtering in plots.",
+    "",
+    "# Before running plots, check the indicator ranges below to determine if you need to change y_max.",
+    "# Note these data are approximations; ranges reflect the full dataset before additional filtering in plots.",
     "# Examine plots carefully to finalize y_max.",
     "# Example to change y_max: generate_lab_seqres_violin(lab_data, raw_data$afp, start_date, end_date, y_max = 250)",
     "",
@@ -379,6 +380,7 @@ generate_kpi_template <- function(output_path, name, edav) {
     'summary(pos_timeliness_check$ontonothq)',
     "",
     "",
+    "# Build plots:",
     culture_violin, itd_violin, seqship_violin, seqres_violin, timely_violin, "\n",
     "# Generate C1 KPI tile ----",
     kpi_tile, "\n",

From 678df67216c30e45b6b5973a9eac418307f39a94 Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 15:53:04 -0400
Subject: [PATCH 27/29] Update R-CMD-check.yaml

change to what is an error in github actions check
---
 .github/workflows/R-CMD-check.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d935b2a0..871aa21d 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -49,3 +49,4 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'

From a5c6c1afee74ec78d43861e957d5c0af8da746ff Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 16:10:34 -0400
Subject: [PATCH 28/29] Update kpi.main.functions.R

changes to kpi template
---
 R/kpi.main.functions.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/kpi.main.functions.R b/R/kpi.main.functions.R
index 2557b0ab..4bbd522e 100644
--- a/R/kpi.main.functions.R
+++ b/R/kpi.main.functions.R
@@ -346,11 +346,12 @@ generate_kpi_template <- function(output_path, name, edav) {
     "",
     "# Before running plots, check the indicator ranges below to determine if you need to change y_max.",
     "# Note these data are approximations; ranges reflect the full dataset before additional filtering in plots.",
+    "# Note: some range checks use internal helper functions from sirfunctions.",
     "# Examine plots carefully to finalize y_max.",
     "# Example to change y_max: generate_lab_seqres_violin(lab_data, raw_data$afp, start_date, end_date, y_max = 250)",
     "",
-    "# Build base dataset for lab violin date checks",
-    'lab_kpi_check <- generate_kpi_lab_timeliness(lab_data, start_date, end_date, raw_data$afp)',
+    "# Build base dataset for lab violin range checks",
+    'lab_kpi_check <- sirfunctions:::generate_kpi_lab_timeliness(lab_data, start_date, end_date, raw_data$afp)',
     "",
     "# For generate_lab_culture_violin()",
     "# Default y_max is 60",
@@ -374,13 +375,12 @@ generate_kpi_template <- function(output_path, name, edav) {
     "",
     "# For generate_timely_det_violin()",
     "# Default y_max is dynamic to the max of ontonothq",
-    "# Uses internal processing; this check approximates the plotted data.",
     'pos_timeliness_check <- sirfunctions:::generate_pos_timeliness(raw_data, start_date, end_date)',
     'range(pos_timeliness_check$ontonothq, na.rm = TRUE)',
     'summary(pos_timeliness_check$ontonothq)',
     "",
     "",
-    "# Build plots:",
+    "# Build plots ----",
     culture_violin, itd_violin, seqship_violin, seqres_violin, timely_violin, "\n",
     "# Generate C1 KPI tile ----",
     kpi_tile, "\n",

From b0bca89c9aa74039d4f4e61bebcd1b69be85128b Mon Sep 17 00:00:00 2001
From: Michelle Sloan <jtq4@cdc.gov>
Date: Wed, 15 Apr 2026 16:49:57 -0400
Subject: [PATCH 29/29] Increment version number to 2.1.7

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 33b28cc9..ab11f694 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sirfunctions
 Title: Key Functions to Analyze Global Polio Surveillance Data
-Version: 2.1.6
+Version: 2.1.7
 Authors@R: c(
     person("Nishant", "Kishore", , "ynm2@cdc.gov", role = c("aut"),
            comment = c(ORCID = "0000-0003-0408-2747")),