From 7af1a1cecfc0968686fc4f6a34caf886cf22d9fb Mon Sep 17 00:00:00 2001
From: Hugo Gruson <Bisaloo@users.noreply.github.com>
Date: Fri, 7 Jul 2023 15:16:53 -0500
Subject: [PATCH] Use dplyr::case_when() rather than nested ifelse()

---
 R/demographics.R    | 17 ++++++-------
 R/endemic_channel.R | 59 +++++++++++++++++++++------------------------
 2 files changed, 34 insertions(+), 42 deletions(-)

diff --git a/R/demographics.R b/R/demographics.R
index 5e7df8d2..fa2c5a1f 100644
--- a/R/demographics.R
+++ b/R/demographics.R
@@ -346,16 +346,13 @@ describe_occupation <- function(isco_codes, output_level) {
   path <- system.file("data", "isco88_table.rda", package = "epiCo")
   load(path)
   isco88_table <- isco88_table
-  input_level <- ifelse(isco_codes == 0 | isco_codes == 110, "Armed Forces",
-    ifelse(nchar(isco_codes) == 1, "major",
-      ifelse(nchar(isco_codes) == 2, "sub_major",
-        ifelse(nchar(isco_codes) == 3, "minor",
-          ifelse(nchar(isco_codes) == 4, "unit",
-            NA
-          )
-        )
-      )
-    )
+  input_level <- dplyr::case_when(
+    isco_codes %in% c(0, 110) ~ "Armed Forces",
+    nchar(isco_codes) == 1    ~ "major",
+    nchar(isco_codes) == 2    ~ "sub_major",
+    nchar(isco_codes) == 3    ~ "minor",
+    nchar(isco_codes) == 4    ~ "unit",
+    TRUE                      ~ NA_character_
   )
   tryCatch(
     {
diff --git a/R/endemic_channel.R b/R/endemic_channel.R
index cf9e12a2..57182f37 100644
--- a/R/endemic_channel.R
+++ b/R/endemic_channel.R
@@ -81,47 +81,42 @@ auto_endemic_channel <- function(disease_name, divipola_code, year,
   ## Dates and DIVIPOLA codes preparation and cleaning
 
   disease_data <- disease_data %>% dplyr::mutate(
-    COD_MUN_R = ifelse(.data$COD_DPTO_R == 1,
-      .data$COD_PAIS_O, # 1 indicates residence abroad
-      ifelse(nchar(.data$COD_MUN_R) == 1,
+    COD_MUN_R = dplyr::case_when(
+      .data$COD_DPTO_R == 1 ~ .data$COD_PAIS_O, # 1 indicates residence abroad
+      nchar(.data$COD_MUN_R) == 1 ~
         as.numeric(paste(.data$COD_DPTO_R,
           .data$COD_MUN_R,
           sep = "00"
         )),
-        ifelse(nchar(.data$COD_MUN_R) == 2,
-          as.numeric(paste(.data$COD_DPTO_R,
-            .data$COD_MUN_R,
-            sep = "0"
-          )),
-          ifelse(nchar(.data$COD_MUN_R) == 3,
-            as.numeric(paste0(.data$COD_DPTO_R,
-              .data$COD_MUN_R
-            )),
-            NA
-          )
-        )
-      )
+      nchar(.data$COD_MUN_R) == 2 ~
+        as.numeric(paste(.data$COD_DPTO_R,
+          .data$COD_MUN_R,
+          sep = "0"
+        )),
+      nchar(.data$COD_MUN_R) == 3 ~
+        as.numeric(paste0(.data$COD_DPTO_R,
+          .data$COD_MUN_R
+        )),
+      TRUE ~ NA_real_
     ),
-    COD_MUN_O = ifelse(.data$COD_DPTO_O == 1,
-      .data$COD_PAIS_O, # 1 indicates infection occurred abroad
-      ifelse(nchar(.data$COD_MUN_O) == 1,
+    COD_MUN_O = dplyr::case_when(
+      # 1 indicates infection occurred abroad
+      .data$COD_DPTO_O == 1 ~ .data$COD_PAIS_O,
+      nchar(.data$COD_MUN_O) == 1 ~
         as.numeric(paste(.data$COD_DPTO_O,
           .data$COD_MUN_O,
           sep = "00"
         )),
-        ifelse(nchar(.data$COD_MUN_O) == 2,
-          as.numeric(paste(.data$COD_DPTO_O,
-            .data$COD_MUN_O,
-            sep = "0"
-          )),
-          ifelse(nchar(.data$COD_MUN_O) == 3,
-            as.numeric(paste0(.data$COD_DPTO_O,
-              .data$COD_MUN_O
-            )),
-            NA
-          )
-        )
-      )
+      nchar(.data$COD_MUN_O) == 2 ~
+        as.numeric(paste(.data$COD_DPTO_O,
+          .data$COD_MUN_O,
+          sep = "0"
+        )),
+      nchar(.data$COD_MUN_O) == 3 ~
+        as.numeric(paste0(.data$COD_DPTO_O,
+          .data$COD_MUN_O
+        )),
+      TRUE ~ NA_real_
     ),
     EPI_WEEK = lubridate::epiweek(.data$FEC_NOT),
     EPI_MONTH = lubridate::month(.data$FEC_NOT),