Rename function add_smrtype (#840)

* rename to `add_smrtype` * Rename script to `add_smrtype` * update documentation * Remove TODO comment * Style code * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Megan McNicol <[email protected]>
Public-Health-Scotland · Oct 2, 2023 · 570f395 · 570f395
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Showing 14 changed files with 23 additions and 26 deletions.
diff --git a/R/add_smr_type.R → R/add_smrtype.R b/R/add_smr_type.R → R/add_smrtype.R
@@ -10,15 +10,12 @@
 #' @return A vector of `smrtype`
 #'
 #' @family Codes
-add_smr_type <- function(recid,
-                         mpat = NULL,
-                         ipdc = NULL,
-                         hc_service = NULL,
-                         main_applicant_flag = NULL,
-                         consultation_type = NULL) {
-  # TODO rename this function to `add_smrtype()` to match the name of the
-  # variable. Need to make sure to change all places where it is used as well.
-
+add_smrtype <- function(recid,
+                        mpat = NULL,
+                        ipdc = NULL,
+                        hc_service = NULL,
+                        main_applicant_flag = NULL,
+                        consultation_type = NULL) {
   # Situation where some recids are not in the accepted values
   if (!all(recid %in% c(
     "00B",
@@ -188,7 +185,7 @@ add_smr_type <- function(recid,
 
   if (anyNA(smrtype)) {
     cli::cli_warn(
-      "Some {.var smrtype}s were not properly set by {.fun add_smr_type}."
+      "Some {.var smrtype}s were not properly set by {.fun add_smrtype}."
     )
   }
 

diff --git a/R/process_extract_acute.R b/R/process_extract_acute.R
@@ -45,7 +45,7 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
     dplyr::mutate(
       stay = calculate_stay(year, .data$record_keydate1, .data$record_keydate2),
       # create and populate SMRType
-      smrtype = add_smr_type(recid = .data$recid, ipdc = .data$ipdc)
+      smrtype = add_smrtype(recid = .data$recid, ipdc = .data$ipdc)
     ) %>%
     # Apply new costs for C3 specialty, these are taken from the 2017/18 file
     fix_c3_costs(year) %>%

diff --git a/R/process_extract_ae.R b/R/process_extract_ae.R
@@ -62,7 +62,7 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
     # Create month variable
     dplyr::mutate(
       month = strftime(.data$record_keydate1, "%m"),
-      smrtype = add_smr_type(.data$recid)
+      smrtype = add_smrtype(.data$recid)
     ) %>%
     # Allocate the costs to the correct month
     create_day_episode_costs(.data$record_keydate1, .data$cost_total_net)

diff --git a/R/process_extract_care_home.R b/R/process_extract_care_home.R
@@ -58,7 +58,7 @@ process_extract_care_home <- function(
     dplyr::mutate(
       year = year,
       recid = "CH",
-      smrtype = add_smr_type(recid = "CH")
+      smrtype = add_smrtype(recid = "CH")
     ) %>%
     # compute lca variable from sending_location
     dplyr::mutate(

diff --git a/R/process_extract_cmh.R b/R/process_extract_cmh.R
@@ -32,7 +32,7 @@ process_extract_cmh <- function(data,
     # create recid, year, SMRType variables
     dplyr::mutate(
       recid = "CMH",
-      smrtype = add_smr_type(recid = .data$recid),
+      smrtype = add_smrtype(recid = .data$recid),
       year = year
     ) %>%
     # contact end time

diff --git a/R/process_extract_district_nursing.R b/R/process_extract_district_nursing.R
@@ -37,7 +37,7 @@ process_extract_district_nursing <- function(
     dplyr::mutate(
       year = year,
       recid = "DN",
-      smrtype = add_smr_type(recid = "DN")
+      smrtype = add_smrtype(recid = "DN")
     ) %>%
     # deal with gpprac
     dplyr::mutate(gpprac = convert_eng_gpprac_to_dummy(.data$gpprac))

diff --git a/R/process_extract_gp_ooh.R b/R/process_extract_gp_ooh.R
@@ -62,7 +62,7 @@ process_extract_gp_ooh <- function(year, data_list, write_to_disk = TRUE) {
       # Replace location unknown with NA
       location = dplyr::na_if(.data$location, "UNKNOWN"),
       recid = "OoH",
-      smrtype = add_smr_type(.data$recid, consultation_type = .data$consultation_type),
+      smrtype = add_smrtype(.data$recid, consultation_type = .data$consultation_type),
       kis_accessed = factor(
         dplyr::case_when(
           kis_accessed == "Y" ~ 1L,

diff --git a/R/process_extract_homelessness.R b/R/process_extract_homelessness.R
@@ -37,7 +37,7 @@ process_extract_homelessness <- function(
     dplyr::mutate(
       year = as.character(year),
       recid = "HL1",
-      smrtype = add_smr_type(
+      smrtype = add_smrtype(
         recid = .data$recid,
         main_applicant_flag = .data$main_applicant_flag
       )

diff --git a/R/process_extract_maternity.R b/R/process_extract_maternity.R
@@ -55,7 +55,7 @@ process_extract_maternity <- function(data, year, write_to_disk = TRUE) {
       discondition = factor(.data$discondition,
         levels = c(1L:5L, 8L)
       ),
-      smrtype = add_smr_type(.data$recid, .data$mpat),
+      smrtype = add_smrtype(.data$recid, .data$mpat),
       ipdc = dplyr::case_match(
         .data$smrtype,
         "Matern-IP" ~ "I",

diff --git a/R/process_extract_mental_health.R b/R/process_extract_mental_health.R
@@ -64,7 +64,7 @@ process_extract_mental_health <- function(data, year, write_to_disk = TRUE) {
         .data$record_keydate2
       ),
       # SMR type
-      smrtype = add_smr_type(.data$recid)
+      smrtype = add_smrtype(.data$recid)
     )
 
   mh_processed <- mh_clean %>%

diff --git a/R/process_extract_nrs_deaths.R b/R/process_extract_nrs_deaths.R
@@ -22,7 +22,7 @@ process_extract_nrs_deaths <- function(data, year, write_to_disk = TRUE) {
       recid = "NRS",
       year = year,
       gpprac = convert_eng_gpprac_to_dummy(.data$gpprac),
-      smrtype = add_smr_type(.data$recid)
+      smrtype = add_smrtype(.data$recid)
     )
 
   if (write_to_disk) {

diff --git a/R/process_extract_outpatients.R b/R/process_extract_outpatients.R
@@ -28,7 +28,7 @@ process_extract_outpatients <- function(data, year, write_to_disk = TRUE) {
       # Set recid variable
       recid = "00B",
       # Set smrtype variable
-      smrtype = add_smr_type(.data$recid)
+      smrtype = add_smrtype(.data$recid)
     ) %>%
     dplyr::mutate(gpprac = convert_eng_gpprac_to_dummy(.data$gpprac)) %>%
     # compute record key date2

diff --git a/R/process_extract_prescribing.R b/R/process_extract_prescribing.R
@@ -37,7 +37,7 @@ process_extract_prescribing <- function(data, year, write_to_disk = TRUE) {
       record_keydate1 = end_fy(year),
       record_keydate2 = .data$record_keydate1,
       # Add SMR type variable
-      smrtype = add_smr_type(.data$recid)
+      smrtype = add_smrtype(.data$recid)
     )
 
   # Issue a warning if rows were removed

diff --git a/man/add_smr_type.Rd → man/add_smrtype.Rd b/man/add_smr_type.Rd → man/add_smrtype.Rd