Merge branch 'master' into development

.github/workflows/document.yaml

@@ -35,6 +35,6 @@ jobs:
         shell: Rscript {0}
 
       - name: Commit and push changes
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Update documentation"

.github/workflows/style.yaml

@@ -69,6 +69,6 @@ jobs:
         shell: Rscript {0}
 
       - name: Commit and push changes
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Style code"

NAMESPACE

@@ -14,7 +14,7 @@ export(convert_fyyear_to_year)
 export(convert_hb_to_hbnames)
 export(convert_hscp_to_hscpnames)
 export(convert_numeric_to_date)
-export(convert_sending_location_to_lca)
+export(convert_sc_sending_location_to_lca)
 export(convert_year_to_fyyear)
 export(create_episode_file)
 export(create_homelessness_lookup)

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}."
     )
   }
 

R/convert_ca_to_lca.R

@@ -12,7 +12,7 @@
 #' convert_ca_to_lca(ca)
 #'
 #' @family code functions
-#' @seealso convert_sending_location_to_lca
+#' @seealso convert_sc_sending_location_to_lca
 convert_ca_to_lca <- function(ca_var) {
   lca <- dplyr::case_match(
     ca_var,

R/convert_sending_location_to_lca.R → R/convert_sc_sending_location_to_lca.R

@@ -10,12 +10,12 @@
 #'
 #' @examples
 #' sending_location <- c(100, 120)
-#' convert_sending_location_to_lca(sending_location)
+#' convert_sc_sending_location_to_lca(sending_location)
 #'
 #' @family code functions
 #'
 #' @seealso convert_ca_to_lca
-convert_sending_location_to_lca <- function(sending_location) {
+convert_sc_sending_location_to_lca <- function(sending_location) {
   lca <- dplyr::case_match(
     sending_location,
     100L ~ "01", # Aberdeen City

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) %>%

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)

R/process_extract_care_home.R

@@ -58,11 +58,11 @@ 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(
-      sc_send_lca = convert_sending_location_to_lca(.data$sending_location)
+      sc_send_lca = convert_sc_sending_location_to_lca(.data$sending_location)
     ) %>%
     # bed days
     create_monthly_beddays(year,

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

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))

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,

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
       )

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",

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 %>%

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) {

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

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

R/process_sc_all_alarms_telecare.R

@@ -55,7 +55,7 @@ process_sc_all_alarms_telecare <- function(
       # Create person id variable
       person_id = stringr::str_glue("{sending_location}-{social_care_id}"),
       # Use function for creating sc send lca variables
-      sc_send_lca = convert_sending_location_to_lca(.data$sending_location)
+      sc_send_lca = convert_sc_sending_location_to_lca(.data$sending_location)
     ) %>%
     # when multiple social_care_id from sending_location for single CHI
     # replace social_care_id with latest

R/process_sc_all_home_care.R

@@ -199,7 +199,7 @@ process_sc_all_home_care <- function(
     create_person_id(type = "SC") %>%
     # compute lca variable from sending_location
     dplyr::mutate(
-      sc_send_lca = convert_sending_location_to_lca(.data$sending_location)
+      sc_send_lca = convert_sc_sending_location_to_lca(.data$sending_location)
     )
 
   if (write_to_disk) {

R/process_sc_all_sds.R

@@ -80,7 +80,7 @@ process_sc_all_sds <- function(
       # Create person id variable
       person_id = stringr::str_glue("{sending_location}-{social_care_id}"),
       # Use function for creating sc send lca variables
-      sc_send_lca = convert_sending_location_to_lca(.data$sending_location)
+      sc_send_lca = convert_sc_sending_location_to_lca(.data$sending_location)
     ) %>%
     # when multiple social_care_id from sending_location for single CHI
     # replace social_care_id with latest

tests/testthat/_snaps/convert_sending_location_to_lca.md

@@ -1,7 +1,7 @@
 # Can convert a SC sending location to lca code
 
     Code
-      convert_sending_location_to_lca(c(100L, 110L, 120L, 130L, 355L, 150L, 395L,
+      convert_sc_sending_location_to_lca(c(100L, 110L, 120L, 130L, 355L, 150L, 395L,
         170L, 180L, 190L, 200L, 210L, 220L, 230L, 240L, 250L, 260L, 270L, 280L, 290L,
         300L, 310L, 320L, 330L, 340L, 350L, 360L, 370L, 380L, 390L, 400L, 235L, 999L,
         0L, NA_integer_))

tests/testthat/test-convert_sending_location_to_lca.R

@@ -1,6 +1,6 @@
 test_that("Can convert a SC sending location to lca code", {
   expect_snapshot(
-    convert_sending_location_to_lca(
+    convert_sc_sending_location_to_lca(
       c(
         100L,
         110L,
@@ -44,9 +44,9 @@ test_that("Can convert a SC sending location to lca code", {
 
 test_that("Errors on unexpected input", {
   expect_error(
-    convert_sending_location_to_lca("100")
+    convert_sc_sending_location_to_lca("100")
   )
   expect_error(
-    convert_sending_location_to_lca(c("100", 99L))
+    convert_sc_sending_location_to_lca(c("100", 99L))
   )
 })