Remove incorrect references to rds

R/process_costs_rmd.R

@@ -14,7 +14,8 @@ process_costs_rmd <- function(file_name) {
     stringr::fixed("Rmd", ignore_case = TRUE)
   )) {
     cli::cli_abort(
-      "{.arg file_name} must be an {.code .Rmd} not a {.code .{fs::path_ext(file_name)}}."
+      "{.arg file_name} must be an {.code .Rmd} not a
+      {.code .{fs::path_ext(file_name)}}."
     )
   }
 
@@ -34,7 +35,12 @@ process_costs_rmd <- function(file_name) {
 
   output_file <- get_file_path(
     directory = output_dir,
-    file_name = fs::path_ext_set(stringr::str_glue("{fs::path_ext_remove(file_name)}-{latest_update()}-{date_today}"), "html"),
+    file_name = fs::path_ext_set(
+      stringr::str_glue(
+        "{fs::path_ext_remove(file_name)}-{latest_update()}-{date_today}"
+      ),
+      "html"
+    ),
     check_mode = "write"
   )
 
@@ -55,7 +61,7 @@ process_costs_rmd <- function(file_name) {
 #'
 #' @description This will read and process the
 #' District Nursing cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @param file_path Path to the cost lookup.
 #'
@@ -73,7 +79,7 @@ process_costs_dn_rmd <- function(file_path = get_dn_costs_path()) {
 #'
 #' @description This will read and process the
 #' care homes cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @inheritParams process_costs_dn_rmd
 #'
@@ -91,7 +97,7 @@ process_costs_ch_rmd <- function(file_path = get_ch_costs_path()) {
 #'
 #' @description This will read and process the
 #' GP ooh cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @inheritParams process_costs_dn_rmd
 #'
@@ -109,7 +115,7 @@ process_costs_gp_ooh_rmd <- function(file_path = get_gp_ooh_costs_path()) {
 #'
 #' @description This will read and process the
 #' Home Care cost lookup, it will return the final data
-#' but also write this out as a rds.
+#' and write it to disk.
 #'
 #' @inheritParams process_costs_dn_rmd
 #'

R/process_extract_acute.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' acute extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -61,9 +61,7 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
       levels = 0L:8L
     ))
 
-
-  ## save outfile ---------------------------------------
-  outfile <- acute_clean %>%
+  acute_processed <- acute_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -113,10 +111,11 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
     dplyr::arrange(.data$chi, .data$record_keydate1)
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(get_source_extract_path(year, "Acute", check_mode = "write"))
+    write_file(
+      acute_processed,
+      get_source_extract_path(year, "Acute", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(acute_processed)
 }

R/process_extract_ae.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' A&E extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -237,9 +237,7 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
       .data$keytime2
     )
 
-
-  # Save outfile----------------------------------------
-  outfile <- matched_ae_data %>%
+  ae_processed <- matched_ae_data %>%
     dplyr::select(
       "year",
       "recid",
@@ -294,10 +292,11 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(get_source_extract_path(year, "AE", check_mode = "write"))
+    write_file(
+      ae_processed,
+      get_source_extract_path(year, "AE", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(ae_processed)
 }

R/process_extract_alarms_telecare.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' (year specific) Alarms Telecare extract, it will return the final data
-#' but also write this out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @inheritParams process_extract_care_home
 #'

R/process_extract_care_home.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' (year specific) Care Home extract, it will return the final data
-#' but also write this out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The full processed data which will be selected from to create
 #' the year specific data.

R/process_extract_cmh.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' CMH extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -44,9 +44,7 @@ process_extract_cmh <- function(data,
     # create blank diag 6
     dplyr::mutate(diag6 = NA)
 
-  # Outfile --------------------------------------------
-
-  outfile <- cmh_clean %>%
+  cmh_processed <- cmh_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -73,10 +71,11 @@ process_extract_cmh <- function(data,
     )
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(get_source_extract_path(year, "CMH", check_mode = "write"))
+    write_file(
+      cmh_processed,
+      get_source_extract_path(year, "CMH", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(cmh_processed)
 }

R/process_extract_consultations.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OOH Consultations extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -19,7 +19,7 @@
   # Consultations Data ---------------------------------
   ## Data Cleaning
 
   fnc_consultation_types <- c(
     "ED APPOINTMENT",
     "ED TELEPHONE ASSESSMENT",
     "ED TO BOOK",

R/process_extract_delayed_discharges.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' delayed discharges extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_district_nursing.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' District Nursing extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.

R/process_extract_gp_ooh.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OoH extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param year The year to process, in FY format.
 #' @param data_list A list containing the extracts.

R/process_extract_home_care.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' (year specific) Home Care extract, it will return the final data
-#' but also write this out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @inheritParams process_extract_care_home
 #'

R/process_extract_homelessness.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' homelessness extract, it will return the final data
-#' and optionally write it out as rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process from [read_extract_homelessness()].
 #' @param year The year to process, in FY format.

R/process_extract_maternity.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' maternity extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -50,9 +50,9 @@
     ) %>%
     # Calculate costs
     create_monthly_costs() %>%
     # Add discondition as a factor
     dplyr::mutate(
       discondition = factor(.data$discondition,
         levels = c(1L:5L, 8L)
       ),
       smrtype = add_smr_type(.data$recid, .data$mpat),
@@ -63,10 +63,7 @@
       )
     )
 
-
-  # Save outfile------------------------------------------------
-
-  outfile <- maternity_clean %>%
+  maternity_processed <- maternity_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -113,12 +110,11 @@
     dplyr::arrange(.data$chi, .data$record_keydate1)
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(
-        get_source_extract_path(year, "Maternity", check_mode = "write")
-      )
+    write_file(
+      maternity_processed,
+      get_source_extract_path(year, "Maternity", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(maternity_processed)
 }

R/process_extract_mental_health.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' mental health extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -67,10 +67,7 @@ process_extract_mental_health <- function(data, year, write_to_disk = TRUE) {
       smrtype = add_smr_type(.data$recid)
     )
 
-
-  # Outfile  ---------------------------------------
-
-  outfile <- mh_clean %>%
+  mh_processed <- mh_clean %>%
     dplyr::arrange(.data$chi, .data$record_keydate1) %>%
     dplyr::select(
       "year",
@@ -118,10 +115,11 @@ process_extract_mental_health <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
-    outfile %>%
-      # Save as rds file
-      write_file(get_source_extract_path(year, "MH", check_mode = "write"))
+    write_file(
+      mh_processed,
+      get_source_extract_path(year, "MH", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(mh_processed)
 }

R/process_extract_ooh_diagnosis.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OOH Diagnosis extract, it will return the final data
-#' but also write this out an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -97,13 +97,13 @@
   readcodes_not_matched
 
   # Give an error if any new 'bad' readcodes come up.
   unrecognised_but_ok_codes <- c(
     "@1JX.",
     "@1JXz",
     "@43jS",
     "@65PW",
     "@8CA.",
     "@8CAK",
     "@A795"
   )
 

R/process_extract_ooh_outcomes.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' GP OOH Outcomes extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -31,8 +31,8 @@
         "ADVISED TO CONTACT OWN GP SURGERY/GP TO CONTACT PATIENT" ~ "03",
         "TREATMENT COMPLETED AT OOH/DISCHARGED/NO FOLLOW-UP" ~ "98",
         "REFERRED TO A&E" ~ "21",
         "REFERRED TO CPN/DISTRICT NURSE/MIDWIFE" ~ "22",
         "REFERRED TO MIU" ~ "21",
         "REFERRED TO SOCIAL SERVICES" ~ "24",
         "OTHER HC REFERRAL/ADVISED TO CONTACT OTHER HCP (NON-EMERGENCY)" ~ "29",
         "OTHER" ~ "99",

R/process_extract_outpatients.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' outpatients extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -41,7 +41,7 @@
   # Factors ---------------------------------------
   outpatients_clean <- outpatients_clean %>%
     dplyr::mutate(
       reftype = factor(.data$reftype,
         levels = 1L:3L
       ),
       clinic_type = factor(.data$clinic_type,
@@ -49,11 +49,7 @@
       )
     )
 
-
-  ## save outfile ---------------------------------------
-
-  outfile <-
-    outpatients_clean %>%
+  outpatients_processed <- outpatients_clean %>%
     dplyr::select(
       "year",
       "recid",
@@ -89,12 +85,11 @@
     )
 
   if (write_to_disk) {
-    # Save as rds file
-    outfile %>%
-      write_file(
-        get_source_extract_path(year, "Outpatients", check_mode = "write")
-      )
+    write_file(
+      outpatients_processed,
+      get_source_extract_path(year, "Outpatients", check_mode = "write")
+    )
   }
 
-  return(outfile)
+  return(outpatients_processed)
 }

R/process_extract_prescribing.R

@@ -2,7 +2,7 @@
 #'
 #' @description This will read and process the
 #' prescribing extract, it will return the final data
-#' but also write this out as an rds.
+#' and (optionally) write it to disk.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -50,9 +50,10 @@ process_extract_prescribing <- function(data, year, write_to_disk = TRUE) {
   }
 
   if (write_to_disk) {
-    # Save as rds file
-    pis_clean %>%
-      write_file(get_source_extract_path(year, "PIS", check_mode = "write"))
+    write_file(
+      pis_clean,
+      get_source_extract_path(year, "PIS", check_mode = "write")
+    )
   }
 
   return(pis_clean)