Merge branch 'development' into targets/pass_all_data_to_episode_file

.github/actions/spelling/expect.txt

@@ -26,6 +26,7 @@ Classificat
 cls
 cmh
 CNWs
+Comhairle
 commhosp
 congen
 costincdnas
@@ -112,6 +113,7 @@ ltc
 ltcs
 lubridate
 magrittr
+Matern
 Mcbride
 mcmahon
 MMMYY
@@ -137,6 +139,7 @@ outfile
 pandoc
 patflow
 pattype
+PCEC
 phs
 phsmethods
 phsopendata
@@ -199,6 +202,7 @@ submis
 tadm
 tarchetypes
 tbl
+Telecare
 telecare
 testthat
 thom

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master, main, main-R]
+    branches: [master, main, development]
   pull_request:
-    branches: [master, main, main-R]
+    branches: [master, main, development]
 
 name: R-CMD-check
 

R/add_smr_type.R

@@ -159,28 +159,30 @@ add_smr_type <- function(recid,
       recid == "HL1" & main_applicant_flag == "N" ~ "HL1-Other"
     )
   } else if (all(recid == "OoH")) {
-    smrtype <- dplyr::case_when(
-      consultation_type == "DISTRICT NURSE" ~ "OOH-DN",
-      consultation_type == "DOCTOR ADVICE/NURSE ADVICE" ~ "OOH-Advice",
-      consultation_type == "HOME VISIT" ~ "OOH-HomeV",
-      consultation_type == "NHS 24 NURSE ADVICE" ~ "OOH-NHS24",
-      consultation_type == "PCEC/PCC" ~ "OOH-PCC",
-      consultation_type == "COVID19 ASSESSMENT" ~ "OOH-C19Ass",
-      consultation_type == "COVID19 ADVICE" ~ "OOH-C19Adv",
-      consultation_type == "COVID19 OTHER" ~ "OOH-C19Oth",
+    smrtype <- dplyr::case_match(
+      consultation_type,
+      "DISTRICT NURSE" ~ "OOH-DN",
+      "DOCTOR ADVICE/NURSE ADVICE" ~ "OOH-Advice",
+      "HOME VISIT" ~ "OOH-HomeV",
+      "NHS 24 NURSE ADVICE" ~ "OOH-NHS24",
+      "PCEC/PCC" ~ "OOH-PCC",
+      "COVID19 ASSESSMENT" ~ "OOH-C19Ass",
+      "COVID19 ADVICE" ~ "OOH-C19Adv",
+      "COVID19 OTHER" ~ "OOH-C19Oth",
       .default = "OOH-Other"
     )
   } else {
     # Recids that can be recoded with no identifier
-    smrtype <- dplyr::case_when(
-      recid == "00B" ~ "Outpatient",
-      recid == "04B" ~ "Psych-IP",
-      recid == "AE2" ~ "A & E",
-      recid == "CH" ~ "Care-Home",
-      recid == "CMH" ~ "Comm-MH",
-      recid == "DN" ~ "DN",
-      recid == "NRS" ~ "NRS Deaths",
-      recid == "PIS" ~ "PIS"
+    smrtype <- dplyr::case_match(
+      recid,
+      "00B" ~ "Outpatient",
+      "04B" ~ "Psych-IP",
+      "AE2" ~ "A & E",
+      "CH" ~ "Care-Home",
+      "CMH" ~ "Comm-MH",
+      "DN" ~ "DN",
+      "NRS" ~ "NRS Deaths",
+      "PIS" ~ "PIS"
     )
   }
 

R/aggregate_by_chi_zihao.R → R/aggregate_by_chi.R

@@ -7,7 +7,7 @@
 #' @importFrom data.table .SD
 #'
 #' @inheritParams create_individual_file
-aggregate_by_chi_zihao <- function(episode_file) {
+aggregate_by_chi <- function(episode_file) {
   cli::cli_alert_info("Aggregate by CHI function started at {Sys.time()}")
 
   # Convert to data.table
@@ -191,12 +191,12 @@ vars_contain <- function(data, vars, ignore_case = FALSE) {
   )
 }
 
-#' Aggregate CIS episodes
+#' Aggregate Care Home episodes to ch_cis
 #'
 #' @description Aggregate CH variables by CHI and CIS.
 #'
 #' @inheritParams create_individual_file
-aggregate_ch_episodes_zihao <- function(episode_file) {
+aggregate_ch_episodes <- function(episode_file) {
   cli::cli_alert_info("Aggregate ch episodes function started at {Sys.time()}")
 
   # Convert to data.table

R/convert_ca_to_lca.R

@@ -14,39 +14,40 @@
 #' @family code functions
 #' @seealso convert_sending_location_to_lca
 convert_ca_to_lca <- function(ca_var) {
-  lca <- dplyr::case_when(
-    ca_var == "S12000033" | ca_var == "Aberdeen City" ~ "01",
-    ca_var == "S12000034" | ca_var == "Aberdeenshire" ~ "02",
-    ca_var == "S12000041" | ca_var == "Angus" ~ "03",
-    ca_var == "S12000035" | ca_var == "Argyll & Bute" ~ "04",
-    ca_var == "S12000026" | ca_var == "Scottish Borders" ~ "05",
-    ca_var == "S12000005" | ca_var == "Clackmannanshire" ~ "06",
-    ca_var == "S12000039" | ca_var == "West Dunbartonshire" ~ "07",
-    ca_var == "S12000006" | ca_var == "Dumfries and Galloway" ~ "08",
-    ca_var == "S12000042" | ca_var == "Dundee City" ~ "09",
-    ca_var == "S12000008" | ca_var == "East Ayrshire" ~ "10",
-    ca_var == "S12000045" | ca_var == "East Dunbartonshire" ~ "11",
-    ca_var == "S12000010" | ca_var == "East Lothian" ~ "12",
-    ca_var == "S12000011" | ca_var == "East Renfrewshire" ~ "13",
-    ca_var == "S12000036" | ca_var == "City of Edinburgh" ~ "14",
-    ca_var == "S12000014" | ca_var == "Falkirk" ~ "15",
-    ca_var %in% c("S12000015", "S12000047") | ca_var == "Fife" ~ "16",
-    ca_var %in% c("S12000046", "S12000049") | ca_var == "Glasgow City" ~ "17",
-    ca_var == "S12000017" | ca_var == "Highland" ~ "18",
-    ca_var == "S12000018" | ca_var == "Inverclyde" ~ "19",
-    ca_var == "S12000019" | ca_var == "Midlothian" ~ "20",
-    ca_var == "S12000020" | ca_var == "Moray" ~ "21",
-    ca_var == "S12000021" | ca_var == "North Ayrshire" ~ "22",
-    ca_var %in% c("S12000044", "S12000050") | ca_var == "North Lanarkshire" ~ "23",
-    ca_var == "S12000023" | ca_var == "Orkney" ~ "24",
-    ca_var %in% c("S12000024", "S12000048") | ca_var == "Perth and Kinross" ~ "25",
-    ca_var == "S12000038" | ca_var == "Renfrewshire" ~ "26",
-    ca_var == "S12000027" | ca_var == "Shetland Islands" ~ "27",
-    ca_var == "S12000028" | ca_var == "South Ayrshire" ~ "28",
-    ca_var == "S12000029" | ca_var == "South Lanarkshire" ~ "29",
-    ca_var == "S12000030" | ca_var == "Stirling" ~ "30",
-    ca_var == "S12000040" | ca_var == "West Lothian" ~ "31",
-    ca_var == "S12000013" | ca_var == "Na h-Eileanan Siar" | ca_var == "Comhairle nan Eilean Siar" ~ "32"
+  lca <- dplyr::case_match(
+    ca_var,
+    c("S12000033", "Aberdeen City") ~ "01",
+    c("S12000034", "Aberdeenshire") ~ "02",
+    c("S12000041", "Angus") ~ "03",
+    c("S12000035", "Argyll & Bute") ~ "04",
+    c("S12000026", "Scottish Borders") ~ "05",
+    c("S12000005", "Clackmannanshire") ~ "06",
+    c("S12000039", "West Dunbartonshire") ~ "07",
+    c("S12000006", "Dumfries and Galloway") ~ "08",
+    c("S12000042", "Dundee City") ~ "09",
+    c("S12000008", "East Ayrshire") ~ "10",
+    c("S12000045", "East Dunbartonshire") ~ "11",
+    c("S12000010", "East Lothian") ~ "12",
+    c("S12000011", "East Renfrewshire") ~ "13",
+    c("S12000036", "City of Edinburgh") ~ "14",
+    c("S12000014", "Falkirk") ~ "15",
+    c("S12000015", "S12000047", "Fife") ~ "16",
+    c("S12000046", "S12000049", "Glasgow City") ~ "17",
+    c("S12000017", "Highland") ~ "18",
+    c("S12000018", "Inverclyde") ~ "19",
+    c("S12000019", "Midlothian") ~ "20",
+    c("S12000020", "Moray") ~ "21",
+    c("S12000021", "North Ayrshire") ~ "22",
+    c("S12000044", "S12000050", "North Lanarkshire") ~ "23",
+    c("S12000023", "Orkney") ~ "24",
+    c("S12000024", "S12000048", "Perth and Kinross") ~ "25",
+    c("S12000038", "Renfrewshire") ~ "26",
+    c("S12000027", "Shetland Islands") ~ "27",
+    c("S12000028", "South Ayrshire") ~ "28",
+    c("S12000029", "South Lanarkshire") ~ "29",
+    c("S12000030", "Stirling") ~ "30",
+    c("S12000040", "West Lothian") ~ "31",
+    c("S12000013", "Na h-Eileanan Siar", "Comhairle nan Eilean Siar") ~ "32"
   )
   return(lca)
 }

R/convert_codes_to_name.R

@@ -14,38 +14,39 @@
 #'
 #' @family code functions
 convert_hscp_to_hscpnames <- function(hscp) {
-  hscpnames <- dplyr::case_when(
-    hscp == "S37000001" ~ "Aberdeen City",
-    hscp == "S37000002" ~ "Aberdeenshire",
-    hscp == "S37000003" ~ "Angus",
-    hscp == "S37000004" ~ "Argyll and Bute",
-    hscp == "S37000005" ~ "Clackmannanshire and Stirling",
-    hscp == "S37000006" ~ "Dumfries and Galloway",
-    hscp == "S37000007" ~ "Dundee City",
-    hscp == "S37000008" ~ "East Ayrshire",
-    hscp == "S37000009" ~ "East Dunbartonshire",
-    hscp == "S37000010" ~ "East Lothian",
-    hscp == "S37000011" ~ "East Renfrewshire",
-    hscp == "S37000012" ~ "Edinburgh",
-    hscp == "S37000013" ~ "Falkirk",
-    hscp == "S37000016" ~ "Highland",
-    hscp == "S37000017" ~ "Inverclyde",
-    hscp == "S37000018" ~ "Midlothian",
-    hscp == "S37000019" ~ "Moray",
-    hscp == "S37000020" ~ "North Ayrshire",
-    hscp == "S37000022" ~ "Orkney Islands",
-    hscp == "S37000024" ~ "Renfrewshire",
-    hscp == "S37000025" ~ "Scottish Borders",
-    hscp == "S37000026" ~ "Shetland Islands",
-    hscp == "S37000027" ~ "South Ayrshire",
-    hscp == "S37000028" ~ "South Lanarkshire",
-    hscp == "S37000029" ~ "West Dunbartonshire",
-    hscp == "S37000030" ~ "West Lothian",
-    hscp == "S37000031" ~ "Western Isles",
-    hscp == "S37000032" ~ "Fife",
-    hscp == "S37000033" ~ "Perth and Kinross",
-    hscp == "S37000034" ~ "Glasgow City",
-    hscp == "S37000035" ~ "North Lanarkshire"
+  hscpnames <- dplyr::case_match(
+    hscp,
+    "S37000001" ~ "Aberdeen City",
+    "S37000002" ~ "Aberdeenshire",
+    "S37000003" ~ "Angus",
+    "S37000004" ~ "Argyll and Bute",
+    "S37000005" ~ "Clackmannanshire and Stirling",
+    "S37000006" ~ "Dumfries and Galloway",
+    "S37000007" ~ "Dundee City",
+    "S37000008" ~ "East Ayrshire",
+    "S37000009" ~ "East Dunbartonshire",
+    "S37000010" ~ "East Lothian",
+    "S37000011" ~ "East Renfrewshire",
+    "S37000012" ~ "Edinburgh",
+    "S37000013" ~ "Falkirk",
+    "S37000016" ~ "Highland",
+    "S37000017" ~ "Inverclyde",
+    "S37000018" ~ "Midlothian",
+    "S37000019" ~ "Moray",
+    "S37000020" ~ "North Ayrshire",
+    "S37000022" ~ "Orkney Islands",
+    "S37000024" ~ "Renfrewshire",
+    "S37000025" ~ "Scottish Borders",
+    "S37000026" ~ "Shetland Islands",
+    "S37000027" ~ "South Ayrshire",
+    "S37000028" ~ "South Lanarkshire",
+    "S37000029" ~ "West Dunbartonshire",
+    "S37000030" ~ "West Lothian",
+    "S37000031" ~ "Western Isles",
+    "S37000032" ~ "Fife",
+    "S37000033" ~ "Perth and Kinross",
+    "S37000034" ~ "Glasgow City",
+    "S37000035" ~ "North Lanarkshire"
   )
   return(hscpnames)
 }
@@ -66,22 +67,22 @@ convert_hscp_to_hscpnames <- function(hscp) {
 #'
 #' @family code functions
 convert_hb_to_hbnames <- function(hb) {
-  hbnames <- dplyr::case_when(
-    hb == "S08000015" ~ "Ayrshire and Arran",
-    hb == "S08000016" ~ "Borders",
-    hb == "S08000017" ~ "Dumfries and Galloway",
-    hb == "S08000019" ~ "Forth Valley",
-    hb == "S08000020" ~ "Grampian",
-    hb == "S08000022" ~ "Highland",
-    hb == "S08000024" ~ "Lothian",
-    hb == "S08000025" ~ "Orkney",
-    hb == "S08000026" ~ "Shetland",
-    hb == "S08000028" ~ "Western Isles",
-    hb == "S08000029" ~ "Fife",
-    hb == "S08000030" ~ "Tayside",
-    hb == "S08000031" ~ "Greater Glasgow and Clyde",
-    hb == "S08000032" ~ "Lanarkshire"
+  hbnames <- dplyr::case_match(
+    hb,
+    "S08000015" ~ "Ayrshire and Arran",
+    "S08000016" ~ "Borders",
+    "S08000017" ~ "Dumfries and Galloway",
+    "S08000019" ~ "Forth Valley",
+    "S08000020" ~ "Grampian",
+    "S08000022" ~ "Highland",
+    "S08000024" ~ "Lothian",
+    "S08000025" ~ "Orkney",
+    "S08000026" ~ "Shetland",
+    "S08000028" ~ "Western Isles",
+    "S08000029" ~ "Fife",
+    "S08000030" ~ "Tayside",
+    "S08000031" ~ "Greater Glasgow and Clyde",
+    "S08000032" ~ "Lanarkshire"
   )
-
   return(hbnames)
 }

R/convert_sending_location_to_lca.R

@@ -16,39 +16,40 @@
 #'
 #' @seealso convert_ca_to_lca
 convert_sending_location_to_lca <- function(sending_location) {
-  lca <- dplyr::case_when(
-    sending_location == "100" ~ "01", # Aberdeen City
-    sending_location == "110" ~ "02", # Aberdeenshire
-    sending_location == "120" ~ "03", # Angus
-    sending_location == "130" ~ "04", # Argyll and Bute
-    sending_location == "355" ~ "05", # Scottish Borders
-    sending_location == "150" ~ "06", # Clackmannanshire
-    sending_location == "395" ~ "07", # West Dumbartonshire
-    sending_location == "170" ~ "08", # Dumfries and Galloway
-    sending_location == "180" ~ "09", # Dundee City
-    sending_location == "190" ~ "10", # East Ayrshire
-    sending_location == "200" ~ "11", # East Dunbartonshire
-    sending_location == "210" ~ "12", # East Lothian
-    sending_location == "220" ~ "13", # East Renfrewshire
-    sending_location == "230" ~ "14", # City of Edinburgh
-    sending_location == "240" ~ "15", # Falkirk
-    sending_location == "250" ~ "16", # Fife
-    sending_location == "260" ~ "17", # Glasgow City
-    sending_location == "270" ~ "18", # Highland
-    sending_location == "280" ~ "19", # Inverclyde
-    sending_location == "290" ~ "20", # Midlothian
-    sending_location == "300" ~ "21", # Moray
-    sending_location == "310" ~ "22", # North Ayrshire
-    sending_location == "320" ~ "23", # North Lanarkshire
-    sending_location == "330" ~ "24", # Orkney Islands
-    sending_location == "340" ~ "25", # Perth and Kinross
-    sending_location == "350" ~ "26", # Renfrewshire
-    sending_location == "360" ~ "27", # Shetland Islands
-    sending_location == "370" ~ "28", # South Ayrshire
-    sending_location == "380" ~ "29", # South Lanarkshire
-    sending_location == "390" ~ "30", # Stirling
-    sending_location == "400" ~ "31", # West Lothian
-    sending_location == "235" ~ "32" # Na_h_Eileanan_Siar
+  lca <- dplyr::case_match(
+    sending_location,
+    "100" ~ "01", # Aberdeen City
+    "110" ~ "02", # Aberdeenshire
+    "120" ~ "03", # Angus
+    "130" ~ "04", # Argyll and Bute
+    "355" ~ "05", # Scottish Borders
+    "150" ~ "06", # Clackmannanshire
+    "395" ~ "07", # West Dumbartonshire
+    "170" ~ "08", # Dumfries and Galloway
+    "180" ~ "09", # Dundee City
+    "190" ~ "10", # East Ayrshire
+    "200" ~ "11", # East Dunbartonshire
+    "210" ~ "12", # East Lothian
+    "220" ~ "13", # East Renfrewshire
+    "230" ~ "14", # City of Edinburgh
+    "240" ~ "15", # Falkirk
+    "250" ~ "16", # Fife
+    "260" ~ "17", # Glasgow City
+    "270" ~ "18", # Highland
+    "280" ~ "19", # Inverclyde
+    "290" ~ "20", # Midlothian
+    "300" ~ "21", # Moray
+    "310" ~ "22", # North Ayrshire
+    "320" ~ "23", # North Lanarkshire
+    "330" ~ "24", # Orkney Islands
+    "340" ~ "25", # Perth and Kinross
+    "350" ~ "26", # Renfrewshire
+    "360" ~ "27", # Shetland Islands
+    "370" ~ "28", # South Ayrshire
+    "380" ~ "29", # South Lanarkshire
+    "390" ~ "30", # Stirling
+    "400" ~ "31", # West Lothian
+    "235" ~ "32" # Na_h_Eileanan_Siar
   )
   return(lca)
 }