Merge branch 'mar-23-update' into check_snake_case

R/create_demog_test_flags.R

@@ -3,19 +3,19 @@
 #' @description Create the demographic flags for testing
 #'
 #' @param data a dataframe containing demographic variables e.g. chi
+#' @param chi Specify chi or anon_chi.
 #'
 #' @return a dataframe with flag (1 or 0) for each demographic variable.
 #' Missing value flag from [is_missing()]
 #'
 #' @family flag functions
-create_demog_test_flags <- function(data) {
+create_demog_test_flags <- function(data, chi = c(chi, anon_chi)) {
   data %>%
-    dplyr::arrange(.data$chi) %>%
+    dplyr::arrange({{ chi }}) %>%
     # create test flags
     dplyr::mutate(
-      valid_chi = phsmethods::chi_check(.data$chi) == "Valid CHI",
-      unique_chi = dplyr::lag(.data$chi) != .data$chi,
-      n_missing_chi = is_missing(.data$chi),
+      unique_chi = dplyr::lag({{ chi }}) != {{ chi }},
+      n_missing_chi = is_missing({{ chi }}),
       n_males = .data$gender == 1L,
       n_females = .data$gender == 2L,
       n_postcode = !is.na(.data$postcode) | !.data$postcode == "",

R/process_tests_alarms_telecare.R

@@ -37,14 +37,14 @@ produce_source_at_tests <- function(data,
                                     max_min_vars = c("record_keydate1", "record_keydate2")) {
   test_flags <- data %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(
       n_at_alarms = .data$smrtype == "AT-Alarm",
       n_at_telecare = .data$smrtype == "AT-Tele"
     ) %>%
     create_lca_test_flags(.data$sc_send_lca) %>%
     # remove variables that won't be summed
-    dplyr::select(.data$valid_chi:.data$West_Lothian) %>%
+    dplyr::select(.data$unique_chi:.data$West_Lothian) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_care_home.R

@@ -47,7 +47,7 @@ produce_source_ch_tests <- function(data,
                                     )) {
   test_flags <- data %>%
     # use functions to create HB and partnership flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(
       n_episodes = 1L,
       ch_name_missing = is.na(.data$ch_name),
@@ -60,7 +60,7 @@ produce_source_ch_tests <- function(data,
     ) %>%
     create_lca_test_flags(.data$sc_send_lca) %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_cmh.R

@@ -43,11 +43,11 @@ process_tests_cmh <- function(data, year) {
 produce_source_cmh_tests <- function(data) {
   test_flags <- data %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     create_hb_test_flags(hb_var = .data$hbrescode) %>%
     dplyr::mutate(n_episodes = 1L) %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_district_nursing.R

@@ -65,11 +65,11 @@ produce_source_dn_tests <- function(data,
                                     )) {
   test_flags <- data %>%
     # use functions to create HB and partnership flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     create_hb_test_flags(.data$hbtreatcode) %>%
     create_hb_cost_test_flags(.data$hbtreatcode, .data$cost_total_net) %>%
     # keep variables for comparison
-    dplyr::select(.data$valid_chi:.data$NHS_Lanarkshire_cost) %>%
+    dplyr::select(.data$unique_chi:.data$NHS_Lanarkshire_cost) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_episode_file.R

@@ -73,15 +73,7 @@ produce_episode_file_tests <- function(
   test_flags <- data %>%
     dplyr::group_by(.data$recid) %>%
     # use functions to create HB and partnership flags
-    dplyr::mutate(
-      unique_anon_chi = dplyr::lag(.data$anon_chi) != .data$anon_chi,
-      n_missing_anon_chi = is_missing(.data$anon_chi),
-      n_males = .data$gender == 1L,
-      n_females = .data$gender == 2L,
-      n_postcode = !is.na(.data$postcode) | !.data$postcode == "",
-      n_missing_postcode = is_missing(.data$postcode),
-      missing_dob = is.na(.data$dob)
-    ) %>%
+    create_demog_test_flags(chi = anon_chi) %>%
     create_hb_test_flags(.data$hbtreatcode) %>%
     create_hb_cost_test_flags(.data$hbtreatcode, .data$cost_total_net) %>%
     create_hscp_test_flags(.data$hscp2018) %>%
@@ -111,7 +103,7 @@ produce_episode_file_tests <- function(
 
   test_flags <- test_flags %>%
     # keep variables for comparison
-    dplyr::select("unique_anon_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum", group_by = "recid")
 

R/process_tests_home_care.R

@@ -49,7 +49,7 @@ produce_source_hc_tests <- function(data,
                                     )) {
   test_flags <- data %>%
     # use functions to create HB and partnership flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(
       n_episodes = 1L,
       hc_per = dplyr::if_else(.data$smrtype == "HC-Per", 1L, 0L),
@@ -61,7 +61,7 @@ produce_source_hc_tests <- function(data,
     ) %>%
     create_lca_test_flags(.data$sc_send_lca) %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_homelessness.R

@@ -38,10 +38,10 @@ produce_slf_homelessness_tests <- function(data,
   test_flags <- data %>%
     dplyr::arrange(.data$chi) %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     create_lca_test_flags(.data$hl1_sending_lca) %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_individual_file.R

@@ -60,19 +60,11 @@ produce_individual_file_tests <- function(data) {
 
   test_flags <- data %>%
     # use functions to create HB and partnership flags
-    dplyr::mutate(
-      unique_anon_chi = dplyr::lag(.data$anon_chi) != .data$anon_chi,
-      n_missing_anon_chi = is_missing(.data$anon_chi),
-      n_males = .data$gender == 1L,
-      n_females = .data$gender == 2L,
-      n_postcode = !is.na(.data$postcode) | !.data$postcode == "",
-      n_missing_postcode = is_missing(.data$postcode),
-      missing_dob = is.na(.data$dob)
-    ) %>%
+    create_demog_test_flags(chi = anon_chi) %>%
     create_hb_test_flags(.data$hbrescode) %>%
     create_hb_cost_test_flags(.data$hbrescode, .data$health_net_cost) %>%
     # keep variables for comparison
-    dplyr::select(c("unique_anon_chi":dplyr::last_col())) %>%
+    dplyr::select(c("unique_chi":dplyr::last_col())) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_nrs_deaths.R

@@ -38,10 +38,10 @@ process_tests_nrs_deaths <- function(data, year) {
 produce_source_nrs_tests <- function(data) {
   test_flags <- data %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(n_deaths = 1L) %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_prescribing.R

@@ -41,10 +41,10 @@ process_tests_prescribing <- function(data, year) {
 produce_source_pis_tests <- function(data) {
   test_flags <- data %>%
     # use functions to create HB and partnership flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(n_episodes = 1L) %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/process_tests_sc_demographics.R

@@ -36,7 +36,7 @@ process_tests_sc_demographics <- function(data) {
 produce_sc_demog_lookup_tests <- function(data) {
   data %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(
       n_missing_sending_loc = is.na(.data$sending_location),
       n_missing_sc_id = is.na(.data$social_care_id)

R/process_tests_sds.R

@@ -35,10 +35,10 @@ produce_source_sds_tests <- function(data,
                                      max_min_vars = c("record_keydate1", "record_keydate2")) {
   test_flags <- data %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     create_lca_test_flags(.data$sc_send_lca) %>%
     # remove variables that won't be summed
-    dplyr::select("valid_chi":"West_Lothian") %>%
+    dplyr::select("unique_chi":"West_Lothian") %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 

R/produce_sc_all_episodes_tests.R

@@ -10,7 +10,7 @@
 produce_sc_all_episodes_tests <- function(data) {
   data %>%
     # create test flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     dplyr::mutate(
       n_missing_sending_loc = dplyr::if_else(
         is.na(.data$sending_location),
@@ -24,7 +24,7 @@ produce_sc_all_episodes_tests <- function(data) {
       )
     ) %>%
     # keep variables for comparison
-    dplyr::select(c("valid_chi":dplyr::last_col())) %>%
+    dplyr::select(c("unique_chi":dplyr::last_col())) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")
 }

R/produce_source_extract_tests.R

@@ -33,7 +33,7 @@ produce_source_extract_tests <- function(data,
                                          add_hscp_count = TRUE) {
   test_flags <- data %>%
     # use functions to create HB and partnership flags
-    create_demog_test_flags() %>%
+    create_demog_test_flags(chi = chi) %>%
     create_hb_test_flags(.data$hbtreatcode) %>%
     create_hb_cost_test_flags(.data$hbtreatcode, .data$cost_total_net)
 
@@ -43,7 +43,7 @@ produce_source_extract_tests <- function(data,
 
   test_flags <- test_flags %>%
     # keep variables for comparison
-    dplyr::select("valid_chi":dplyr::last_col()) %>%
+    dplyr::select("unique_chi":dplyr::last_col()) %>%
     # use function to sum new test flags
     calculate_measures(measure = "sum")