Merge branch 'development' into fix_pkgdown

.github/actions/spelling/expect.txt

@@ -168,6 +168,7 @@ readxl
 reasonwait
 recid
 refsource
+renviron
 rlang
 rmarkdown
 roxygen

.github/workflows/lint-changed-files.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   pull_request:
-    branches: [main-R, master, main]
+    branches: [master, main, development]
 
 name: lint-changed-files
 

.github/workflows/test-coverage.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: test-coverage
 

DESCRIPTION

@@ -53,6 +53,8 @@ Imports:
     slfhelper (>= 0.10.0),
     stringdist (>= 0.9.10),
     stringr (>= 1.5.0),
+    tarchetypes (>= 0.7.6),
+    targets (>= 1.2.0),
     tibble (>= 3.2.1),
     tidyr (>= 1.3.0),
     tidyselect (>= 1.2.0),
@@ -61,8 +63,6 @@ Suggests:
     covr (>= 3.6.1),
     roxygen2 (>= 7.2.3),
     spelling (>= 2.2),
-    tarchetypes (>= 0.7.5),
-    targets (>= 0.14.3),
     testthat (>= 3.1.7)
 Remotes: 
     Public-Health-Scotland/phsmethods,

NAMESPACE

@@ -13,6 +13,7 @@ export(convert_hscp_to_hscpnames)
 export(convert_numeric_to_date)
 export(convert_sending_location_to_lca)
 export(convert_year_to_fyyear)
+export(create_episode_file)
 export(create_individual_file)
 export(create_service_use_cohorts)
 export(end_fy)
@@ -41,6 +42,7 @@ export(get_homelessness_completeness_path)
 export(get_it_deaths_path)
 export(get_it_ltc_path)
 export(get_it_prescribing_path)
+export(get_la_code_opendata_lookup)
 export(get_locality_path)
 export(get_lookups_dir)
 export(get_ltcs_path)
@@ -68,7 +70,6 @@ export(get_year_dir)
 export(gzip_files)
 export(is_date_in_fyyear)
 export(is_missing)
-export(la_code_lookup)
 export(last_date_month)
 export(latest_cost_year)
 export(latest_update)
@@ -155,25 +156,14 @@ export(read_sc_all_alarms_telecare)
 export(read_sc_all_care_home)
 export(read_sc_all_home_care)
 export(read_sc_all_sds)
-export(run_episode_file)
+export(setup_keyring)
 export(start_fy)
 export(start_fy_quarter)
 export(start_next_fy_quarter)
 export(write_file)
 importFrom(data.table,.N)
 importFrom(data.table,.SD)
 importFrom(magrittr,"%>%")
-importFrom(readr,col_character)
-importFrom(readr,col_date)
-importFrom(readr,col_datetime)
-importFrom(readr,col_double)
-importFrom(readr,col_factor)
-importFrom(readr,col_integer)
-importFrom(readr,col_logical)
-importFrom(readr,col_number)
-importFrom(readr,col_time)
-importFrom(readr,cols)
-importFrom(readr,cols_only)
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(tibble,tibble)

R/add_nsu_cohort.R

@@ -2,13 +2,17 @@
 #'
 #' @param data The input data frame
 #' @param year The year being processed
+#' @param nsu_cohort The NSU data for the year
 #'
 #' @return A data frame containing the Non-Service Users as additional rows
 #' @export
 #'
 #' @family episode_file
 #' @seealso [get_nsu_path()]
-add_nsu_cohort <- function(data, year) {
+add_nsu_cohort <- function(
+    data,
+    year,
+    nsu_cohort = read_file(get_nsu_path(year))) {
   year_param <- year
 
   if (!check_year_valid(year, "NSU")) {
@@ -29,9 +33,9 @@ add_nsu_cohort <- function(data, year) {
     )
   )
 
-  matched <- dplyr::full_join(data,
-    # NSU cohort file
-    read_file(get_nsu_path(year)) %>%
+  matched <- dplyr::full_join(
+    data,
+    nsu_cohort %>%
       dplyr::mutate(
         dob = as.Date(.data[["dob"]]),
         gpprac = convert_eng_gpprac_to_dummy(.data[["gpprac"]])
@@ -110,7 +114,6 @@ add_nsu_cohort <- function(data, year) {
         .data[["chi"]]
       )
     ) %>%
-    # Remove the additional columns
     dplyr::select(-dplyr::contains("_nsu"), -"has_chi")
 
   return(return_df)

R/compute_mid_year_age.R

@@ -20,7 +20,7 @@
 compute_mid_year_age <- function(fyyear, dob) {
   age_intervals <- lubridate::interval(
     start = dob,
-    end = as.Date(midpoint_fy(fyyear))
+    end = midpoint_fy(fyyear)
   )
 
   ages <- lubridate::as.period(age_intervals)$year