Merge Sept update 23 into master

.Rbuildignore

@@ -22,3 +22,4 @@
 ^_targets\.R$
 ^_targets\.yaml$
 ^_SPSS_archived$
+^run_targets_

.github/actions/spelling/expect.txt

@@ -29,6 +29,7 @@ Classificat
 cls
 cmh
 CNWs
+Comhairle
 codecov
 commhosp
 congen
@@ -97,6 +98,7 @@ hjust
 hms
 homecare
 homev
+hscdiip
 hscp
 hscpnames
 htmlwidgets
@@ -115,13 +117,15 @@ keyring
 keytime
 keytimex
 kis
+lazydt
 lgl
 lintr
 los
 ltc
 ltcs
 lubridate
 magrittr
+Matern
 markdownguide
 Mcbride
 mcmahon
@@ -148,6 +152,7 @@ outfile
 pandoc
 patflow
 pattype
+PCEC
 phs
 phsmethods
 phsopendata
@@ -177,6 +182,7 @@ reasonwait
 recid
 reflectoring
 refsource
+renviron
 rlang
 rmarkdown
 roxygen
@@ -215,6 +221,7 @@ 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
 

.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

@@ -50,9 +50,11 @@ Imports:
     rmarkdown (>= 2.17),
     rstudioapi (>= 0.14),
     scales (>= 1.2.0),
-    slfhelper (>= 0.9.0),
+    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

@@ -1,6 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(add_homelessness_date_flags)
+export(add_homelessness_flag)
+export(add_hri_variables)
 export(add_nsu_cohort)
 export(check_year_format)
 export(clean_up_free_text)
@@ -13,6 +16,8 @@
 export(convert_numeric_to_date)
 export(convert_sending_location_to_lca)
 export(convert_year_to_fyyear)
+export(create_episode_file)
+export(create_homelessness_lookup)
 export(create_individual_file)
 export(create_service_use_cohorts)
 export(end_fy)
@@ -29,6 +34,7 @@
 export(get_dev_dir)
 export(get_dn_costs_path)
 export(get_dn_raw_costs_path)
+export(get_existing_data_for_tests)
 export(get_file_path)
 export(get_gp_ooh_costs_path)
 export(get_gp_ooh_raw_costs_path)
@@ -49,6 +55,7 @@
 export(get_readcode_lookup_path)
 export(get_sc_at_episodes_path)
 export(get_sc_ch_episodes_path)
+export(get_sc_client_lookup_path)
 export(get_sc_demog_lookup_path)
 export(get_sc_hc_episodes_path)
 export(get_sc_sds_episodes_path)
@@ -59,9 +66,7 @@
 export(get_slf_chi_deaths_path)
 export(get_slf_deaths_lookup_path)
 export(get_slf_dir)
-export(get_slf_ep_temp_path)
 export(get_slf_gpprac_path)
-export(get_slf_indiv_temp_path)
 export(get_slf_postcode_path)
 export(get_source_extract_path)
 export(get_sparra_path)
@@ -132,8 +137,10 @@
 export(process_tests_outpatients)
 export(process_tests_prescribing)
 export(process_tests_sc_ch_episodes)
+export(process_tests_sc_client_lookup)
 export(process_tests_sc_demographics)
 export(process_tests_sds)
+export(produce_episode_file_tests)
 export(produce_source_extract_tests)
 export(produce_test_comparison)
 export(read_extract_acute)
@@ -157,7 +164,7 @@
 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)

NEWS.md

@@ -1,6 +1,50 @@
-# March 2023 Update - Unreleased
+# September 2023 Update - Unreleased
+* Update of 2017/18 onwards to include bug fixes within the files. 
+* New 2023/24 files.
+  *No social care data available for new 2023/24 file.
+* New NSU cohort for 2022/23 file.
+* SPD and SIMD updated.
+* Re addition of:
+  * HRIs in individual file.
+  * Homelessness Flags.
+* Bug fixes: 
+  * Blank `datazone` in A&E. This has been fixed and was due to PC8 postcode format matching onto SLF pc lookup. 
+  * Large increase in preventable beddays. This was caused due to an SPSS vs R logic difference. Uses SPSS logic which 
+    brings the difference down to `3.3%`. 
+  * Issue with `locality` which showed `locality` in each row instead of its true `locality`. This has now been fixed. 
+  * Duplicated CHI in the individual file. The issue was identified when trying to include HRIs. This has now been corrected. 
+* Internal changes to SLF development: 
+  * `DN` and `CMH` data are now archived in an HSCDIIP folder as the BOXI datamart is now closed down for these. Function `get_boxi_extract_path` has been updated to reflect this. 
+  * Tests updated to include `HSCP`count. 
+  * Tests created for `Delayed Discharges` extract and `Social care Client lookup`.
 
 
+# June 2023 Update - Released 24-Jul-2023
+* 2011/12 -> 2013/14 – These files have not been altered, other than to make them available in a new file type (parquet).
+* 2017/18 – These files have been recreated using our new R pipeline, but the data has not changed. We did this so that we would have a good comparator file.
+* 2018/19 -> 2022/23 – These files have been recreated using the R pipeline and are also using updated data (as in a ‘normal’ update).
+* Files changed into parquet format. 
+* SLFhelper updated. 
+* Removal of `keydate1_dateformat` and `keydate2_dateformat`.
+* `dd_responsible_lca` – This variable now uses CA2019 codes instead of the 2-digit ‘old’ LCA code.
+* Preventable beddays - not able to calculate these correctly. * Death fixes not included.
+* Variables not ordered in R like they used to be in SPSS.
+* End of HHG.
+* New variable `ch_postcode`.
+* rename of variables `cost_total_net_incdnas`, `ooh_outcome.1`, `ooh_outcome.2`, `ooh_outcome.3`, `ooh_outcome.4`, `totalnodncontacts`. 
+* HRI's not included. 
+* Homelessness flags not included. 
+* Keep_population flag not included. 
+
+
+# March 2023 Update - Released 10-Mar-2023
+* 2021/22 episode and individual files refreshed with updated activity.
+* 2022/23 file updated and contains data up to the end of Q3. 
+* Social care data is available for 2022/23. 
+* Typo in the variable name `ooh_covid_assessment`
+* Next update in May as a test run in R but won't be released. 
+* Next release in June. 
+
 # December 2022 Update - Released 07-Dec-2022
 * Now using the 2022v2 Scottish Postcode Directory.
 * Now using the 2020 Urban Rural classifications (instead of the older 2016 ones), this means variables such as `URx_2016` will now be called `URx_2020`.

R/00-update_refs.R

@@ -7,7 +7,7 @@
 #'
 #' @family initialisation
 latest_update <- function() {
-  "Jun_2023"
+  "Sep_2023"
 }
 
 #' Previous update
@@ -34,11 +34,11 @@
 
   latest_update_date <- lubridate::my(latest_update())
 
   previous_update_year <- lubridate::year(
     latest_update_date - lubridate::period(months_ago, "months")
   )
 
   previous_update_month <- lubridate::month(
     latest_update_date - lubridate::period(months_ago, "months"),
     label = TRUE,
     abbr = TRUE
@@ -61,7 +61,7 @@
 #'
 #' @family initialisation
 get_dd_period <- function() {
-  "Jul16_Mar23"
+  "Jul16_Jun23"
 }
 
 #' The latest financial year for Cost uplift setting
@@ -74,5 +74,5 @@
 #'
 #' @family initialisation
 latest_cost_year <- function() {
-  "2223"
+  "2324"
 }