Merge pull request #48 from Public-Health-Scotland/dec24-mi-release

Dec24 mi release

code/00_setup-environment.R

@@ -26,8 +26,8 @@
 test_output <- TRUE
 
 # UPDATE - Last day in reporting period (ddmmyyyy)
-end_date <- lubridate::dmy(30062024)
-previous_end_date <- lubridate::dmy(31032024)
+end_date <- lubridate::dmy(30092024)
+previous_end_date <- lubridate::dmy(30062024)
 
 # UPDATE - Most recent Date of publication (ddmmyyyy)
 # Need this for set up of some folder structure
@@ -79,8 +79,7 @@ cl_out <- case_when(
 ### 3 - SIMD Lookup ----
 
 simd <- function(){
-  read_rds(glue("{cl_out}/lookups/Unicode/",
-                "Deprivation/postcode_2024_1_simd2020v2.rds")) %>%
+  simd <- read_rds(get_simd_path()) %>% 
     clean_names() %>%
     select(pc7, simd = simd2020v2_sc_quintile) %>%
     mutate(
@@ -90,6 +89,8 @@ simd <- function(){
         TRUE ~ as.character(simd)
       )
     )
+
+  return(simd)
 }
 
 

code/01_data-preparation.R

@@ -69,7 +69,7 @@ pds <-
   )
 
 
-### 4 - Save out error summary
+### 4 - Save out error summary ----
 
 err <- pds %>%
   mutate(health_board = if_else(is.na(health_board),
@@ -182,7 +182,7 @@ dupes <-
   write_file(path = get_mi_data_path("dupe_data", ext = "csv", test_output = test_output))
 0 # this zero stops script from running IF write_file is overwriting an existing file, re-run the section without this line and enter 1 in the console, when prompted, to overwrite file.
 
-### 7 - Remove duplicate records ---
+### 7 - Remove duplicate records ----
 pds %<>%
 
   filter(dupe_keep == 1) %>%
@@ -195,7 +195,7 @@ pds %<>%
   select(-contains("dupe"))
 
 
-### 8 - Save data ---
+### 8 - Save data ----
 
 pds %>% 
 write_file(path = get_mi_data_path("clean_data", ext = "rds", test_output = test_output))

code/04_ldp_tests.R

@@ -22,13 +22,14 @@ source(here::here("functions", "produce_tests.R"))
 # Read latest data---
 latest_data <- read_rds(get_mi_data_path(type = "final_data", 
                                          "rds", 
-                                         test_output = FALSE)) %>% 
+                                         test_output = test_output)) %>% 
               # Remove codes from board and IJB
               clean_geog_codes()
 
 # read previous years data---
 previous_data <- read_rds(get_mi_data_path(type = "final_data", 
                                            "rds", 
+                                           test_output = FALSE,
                                            previous_data = TRUE)) %>% 
               # Remove codes from board and IJB
               clean_geog_codes()

management-report/markdown/management-report.Rmd

@@ -61,8 +61,6 @@ This report has been produced by Public Health Scotland (PHS) and contains analy
 
 <span style="color:red"> **The information contained in this report is for management information only and should not be distributed widely.** </span>
 
-**Please note that both the Dementia Post Diagnostic Support service provision and data submission to PHS have been affected by the COVID-19 pandemic.**
-
 These reports reflect the [Dementia PDS dataset](https://publichealthscotland.scot/media/20921/2023-12-14-dementia-pds-definitions-and-recording-guidance-v14.pdf) effective 01 April 2019 and contain data for individuals diagnosed with dementia between **`r format(dmy(01042016), "%d %B %Y")`** and **`r format(end_date, "%d %B %Y")`** who were referred for post diagnostic support.
 
 Data are submitted to PHS by health boards on a quarterly basis. Each health board provides updated information for all individuals referred for post diagnostic support with a diagnosis date from `r format(start_date, "%d %B %Y")` onwards. Therefore, data for diagnoses from this date onwards are refreshed in each management report and are based on the most recently submitted data. 
@@ -103,6 +101,8 @@ Row
 
 *Please note the following:*
 
+**Please note that both the Dementia Post Diagnostic Support service provision and data submission to PHS were affected by the COVID-19 pandemic.**
+
 **NHS Orkney** – NHS Orkney had no referrals in *2022/23* (*Q3* and *Q4*) and *2023/24* (*Q1* and *Q2*) as they were unable to access a consultant psychiatrist.
 
 **NHS Shetland** - NHS Shetland did not have a PDS worker in post from *2022/23 Q1* through *2023/24 Q3*. As a result not all people referred to PDS could be allocated or contacted by a PDS worker within 12 months of diagnosis, hence they have been recorded as not having met the standard. A PDS worker was assigned in *2023/24 Q4* and the PDS service in Shetland has resumed.

management-report/markdown/subpage-hb.Rmd

@@ -29,6 +29,13 @@ qt_text <-
     }
   }
 
+# text to state impact of Covid 19
+covid_text <-
+  case_when(
+    str_sub(sel_fy, 1, 4) == "2020" ~
+    "**Please note that both the Dementia Post Diagnostic Support service provision and data submission to PHS have been affected by the COVID-19 pandemic.**",
+    TRUE ~ ""
+  )
 
 # Text to explain incomplete years / referrals still ongoing
 latest_final_year <- dmy(paste0("0104",substr(finalised_years[length(finalised_years)],1,4)))
@@ -209,7 +216,7 @@ Row
 
 ### **Note**
 
-**Please note that both the Dementia Post Diagnostic Support service provision and data submission to PHS have been affected by the COVID-19 pandemic.**
+`r covid_text`
 
 `r completeness_text`
 

management-report/markdown/subpage-scotland.Rmd

@@ -29,6 +29,14 @@ qt_text <-
     }
   }
 
+# text to state impact of Covid 19
+covid_text <-
+  case_when(
+    str_sub(sel_fy, 1, 4) == "2020" ~
+    "**Please note that both the Dementia Post Diagnostic Support service provision and data submission to PHS have been affected by the COVID-19 pandemic.**",
+    TRUE ~ ""
+    )
+
 # Text to explain incomplete years / referrals still ongoing
 latest_final_year <- dmy(paste0("0104",substr(finalised_years[length(finalised_years)],1,4)))
 
@@ -205,7 +213,7 @@ Row
 
 ### **Note**
 
-**Please note that both the Dementia Post Diagnostic Support service provision and data submission to PHS have been affected by the COVID-19 pandemic.**
+`r covid_text`
 
 `r completeness_text`