fix minor conflict

Merge branch 'main' into bex # Conflicts: # 01_control/control_mmi.R
Public-Health-Scotland · Sep 26, 2024 · b4dba3d · b4dba3d
2 parents 4555ea1 + d42cbd4
commit b4dba3d
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Showing 4 changed files with 51 additions and 6 deletions.
diff --git a/01_control/control_mmi.R b/01_control/control_mmi.R
@@ -22,25 +22,34 @@ source("./07_publication/script/chapters/3_set_constants.R")
 
 # Step 3 - Analyse Data ---------------------------------------------------
 
+summarise_referrals()
+summarise_non_acceptance()
+
 summarise_appointments_att() # key output "/appointments_att/apps_att_mth_hb.parquet"
 summarise_patients_seen() # key outputs "/patients_seen/pat_seen_unadj_wait_grp_mth.parquet' and "/patients_seen/pat_seen_adj_wait_grp_mth.parquet'
 
 summarise_open_cases()
-summarise_referrals()
-summarise_non_acceptance()
 
 # Step 4 - Excel summaries ------------------------------------------------# being used?
 
+compile_referrals_summary()
+compile_non_acceptance_summary()
+compile_appointments_summary()
+
 compile_pat_seen_adj_summary()
 compile_pat_seen_unadj_summary()
 compile_appointments_summary()
 
 compile_open_cases_summary()
-compile_referrals_summary()
-compile_non_acceptance_summary()
 
 # Step 5 - Create plots ---------------------------------------------------
 #
 #create_plots_patients_seen("PT")
 #create_plots_patients_seen("CAMHS")
 
+
+# Step 6 - Create MMI excel doc -------------------------------------------
+
+
+
+
diff --git a/01_control/control_pre_shorewise.R b/01_control/control_pre_shorewise.R
@@ -81,7 +81,14 @@ df_captnd_checked <- rbind.fill(
   df_checked_dis) |> 
   save_captnd_checked()
 
-
+rm(df_checked_demo,
+   df_checked_ref,
+   df_checked_apps,
+   df_checked_unav,
+   df_checked_diag,
+   df_checked_dis, 
+   df_captnd_checked, 
+   df)
 
 # 4 - Create DQ heatmap reports -------------------------------------------
 

diff --git a/10_pre_shorewise_scripts/dq_reporting/arrange_dq_df.R b/10_pre_shorewise_scripts/dq_reporting/arrange_dq_df.R
@@ -10,7 +10,7 @@
 arrange_dq_df <- function(df){
 
   level_order_hb2 <- setdiff(level_order_hb, "NHS Scotland")
-  level_order_hb2 <- c("NHS Scotland", test)
+  level_order_hb2 <- c("NHS Scotland", level_order_hb2)
 
   df_arranged <- df |>  
     mutate(hb_name = factor(hb_name, levels = level_order_hb2),

diff --git a/10_pre_shorewise_scripts/dq_reporting/update_dq_values.R b/10_pre_shorewise_scripts/dq_reporting/update_dq_values.R
@@ -94,6 +94,35 @@ update_dq_values <- function(wb){
             startCol = 2, startRow = 2, #headerStyle = style_text,
             colNames = FALSE, withFilter = FALSE,  keepNA = TRUE, na.string = "-")
 
+  # trend - alternative table with tic marks
+  df_trend2 <- read_parquet(paste0(pre_shorewise_output_dir, "/02_data_quality/captnd_dq_clean_all.parquet")) |> 
+    mutate(header_date_month =  format(as.Date(header_date_month), "%b %Y"),
+           value = str_to_title(value),
+           value = factor(value, levels = c("Known", "Missing", "Invalid", "Not Known"))) |> 
+    arrange(header_date_month, dataset_type, hb_name, variable, value) |> 
+    select(Month = header_date_month, 
+           Dataset = dataset_type, 
+           `Health Board` = hb_name, 
+           Variable = variable,
+           `Submission Status` = submission_status, 
+           PMS = pms,
+           `DQ Assessment` = value,
+           -count, -total, Proportion = proportion) |> 
+    pivot_wider(names_from = Month, values_from = Proportion)
+
+  export(df_trend2, 
+         file = paste0(pre_shorewise_output_dir, "/02_data_quality/captnd_dq_trend_summary"),
+         format = "xlsx")
+
+  # deleteData(wb, sheet = "Trend Summary", cols = 2:14, rows = 2:19681, gridExpand = TRUE)
+
+  # writeData(wb, sheet = "Trend Summary",
+  #           x = df_trend2,
+  #           startCol = 2, startRow = 2, #headerStyle = style_text,
+  #           colNames = FALSE, withFilter = FALSE,  keepNA = TRUE, na.string = "-")
+
+
+
   # update references
   vec_hb <- unique(df_trend$`Health Board`)
   writeData(wb, sheet = "Refs",