mmi working

01_control/control_mmi.R

@@ -40,7 +40,7 @@ compile_referrals_summary()
 compile_non_acceptance_summary()
 
 # Step 5 - Create plots ---------------------------------------------------
-# 
-# create_plots_patients_seen("PT")
-# create_plots_patients_seen("CAMHS")
+#
+#create_plots_patients_seen("PT")
+#create_plots_patients_seen("CAMHS")
 

04_check_modify/add_rtt_eval.R

@@ -48,7 +48,7 @@ add_rtt_eval <- function(df, evalAllData=FALSE) {
         ref_acc_last_reported == 1 &
         any(
             !is.na(!!sym(treat_start_date_o))
-        ) ~ 'seen - active',
+        ) ~ 'seen - active', # not how treat_start_date is really meant to be used..?
 
       #other case is patients seen whose treatment is ongoing
       has_ref_rec_date_opti == TRUE &
@@ -68,7 +68,7 @@ add_rtt_eval <- function(df, evalAllData=FALSE) {
         ref_acc_last_reported == 1 &
         any(
             !is.na(!!sym(treat_start_date_o))
-        ) ~ 'seen - closed',
+        ) ~ 'seen - closed', # not how treat_start_date is really meant to be used..?
 
       #next case is patients seen whose treatment is finished
       has_ref_rec_date_opti == TRUE &
@@ -135,15 +135,15 @@ add_rtt_eval <- function(df, evalAllData=FALSE) {
         any(
           !is.na(!!sym(app_date_o)) &
             !!sym(att_status_o) == 1 
-        ) ~ 'rtt not possible - attended app but no purpose',
+        ) ~ 'rtt not possible - attended app but no purpose', # this isn't dependent on only FIRST treatment app
 
       #rtt not possible - no app attendance information
       has_any_app_date == TRUE &
         has_ref_rec_date_opti == TRUE &
         #is_case_closed == FALSE &
         ref_acc_last_reported == 1 &
         (!!sym(att_status_o) == 99 | is.na(!!sym(att_status_o))) 
-      ~ 'rtt not possible - app date but no attendance status',
+      ~ 'rtt not possible - app date but no attendance status', # this isn't dependent on only FIRST treatment app
 
 
       #case closed due to no attendance
@@ -154,7 +154,7 @@ add_rtt_eval <- function(df, evalAllData=FALSE) {
         any(
           !is.na(!!sym(app_date_o)) &
             !!sym(att_status_o) %in% c(2,3,5,8) 
-        ) ~ 'case closed due to non attendance',
+        ) ~ 'case closed due to non attendance', # would this flag any closed case where ANY (rather than ALL) nonattendance had occurred?
 
       #patients waiting no attendance
       has_any_app_date == TRUE &
@@ -164,7 +164,7 @@ add_rtt_eval <- function(df, evalAllData=FALSE) {
         any(
           !is.na(!!sym(app_date_o)) &
             !!sym(att_status_o) %in% c(2,3,5,8) 
-        ) ~ 'waiting - not attended',
+        ) ~ 'waiting - not attended', # again ANY or ALL apps non-attended being flagged here?
 
       #case closed prior to app
       has_any_app_date == FALSE &

06_calculations/calculate_adjusted_rtt_waits.R

@@ -36,7 +36,7 @@ calculate_adjusted_rtt_waits <- function(df){
   df_reset <- df_rtt |>
     mutate(dna_date = if_else(#app_purpose %in% c(2, 3) & removing - should reset for treatment and assessment app d/cna/w
                                 att_status %in% c(3, 5, 8) &
-                                app_date < first_treat_app,
+                                app_date < first_treat_app, # should this <= instead?
                               app_date, NA_Date_)) |> # makes a column with dates for any D/CNA/W # will need to add cancellation date here
 
     filter(!is.na(dna_date)) |> # removes gaps between dnas so lag doesn't get interrupted

07_publication/script/chapters/2_load_functions.R

@@ -69,3 +69,5 @@ source('./07_publication/script/functions/get_forpub_refs_agesex.R')
 #### Functions for MMI only ----------------------------------------------------
 
 source('./07_publication/script/functions/summarise_patients_seen.R')
+source('./07_publication/script/functions/compile_pat_seen_adj_excel_summary.R')
+source('./07_publication/script/functions/compile_pat_seen_unadj_excel_summary.R')

07_publication/script/chapters/3_set_constants.R

@@ -35,6 +35,7 @@ apps_att_dir <- paste0(shorewise_pub_data_dir, "/appointments_att/")
 basic_opti_dir <- paste0(shorewise_pub_data_dir, "/basic_v_opti/")
 markdown_dir <- paste0(root_dir, "/markdown/")
 open_dir <- paste0(shorewise_pub_data_dir, "/open_cases/")
+pat_seen_dir <- paste0(shorewise_pub_data_dir, "/patients_seen/")
 
 # 4 - Reference -----------------------------------------------------------
 
@@ -65,8 +66,8 @@ df_ds_hb_name <- cross_join(as.data.frame(vec_dataset_type),
   rename(dataset_type = vec_dataset_type,
          hb_name = hb_vector) |> 
   mutate(hb_name = factor(hb_name, levels = hb_vector))
-  filter(!(#dataset_type == "CAMHS" & 
-             hb_name == "NHS 24")) # remove invalid combo
+  # filter(!(#dataset_type == "CAMHS" & 
+  #            hb_name == "NHS 24")) # remove invalid combo
 
 # with time columns
 df_time <- data.frame(month = date_range) |> 

07_publication/script/functions/compile_pat_seen_adj_excel_summary.R

@@ -13,20 +13,20 @@ compile_pat_seen_adj_summary <- function(){
   #filnames <- list.files(ref_dir)
 
   #  load parquet files 
-  p1 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_all.parquet"))
-  p2 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_all_sex.parquet"))
-  p3 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_all_age.parquet"))
-  p4 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_all_simd.parquet"))
+  p1 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_all.parquet"))
+  p2 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_all_sex.parquet"))
+  p3 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_all_age.parquet"))
+  p4 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_all_simd.parquet"))
 
-  p5 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_mth.parquet"))
-  p6 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_mth_sex.parquet"))
-  p7 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_mth_age.parquet"))
-  p8 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_mth_simd.parquet"))
+  p5 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_mth.parquet"))
+  p6 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_mth_sex.parquet"))
+  p7 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_mth_age.parquet"))
+  p8 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_mth_simd.parquet"))
 
-  p9 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_qt.parquet"))
-  p10 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_qt_sex.parquet"))
-  p11 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_qt_age.parquet"))
-  p12 <- read_parquet(paste0(pat_seen_dir, "adj_wait_grp_qt_simd.parquet"))
+  p9 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_qt.parquet"))
+  p10 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_qt_sex.parquet"))
+  p11 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_qt_age.parquet"))
+  p12 <- read_parquet(paste0(pat_seen_dir, "pat_seen_adj_wait_grp_qt_simd.parquet"))
 
   # name tabs
   list_tabs <- list(

07_publication/script/functions/compile_pat_seen_unadj_excel_summary.R

@@ -13,20 +13,20 @@ compile_pat_seen_unadj_summary <- function(){
   #filnames <- list.files(ref_dir)
 
   #  load parquet files 
-  p1 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_all.parquet"))
-  p2 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_all_sex.parquet"))
-  p3 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_all_age.parquet"))
-  p4 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_all_simd.parquet"))
+  p1 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_all.parquet"))
+  p2 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_all_sex.parquet"))
+  p3 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_all_age.parquet"))
+  p4 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_all_simd.parquet"))
 
-  p5 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_mth.parquet"))
-  p6 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_mth_sex.parquet"))
-  p7 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_mth_age.parquet"))
-  p8 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_mth_simd.parquet"))
+  p5 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_mth.parquet"))
+  p6 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_mth_sex.parquet"))
+  p7 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_mth_age.parquet"))
+  p8 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_mth_simd.parquet"))
 
-  p9 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_qt.parquet"))
-  p10 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_qt_sex.parquet"))
-  p11 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_qt_age.parquet"))
-  p12 <- read_parquet(paste0(pat_seen_dir, "unadj_wait_grp_qt_simd.parquet"))
+  p9 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_qt.parquet"))
+  p10 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_qt_sex.parquet"))
+  p11 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_qt_age.parquet"))
+  p12 <- read_parquet(paste0(pat_seen_dir, "pat_seen_unadj_wait_grp_qt_simd.parquet"))
 
   # name tabs
   list_tabs <- list(