Merge pull request #421 from Public-Health-Scotland/bex

reorganise publications folder

07_publication/archive/chapters/2_load_functions.R

@@ -0,0 +1,24 @@
+
+######################.
+### Load functions ###
+######################.
+
+# Author: Charlie Smith
+# Date: 2023-11-14
+
+
+source('./02_setup/save_df_as_parquet.R')
+source("./07_publication/script/functions/retrieve_save_data.R")
+source('./07_publication/script/functions/get_referrals_quarterly.R')
+source('./07_publication/script/functions/get_referrals_monthly_sco.R')
+source('./07_publication/script/functions/get_referrals_sex_age.R')
+source('./07_publication/script/functions/get_referrals_simd.R')
+
+source('./07_publication/script/functions/create_table_refs_quarterly.R')
+source('./07_publication/script/functions/get_annual_summary_figures.R')
+
+source('./07_publication/script/functions/make_chart_referrals_sco.R')
+source('./07_publication/script/functions/make_chart_referrals_sex_age.R')
+source('./07_publication/script/functions/make_chart_referrals_rate_simd.R')
+
+source('./07_publication/script/functions/compile_excel_doc.R')

07_publication/archive/chapters/3_set_constants.R

@@ -0,0 +1,67 @@
+
+#####################.
+### Set constants ###
+#####################.
+
+# Author: Charlie Smith
+# Date: 2023-11-14
+
+
+
+
+# 1 - Establish data time frame -------------------------------------------
+
+month_end <- ymd(month_end)
+month_start <- ymd(month_end) - months(14)
+date_range <- seq.Date(from = month_start, to = month_end, by = "month")
+
+range_12_month <- seq.Date(from = month_end - months(11), to = month_end, by = "month")
+
+# 2 - Production data -----------------------------------------------------
+publication_month <- month_end + months(3)
+
+
+production_date <- Sys.Date()
+production_month <- format(as.Date(production_date), "%B %Y")
+
+# 3 - Set safe place to save working data ---------------------------------
+
+data_working_safe <- "../../../output/publication/data/"
+
+reference_files_dir <- paste0(data_working_safe, 'reference_files/')
+dir.create(paste0(data_working_safe, publication_month, '_release'))
+
+data_working_safe <- paste0(data_working_safe, publication_month, '_release/')
+
+
+
+
+# 4 - Reference -----------------------------------------------------------
+
+# create HB vector
+hb_vector <- c("NHS Scotland",
+               "NHS Ayrshire and Arran", 
+               "NHS Borders", 
+               "NHS Dumfries and Galloway",
+               "NHS Fife",
+               "NHS Forth Valley", 
+               "NHS Grampian",
+               "NHS Greater Glasgow and Clyde",
+               "NHS Highland",
+               "NHS Lanarkshire", 
+               "NHS Lothian", 
+               "NHS Orkney",
+               "NHS Shetland", 
+               "NHS Tayside", 
+               "NHS Western Isles",
+               "NHS 24")
+
+
+# chart dimensions
+chart_width <- 24
+chart_height <- 16
+
+
+# 6 - Get next pub date ---------------------------------------------------
+# (6 months after month_end, 1st Tuesday)
+# next_pub_date <- id_next_pub(data_last = month_end)

07_publication/script/chapters/2_load_functions.R

@@ -7,18 +7,60 @@
 # Date: 2023-11-14
 
 
+
 source('./02_setup/save_df_as_parquet.R')
-source("./07_publication/script/functions/retrieve_save_data.R")
-source('./07_publication/script/functions/get_referrals_quarterly.R')
-source('./07_publication/script/functions/get_referrals_monthly_sco.R')
-source('./07_publication/script/functions/get_referrals_sex_age.R')
-source('./07_publication/script/functions/get_referrals_simd.R')
 
-source('./07_publication/script/functions/create_table_refs_quarterly.R')
-source('./07_publication/script/functions/get_annual_summary_figures.R')
+source('./07_publication/update_2024_06/functions/add_sex_description.R')
+source('./07_publication/update_2024_06/functions/append_quarter_ending.R')
+source('./07_publication/update_2024_06/functions/summarise_by_quarter.R')
+source('./07_publication/update_2024_06/functions/add_proportion_ds_hb.R')
+source('./07_publication/update_2024_06/functions/add_hb_region.R')
+source("./07_publication/update_2024_06/functions/get_appointments_df.R")
+source("./07_publication/update_2024_06/functions/get_basic_data_referrals_df.R")
+source('./07_publication/update_2024_06/functions/tidy_age_group_order.R')
+
+source('./07_publication/update_2024_06/functions/summarise_referrals.R')
+#source('./07_publication/update_2024_06/functions/referrals_by_source.R')
+source('./07_publication/update_2024_06/functions/non_acceptance.R')
+source('./07_publication/update_2024_06/functions/non_acceptance_reason.R')
+source('./07_publication/update_2024_06/functions/non_acceptance_action.R')
+
+source('./07_publication/update_2024_06/functions/summarise_referrals_basic_opti.R')
+source('./07_publication/update_2024_06/functions/summarise_appointments_att.R')
+
+source('./07_publication/update_2024_06/functions/compile_referrals_excel_summary.R')
+source('./07_publication/update_2024_06/functions/compile_ref_source_excel_summary.R')
+source('./07_publication/update_2024_06/functions/compile_non_acceptance_summary.R')
+source('./07_publication/update_2024_06/functions/compile_non_acceptance_reason_summary.R')
+source('./07_publication/update_2024_06/functions/compile_non_acceptance_action_summary.R')
+source('./07_publication/update_2024_06/functions/compile_appointments_excel_summary.R')
+source('./07_publication/update_2024_06/functions/compile_basic_opti_excel_summary.R')
+
+
+source('./07_publication/update_2024_06/functions/create_table_referrals_quarterly.R')
+source('./07_publication/update_2024_06/functions/create_table_acc_rate.R')
+#source('./07_publication/update_2024_06/functions/create_table_acc_reason_action.R')
+source('./07_publication/update_2024_06/functions/create_table_app_att.R')
+source('./07_publication/update_2024_06/functions/create_table_basic_opti.R')
+
+source('./07_publication/update_2024_06/functions/create_bar_chart_rej_reason.R')
+source('./07_publication/update_2024_06/functions/create_bar_chart_rej_action.R')
+source('./07_publication/update_2024_06/functions/create_bar_chart_dna_simd.R')
+source('./07_publication/update_2024_06/functions/create_trend_plot_dna_rate.R')
+
+source('./07_publication/update_2024_06/functions/create_pub_function.R')
+source('./07_publication/update_2024_06/functions/identify_next_publication_date.R')
+
+# compile data tables functions
+source('./07_publication/update_2024_06/functions/compile_publication_data_tables.R')
+source('./07_publication/update_2024_06/functions/update_dt_wording.R')
+source('./07_publication/update_2024_06/functions/update_dt_values.R')
+source('./07_publication/update_2024_06/functions/protect_worksheets.R')
+
+source('./07_publication/update_2024_06/functions/summarise_referrals_sex_age.R')
+source('./07_publication/update_2024_06/functions/create_stemleaf_ref_sex_age.R')
+source('./07_publication/update_2024_06/functions/create_bar_chart_refs_simd.R')
+
+source('./07_publication/update_2024_06/functions/get_forpub_refs_agesex.R')
 
-source('./07_publication/script/functions/make_chart_referrals_sco.R')
-source('./07_publication/script/functions/make_chart_referrals_sex_age.R')
-source('./07_publication/script/functions/make_chart_referrals_rate_simd.R')
 
-source('./07_publication/script/functions/compile_excel_doc.R')

07_publication/script/chapters/3_set_constants.R

@@ -26,21 +26,20 @@ production_month <- format(as.Date(production_date), "%B %Y")
 
 # 3 - Set safe place to save working data ---------------------------------
 
-data_working_safe <- "../../../output/publication/data/"
-
-reference_files_dir <- paste0(data_working_safe, 'reference_files/')
-dir.create(paste0(data_working_safe, publication_month, '_release'))
-
-data_working_safe <- paste0(data_working_safe, publication_month, '_release/')
-
-
+ref_dir <- paste0(shorewise_pub_data_dir, "/referrals/")
+ref_source_dir <- paste0(shorewise_pub_data_dir, "/referrals_by_ref_source/")
+non_acc_dir <- paste0(shorewise_pub_data_dir, "/non_acceptance/")
+non_acc_reason_dir <- paste0(shorewise_pub_data_dir, "/non_acceptance_reason/")
+non_acc_action_dir <- paste0(shorewise_pub_data_dir, "/non_acceptance_action/")
+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/")
 
 
 # 4 - Reference -----------------------------------------------------------
 
 # create HB vector
-hb_vector <- c("NHS Scotland",
-               "NHS Ayrshire and Arran", 
+hb_vector <- c("NHS Ayrshire and Arran", 
                "NHS Borders", 
                "NHS Dumfries and Galloway",
                "NHS Fife",
@@ -54,14 +53,86 @@ hb_vector <- c("NHS Scotland",
                "NHS Shetland", 
                "NHS Tayside", 
                "NHS Western Isles",
-               "NHS 24")
+               "NHS 24",
+               "NHS Scotland")
 
 
-# chart dimensions
-chart_width <- 24
-chart_height <- 16
+vec_dataset_type <- c("CAMHS", "PT")
+
+# create complete ds 
+df_ds_hb_name <- cross_join(as.data.frame(vec_dataset_type), 
+                            as.data.frame(hb_vector)) |> 
+  rename(dataset_type = vec_dataset_type,
+         hb_name = hb_vector) |> 
+  filter(!(#dataset_type == "CAMHS" & 
+             hb_name == "NHS 24")) # remove invalid combo
 
 
-# 6 - Get next pub date ---------------------------------------------------
-# (6 months after month_end, 1st Tuesday)
-# next_pub_date <- id_next_pub(data_last = month_end)
+# 5. Plotting constants -------------------------------------------------------
+
+# chart dimensions
+chart_width = 18 # changed to scale better on a4 page # 24
+chart_height = 12 # changed to scale better on a4 page # 16
+bar_width = 0.5
+
+# custom plotting theme (does not set legend formatting, 
+# requires panel.grid.major.x/y to be manually defined depending on orientation of plot)
+
+theme_captnd <- function(){
+  font <- "Arial"
+  theme_minimal() %+replace%
+    theme(
+      panel.grid.major = element_blank(),
+      panel.grid.minor = element_blank(),
+      panel.background = element_rect(fill = "white"),
+      panel.border = element_rect(colour = "grey95", fill = NA, linewidth = 0.75),
+      plot.caption = element_text(size = 10, hjust = 1, margin = margin(t = 10)),
+      axis.title.x = element_text(size = 12, face = "bold",
+                                  margin = margin(t = 15)),
+      axis.title.y = element_text(size = 12, face = "bold",
+                                  margin = margin(r = 15), angle = 90),
+      axis.text.x = element_text(size = 11, color = "black"),
+      axis.text.y = element_text(size = 11, color = "black", hjust = 1),
+      axis.ticks = element_line(colour = "grey90")
+    )
+}
+
+
+
+# 6 - Get date labels for publication doc ----------------------------
+
+# date labels
+date_label <- format(as.Date(month_end), "%B %Y")
+date_label_qt <- format((as.Date(month_end) %m-% months(3)), "%B %Y")
+date_label_yr <- format((as.Date(month_end) %m-% months(12)), "%B %Y")
+date_label_5qt <- format((as.Date(month_end) %m-% months(14)), "%B %Y")
+
+# set pub_date as 3 months after month_end
+pub_month <- as.Date(month_end %m+% months(3))
+## Get next pub date and prev pub date
+# (6 months after pub_date, 1st Tuesday)
+next_pub_date <- id_next_pub(pub_month)
+# (6 months after 1yr before pub_date, 1st Tuesday)
+prev_pub_date <- id_next_pub(pub_month - months(12))
+
+#pub_date for this publication itself
+pub_date <- id_next_pub(pub_month -months(6))
+
+
+
+
+# 7 - Constants for data tables -------------------------------------------
+
+
+# # password for locking worksheets (doesn't seem to work...)
+# str_password <- "13_DunDee_$dollar$"
+# 
+# dq_template_1 = "dq_info_only_template.xlsx" # DQ Report template
+# dq_template_1_update = "dq_report_template_DO_NOT_EDIT.xlsx"
+# dq_template_2 = "record_trend_only_template.xlsx" # Record Counts Report template
+# 
+# # set text font and size for added text
+style_text <- createStyle(fontName = 'Arial', fontSize = 11)
+style_date <- createStyle(numFmt = "mmm-yy", fontName = 'Arial', fontSize = 11, halign = "left")
+style_count <- createStyle(numFmt = "#,##0", fontName = 'Arial', fontSize = 11, halign = "right")
+style_percent <- createStyle(numFmt = "PERCENT", fontName = 'Arial', fontSize = 11, halign = "right")