update publication functions with test directory

Public-Health-Scotland · Aug 2, 2024 · 0315a54 · 0315a54
1 parent 364fe18
commit 0315a54
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Showing 6 changed files with 20 additions and 22 deletions.
diff --git a/code/publication/01_create-pub-basefile.R b/code/publication/01_create-pub-basefile.R
@@ -30,7 +30,7 @@ create_final_data(
 
 ### 2 - Restructure data file ----
 
-basefile <- read_rds(get_mi_data_path(type = "final_data", ext = "rds")) %>% 
+basefile <- read_rds(get_mi_data_path(type = "final_data", ext = "rds", test_output = test_output)) %>% 
 
   # Select only FY to be included in pub
   filter(fy %in% fy_in_pub) %>%
@@ -81,6 +81,6 @@ basefile <- read_rds(get_mi_data_path(type = "final_data", ext = "rds")) %>%
 
 ### 3 - Save file ----
 basefile %>% 
-write_rds(get_pub_data_path(), compress = "gz")
+write_rds(get_pub_data_path(test_output = test_output), compress = "gz")
 
 ### END OF SCRIPT ###
diff --git a/code/publication/02_create-figures.R b/code/publication/02_create-figures.R
@@ -22,7 +22,7 @@ source(here("functions", "ggplot_themes.R"))
 
 ### 2 - Read in data ----
 
-basefile <- read_rds(get_pub_data_path())
+basefile <- read_rds(get_pub_data_path(test_output = test_output))
 
 
 # Load expected diagnoses reference file
@@ -89,7 +89,7 @@ c1 <-
   ) +
   ylab("")
 
-ggsave(get_pub_figures_path(type = "c1"),
+ggsave(get_pub_figures_path(type = "c1", test_output = test_output),
   plot = c1,
   height = 6,
   width = 6,
@@ -128,7 +128,7 @@ c2 <-
   xlab("Percentage of Referrals Achieved LDP Standard") +
   ylab("")
 
-ggsave(get_pub_figures_path(type = "c2"),
+ggsave(get_pub_figures_path(type = "c2", test_output = test_output),
   plot = c2,
   height = 6,
   width = 6,
@@ -137,9 +137,7 @@ ggsave(get_pub_figures_path(type = "c2"),
 )
 
 # Save chart for twitter
-ggsave(
-  here("publication", "output", pub_date,
-       paste0(pub_date, "_dementia-pds_twitter-chart.png")),
+ggsave(get_pub_figures_path(type = "twitter", test_output = test_output),
   plot = c2,
   height = 6,
   width = 6,
@@ -158,7 +156,7 @@ summary <-
   theme(axis.title.x = element_text(size = 7.5),
         axis.text = element_text(size = 7.5))
 
-ggsave(get_pub_figures_path(type = "summary"),
+ggsave(get_pub_figures_path(type = "summary", test_output = test_output),
   plot = summary,
   height = 5,
   width = 5,
@@ -199,7 +197,7 @@ c3 <-
   xlab("Percentage of Referrals Achieved LDP Standard") +
   ylab("")
 
-ggsave(get_pub_figures_path(type = "c3"),
+ggsave(get_pub_figures_path(type = "c3", test_output = test_output),
   plot = c3,
   height = 9,
   width = 6,
@@ -257,7 +255,7 @@ c4 <-
   ylab(str_wrap("Percentage of total referrals", width = 10))
 
 # Save chart to output folder
-ggsave(get_pub_figures_path(type = "c4"),
+ggsave(get_pub_figures_path(type = "c4", test_output = test_output),
   plot = c4,
   width = 6.8,
   height = 3.5,
@@ -327,7 +325,7 @@ c5 <-
   ylab(str_wrap("Percentage of Referrals Achieved LDP Standard", width = 10))
 
 # Save chart to output folder
-ggsave(get_pub_figures_path(type = "c5"),
+ggsave(get_pub_figures_path(type = "c5", test_output = test_output),
   plot = c5,
   width = 6.8,
   height = 3.5,
@@ -383,7 +381,7 @@ c6 <-
   ylab(str_wrap("Percentage of total referrals", width = 10))
 
 # Save chart to output folder
-ggsave(get_pub_figures_path(type = "c6"),
+ggsave(get_pub_figures_path(type = "c6", test_output = test_output),
   plot = c6,
   width = 6.8,
   height = 3.5,
@@ -445,7 +443,7 @@ c7 <-
   ylab(str_wrap("Percentage of Referrals Achieved LDP Standard", width = 10))
 
 # Save chart to output folder
-ggsave(get_pub_figures_path(type = "c7"),
+ggsave(get_pub_figures_path(type = "c7", test_output = test_output),
   plot = c7,
   width = 6.8,
   height = 3.5,

diff --git a/code/publication/03-knit-markdown.R b/code/publication/03-knit-markdown.R
@@ -19,7 +19,7 @@ source(here::here("code", "publication", "00_setup-pub-environment.R"))
 
 render(
   input = here("publication", "markdown", "summary.Rmd"),
-  output_file = get_pub_output_path(output_name = "pub_summary")
+  output_file = get_pub_output_path(output_name = "pub_summary", test_output = test_output)
 )
 
 ### 2 - load environment file and load functions then knit REPORT ----
@@ -28,7 +28,7 @@ source(here::here("code", "publication", "00_setup-pub-environment.R"))
 
 rmarkdown::render(
   input = here("publication", "markdown", "report.Rmd"),
-  output_file = get_pub_output_path(output_name = "pub_report")
+  output_file = get_pub_output_path(output_name = "pub_report", test_output = test_output)
 )
 
 ### END OF SCRIPT ###
diff --git a/code/publication/04_create-excel-tables.R b/code/publication/04_create-excel-tables.R
@@ -18,7 +18,7 @@ source(here::here("code", "publication", "00_setup-pub-environment.R"))
 
 ### 2 - Load data ----
 
-pds <- read_rds(get_pub_data_path())
+pds <- read_rds(get_pub_data_path(test_output = test_output))
 
 expected <- read_csv(get_exp_diagnoses_path()) %>%
   select(-health_board)
@@ -195,7 +195,7 @@ writeData(wb,
 sheetVisibility(wb)[10:11] <- "hidden"
 
 saveWorkbook(wb,
-             get_pub_output_path(output_name = "excel_tables"),
+             get_pub_output_path(output_name = "excel_tables", test_output = test_output),
              overwrite = TRUE)
 
 

diff --git a/code/publication/05_create-discovery-data.R b/code/publication/05_create-discovery-data.R
@@ -18,7 +18,7 @@ source(here::here("code", "publication", "00_setup-pub-environment.R"))
 
 ### 2 - Load data ----
 
-pds <- read_rds(get_pub_data_path())
+pds <- read_rds(get_pub_data_path(test_output = test_output))
 
 
 ### 3 - Restructure data ----
@@ -53,7 +53,7 @@ discovery <-
 
 write_csv(
   discovery,
-  get_pub_output_path(output_name = "discovery_data"))
+  get_pub_output_path(output_name = "discovery_data", test_output = test_output))
 
 
 ### END OF SCRIPT ###
diff --git a/publication/markdown/report.Rmd b/publication/markdown/report.Rmd
@@ -32,7 +32,7 @@ format_perc <- function(x, dp = 1){
 
 # LDP Dataset
 pds <- 
-  read_rds(get_pub_data_path()) %>% 
+  read_rds(get_pub_data_path(test_output = test_output)) %>% 
   filter(ijb != "Unknown" & referrals > 0)
 
 # Expected Diagnoses (Incidence)
@@ -41,7 +41,7 @@ exp <- read_csv(get_exp_diagnoses_path()) %>%
 
 # Error rates 
 err <- 
-  read_rds(get_mi_data_path(type = "error_data", ext = "rds")) %>% 
+  read_rds(get_mi_data_path(type = "error_data", ext = "rds", test_output = test_output)) %>% 
   filter(health_board == "Scotland" & fy %in% fy_in_pub) %>%
   mutate(perc = format_perc(total_errors / records * 100)
   ) %>%