transfer from old repo

1 PA Decline/flowchart.R

@@ -0,0 +1,48 @@
+create_flowchart <- function(data, export.path = NULL) {
+  out <- data |> 
+    dplyr::select(pase_0,pase_4) |> 
+    dplyr::mutate(id= dplyr::row_number(),
+                  exclude=is.na(pase_0)|is.na(pase_4),
+                  exclude_reason=factor(dplyr::case_when(
+      is.na(pase_0) ~ "Pre-stroke PASE missing",
+      is.na(pase_4) ~"Post-stroke PASE missing"
+    ),levels=c( "Pre-stroke PASE missing","Post-stroke PASE missing")),
+    ) |> 
+    consort::consort_plot(
+    orders = c(
+      id = "Complete TALOS cohort",
+      exclude_reason = "Excluded",
+      id = "Main dataset"
+    ),
+    side_box = c("exclude_reason"),
+    labels = c(
+      "1" = "Identification",
+      "2" = "Inclusion",
+      "3" = "Complete data"
+    )
+  )
+  
+  if (!is.null(export.path)) {
+    out |> export_consort_dot(path = export.path)
+  } else {
+    plot(out)
+  }
+}
+
+source(here::here("2 Longterm/data.R"))
+# The original functions from DST unedited
+source(here::here("1 PA Decline/Fra DDV/functions200411.R"))
+source(here::here("1 PA Decline/Fra DDV/functions240418.R"))
+# Modified functions to overwrite original
+source(here::here("R/functions.R"))
+
+df <- df_ddv |>
+  dplyr::tibble() |>
+  dplyr::mutate_all(as.character) |>
+  ready_clin() |>
+  data_formatting()|>
+  get_vars(c("clin","lifestyle","ses", "assess.pred"))  |> 
+  dplyr::mutate(exclude=ifelse(is.na(pase_0)|is.na(pase_4),"Excluded","Included"),
+                age=as.numeric(age))
+
+df |> create_flowchart()