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()