gabrielburcea

get_fct_recode <- function(path_config_fl) {

  mapp_col <- readRDS(file.path(path_config_fl, "mapp_col.rds"))
  
  list_config_fls <- Sys.glob(file.path(path_config_fl, "*.rds"))
  
  mapp_col <- mapp_col %>% dplyr::mutate(file_name_config = file.path(path_config_fl, paste0(common, "_levels.rds")), 
                                         list_config_fct = dplyr::if_else(file_name_config %in% list_config_fls, file_name_config, NA_character_)) %>%
    dplyr::select(-file_name_config)
  

gabrielburcea

occupancy_fct <- function(start_date = as.Date("2016-06-01", tz = "Europe/London"),
                          end_date = as.Date("2016-06-08", tz = "Europe/London"),
                          data){

  dt_los <- data %>%
    dplyr::select(spell_number, spell_start, spell_end) %>%
    dplyr::mutate(Same_day_discharge = as.numeric(difftime(spell_end, spell_start, unit = c("min"))))


  dt_calc <- dt_los %>%

gabrielburcea

occupancy_fct <- function(start_date = as.Date("2016-06-01", tz = "Europe/London"),
                          end_date = as.Date("2016-06-08", tz = "Europe/London"),
                          data){

  dt_los <- data %>%
    dplyr::select(spell_number, spell_start, spell_end) %>%
    dplyr::mutate(Same_day_discharge = as.numeric(difftime(spell_end, spell_start, unit = c("min"))))


  dt_calc <- dt_los %>%

gabrielburcea

los_distrib_with_better_breaks <- function(data, plot_chart){
  
  
  
  # renaming the variables I am interested in 
  df_rename <- df %>%
    select(PAT_CODE, START_DATETIME, END_DATETIME, episode.order, Admission.Type, disch.ward.type, WARD_CODE) %>%
    dplyr::rename(IDcol = PAT_CODE, Admissions = START_DATETIME, 
                  Discharges = END_DATETIME, Episode_number = episode.order, Ward_code = WARD_CODE, 
                  Admission_type = Admission.Type, Discharge_ward_type = disch.ward.type)

gabrielburcea

los_distrib_1_month_with_breaks_provided <- function(data, plot_chart){

  # renaming the variables I am interested in 
  # renaming the variables I am interested in 
  df_rename <- data %>%
    select(PAT_CODE, START_DATETIME, END_DATETIME, episode.order, Admission.Type, disch.ward.type, WARD_CODE) %>%
    dplyr::rename(IDcol = PAT_CODE, Admissions = START_DATETIME, 
                  Discharges = END_DATETIME, Episode_number = episode.order, Ward_code = WARD_CODE, 
                  Admission_type = Admission.Type, Discharge_ward_type = disch.ward.type)
  

gabrielburcea

  # renaming the variables I am interested in 
  df_rename <- df %>%
    select(PAT_CODE, START_DATETIME, END_DATETIME, episode.order, AGE_BAND, SEX, spell.type, WARD_CODE, spell.end.ward) %>%
    dplyr::rename(IDcol = PAT_CODE, Admissions = START_DATETIME, PatientType = spell.type, 
                  Discharges = END_DATETIME, EpisodeNumber = episode.order, Ward = WARD_CODE,
                  Gender = SEX, AgeBand = AGE_BAND, LastWard = spell.end.ward)

  
  #df_subset <- df_subset %>%
    #filter(EpisodeStart > StartDate & EpisodeEnd < EndDate) 

gabrielburcea

 melt_for_plt <- melt(total_adm_disch_non_emerg)
  
  
  plot_adm_disc <-ggplot(melt_for_plt, aes(Week_Day, value, group = variable)) + #shape = Event,  colour = Event
    #geom_bar(stat = "identity", position = "identity" , alpha=0.4, width = 0.5, fill = "slateblue4") + 
    geom_line(aes(linetype = variable, color = variable), size = 1.0) +
    geom_point(aes(shape = variable), size = 1.0) +
    scale_shape_manual(values = c(7, 6, 5)) +
    scale_linetype_manual(values = c("solid", "solid" , "twodash")) +
    scale_color_manual(values=c("red", "black",  "black")) +

gabrielburcea

  # function to select the columns I need

  rename_fct <- function(data, oldnames, newnames){
    data_names <- colnames(data)
    data_names[which(data_names %in% oldnames)] <- newnames
    colnames(data) <- data_names
    data
  }
  
  data <- rename_fct(df, c("PAT_CODE", "WARD_CODE", "START_DATETIME", "END_DATETIME", "AGE_BAND", "SEX",    "episode.order", "spell.end.ward"), 

gabrielburcea

dput(head(ae_att_df, 10))

gabrielburcea

 ############################
  # calculating total time by using difftime - length of stay
  ################################
  dt_los <- dt_subset %>%
    mutate(LOS = as.numeric(difftime(end_datetime, start_datetime, units = c("days")))) %>% # or minutes? 
    select(pat_code, LOS, admission.type, disch.ward.type) %>%
    na.omit()