slide 46 - Admissions and Discharges

gistfile1.txt

##############################
# Admissions and Discharges 
##############################

####################
#reading the data ##
####################
data <- read.csv("df.csv", header = TRUE)

head(data, 10)
data$X <- NULL
##################################
# Importing the libraries I need##
##################################
library(lubridate)
library(tidyverse)
##################################
##################################


#######################################################

# Code that converts all the columns names to lowercase 

df_tolower <-  function(x) { 
  colnames(x) <- tolower(colnames(x)) 
  x
  
}

#####################################################

df <- df_tolower(data)



########################################
########################################
#function to transform the variables POSITXlt into POSITct 
change_col_to_ct <- function(df, col_name) {
  df[,col_name] <- as.POSIXct(df[,col_name])
  df
}

##################################
##################################
# example applying the change col to POSITct 
dt_sub <- df %>%  
  change_col_to_ct("start_datetime")%>%
  change_col_to_ct("end_datetime")
  
#################################
#################################
str(dt_sub)
#################################


################################################################################################################
# subseting data set 
################################################################################################################
dt_rmds<- dt_sub[c("pat_code", "start_datetime", "end_datetime", "spell.type", "ward_code", "episode.order", "spell.number")]



dt_JM2016<- subset(dt_rmds, (start_datetime >= as.POSIXct("2014-01-01 00:00:00") & start_datetime <= as.POSIXct("2014-04-01 23:59:00")) | 
                     (end_datetime >= as.POSIXct("2014-01-01 00:00:00") & end_datetime <= as.POSIXct("2014-04-01 23:59:00"))) 



#Choose EpisodeNumber == 1 (which has different spell numbers). 
#Each row has an episode number attached, with subsequent row == having the same PSeudoId
#That means it has the same number of episode for multiple spells within the Episode. 
#With thi, there are different AdmissionTimes, but different number for Discharge Time. 
# As a consequence, Yet I am interested only in the Episode number one 

#########################################################
### Obtaining the data needed for the two charts 46 $ 57 
########################################################
dt_spell <- dt_JM2016 %>% dplyr::filter(episode.order ==1)
names(dt_spell)

as.data.frame(dt_spell)



################
# 
################
# Selecting the variables I need 
dt_AdmiD_DischD <- dt_spell[c("pat_code","start_datetime", "end_datetime", "spell.number")]


# get the count of Admission and Discharges. with gather function
dt_spell_1 <- dt_AdmiD_DischD %>%
  group_by(pat_code) %>%
  gather(value= "count", key= Event, start_datetime,end_datetime)

# finding the days of the week from the dates 
dt_spell_1$EventDay <- lubridate::wday(dt_spell_1$count, label = TRUE)

dt_spell_1$count <- NULL


# get the counts 
sum_for_plot <- dt_spell_1 %>% 
  group_by(EventDay, Event) %>% 
  dplyr::summarize(Count=n()) %>%
  dplyr::mutate(Percent = Count / sum(Count))



# getting the mean ? I have the feeling this is not doing what I meant to? 

avg_tbl <- sum_for_plot %>%
  group_by(EventDay, Event) %>%
  dplyr::summarize(avg = mean(Count, na.rm=TRUE))

#######################################
# check the averages - it is not good #
#######################################

p1 <-ggplot(avg_tbl, aes(EventDay, avg, group= Event, shape = Event, colour = Event))
p1 + geom_bar(stat = "identity", position = "identity" , alpha=0.1, width = 0.4, colour="white", lwd = 0.5) + 
  geom_line()+
  scale_colour_manual(name = "Event",
                      breaks = c("Admissions", "Discharges"),
                      labels = c("Admissions", "Discharges"),
                      values = c("blue" , "red")) +
  geom_point()+
  xlim("Mon", "Tue", "Wed", "Thu", "Fri", "Sat", "Sun")+
  labs(title = "Admissions and Discharges by days of the week, 1st of Jan to 31st of March 2014",
       subtitle = "Number of daily hospital arrivals and discharges(incl.only the emergency cases) by the day of the week.
Note: results are intended for management information only",
       y = "Count", x = "Days of the week", caption = "Source: CLAHRC") +
  theme(axis.title.y = element_text(margin = margin(t = 0, r = 21, b = 0, l = 0)),
        plot.title = element_text(size = 10, face = "bold"),
        plot.subtitle = element_text(size = 7))