# the data frame SpecGroup.rda should be loaded

# example how to create a stacked bar-plot by grouping the data from the SpecGroup.rda file

# first address the capitals, by making them all the same:
SpecGroup$Speciality <- ifelse(SpecGroup$Speciality=="oncology", "Oncology",SpecGroup$Speciality) 

SpecGroup$Speciality <- ifelse(SpecGroup$Speciality=="Ortho", "Orthopaedics",SpecGroup$Speciality) 
SpecGroup$Speciality <- ifelse(SpecGroup$Speciality=="ortho", "Orthopaedics",SpecGroup$Speciality) 

# this dataframe now has duplicate values (which complicate the plot)!!
# to add the duplicates grouped by Month, Group and Speciality adding the variable Number; use the ddply function in the plyr package:
# call the new dataframe SpecGroup1
library(plyr)
SpecGroup1<-ddply(SpecGroup,c("Month","Group","Speciality"),numcolwise(sum)) # add as defined similar to the unique function

# for the data labels (numbers on top of the bars) to be postioned correctly it is necessary to calculate the cumsum
# use the ddply in the plyr package function for this:
# calculate the cumsum in a new dataframe called SpecGroup2
SpecGroup2<-ddply(SpecGroup1, c("Speciality","Month"),transform,ypos=cumsum(Number))

# Rather than having the month and year, create month names for the plot: 
# Again use the plyr package for this and save it as a new variable in the same dataframe (but without a capital letter):
SpecGroup2$month<-mapvalues(SpecGroup2$Month,from=c('01/2016','02/2016','03/2016','04/2016','05/2016','06/2016','07/2016','08/2016','09/2016','10/2016','11/2016','12/2016'),to=c('Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec'))

# now create a stacke bar plot with facets
dev.new() # new plot window
ggplot(SpecGroup2, aes(x=month, y= Number,fill=Group)) + # a bar plot using the SpecGroup2 dataframe with variables month and Number and the Group as fill
geom_bar(stat='identity',position='stack')+ # define a stacked bar plot
facet_grid(~Speciality)+ # define a facet to group the data further
theme_bw(base_size=12)+ # remove grey scales and set the font size
geom_text(aes(y=ypos,label=Number),vjust=1.0, color="white", size=3.5) + # make sure tha labels are correctly positined as defined above with the ypos variable
ggtitle(label = 'MDT Activity 2016') + # give the plot a title
xlab(label = 'Month') + # x axis label
ylab(label = 'Number')+ # y axis label
scale_x_discrete(limits = c('Jan','Feb','Mar','Apr','May','Jun')) # define the scale so that only these months show