Author: Daniel Gardiner
Contact: daniel.gardiner@phe.gov.uk
Date: 06.03.2018
Credit: this function is loosely based on the plotIncidence function created as part of the GRINDER hackathon https://github.com/Hackout2/time
Functon to plot epicurve
Arguments:
x: a data frame
date.col: a character specifying the column containing dates
time.period: a character of the desired time period for the epicurve, this can either be day, year, month, year.month, iso.year, iso.week, iso.year.week, use.date.col.as.is NOTE: if time.period = use.date.col.as.is the date.col will be treated as a factor and will be used as the x-axis
fill.by: a character specifying the column to stratify by fill colour
split.by: a character specifying the column to stratify by faceting
shade.by: a character specifying the column to stratify by shade colour
start.at: a character in the format "yyyy-mm-dd" to specify the start date for the epicurve
stop.at: a character in the format "yyyy-mm-dd" to specify the stop date for the epicurve
xlab: a character specifying the x-axis label for the epicurve
ylab: a character specifying the y-axis label for the epicurve
fill.by.legend.title: a character specifying the fill legend title
shade.by.legend.title: a character specifying the shade legend title
angle: a numeric to specify the x-axis label angel for the epicurve
col.pal: a numeric specifying the colour palette (range 1-8 inclusive) OR a character stating 'phe' to use the phe colour palette
label.breaks: a numeric specifying the interval for x-axis label breaks
epi.squares: a logical specifying if episquares should be used on the epicurve
blank.background: a logical specifying if the figure background should be blank
na.rm: a logical specifying if missing dates should be removed from the epicurve
