plotIncidence: Plot incidence time series using histograms

In Hackout2/incidence: Computation and Visualisation of Incidence from Line Lists

Description

This function provides advanced plotting facilities for incidence time series using ggplot2

Usage

plotIncidence(x, dates, bin = 7, fill.by = NULL, split.by = NULL,
  shade.by = NULL, start.at = NULL, stop.at = NULL, xlab = NULL,
  ylab = "Incidence", date.format = "%d %b %Y", angle = 45,
  xbreaks = "1 week", col.pal = 1)

Arguments

x	a data.frame containing the data to be plotted.
dates	a character string or an integer indicating which column contains the dates to use
bin	an integer indicating the size of the time window (in days) to use for the incidence computation
fill.by	a character string or an integer indicating which column to use to color the bars
split.by	a character string or an integer indicating which column to use to split the charts
shade.by	a character string or an integer indicating which column to use to shade the bars
start.at	a starting date for the incidence; defaults to the earliest date of the dataset
stop.at	a stoping date for the incidence; defaults to the latest date of the dataset
xlab	a label for the x axis
ylab	a label for the y axis
date.format	a character string indicating the format of the dates
angle	an integer indicating the angle of the dates
xbreaks	a character string indicating the time interval between vertical lines
col.pal	an integer between 1 and 8 indicating a color palette to be used; if NULL, the default color palette of ggplot2 is used

Author(s)

Thibaut Jombart [e-mail]

Examples

data("toy")
head(toy)

## basic plot
plotIncidence(toy, dates="dateOfOnset")

## change column indication, and bin size to 2 days
plotIncidence(toy, dates=1, bin=2)
plotIncidence(toy, dates=1, bin=2, split.by="gender", fill.by=3)

Hackout2/incidence documentation built on May 6, 2019, 9:47 p.m.