| Type: | Package |
| Title: | Plot an Epidemic Curve |
| Version: | 2.4-2 |
| Date: | 2021-07-14 |
| Description: | Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data. |
| License: | LGPL-3 |
| Encoding: | UTF-8 |
| URL: | https://github.com/IamKDO/EpiCurve |
| Depends: | ggplot2, dplyr, ISOweek, scales, timeDate |
| Imports: | RColorBrewer, tibble |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2021-07-14 15:52:14 UTC; kdo |
| Author: | Jean Pierre Decorps [aut, cre] |
| Maintainer: | Jean Pierre Decorps <jean.pierre.decorps@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2021-07-14 16:20:05 UTC |
Plot an Epidemic Curve
Description
This function plot an epidemic curve with ggplot2
Usage
EpiCurve(x, date = NULL,freq = NULL, cutvar = NULL,
period = NULL, to.period = NULL, split = 1, cutorder = NULL, colors = NULL,
title = NULL, xlabel = NULL, ylabel=NULL, note=NULL, square = TRUE)
Arguments
x |
data.frame with at least one column with Date type |
date |
character, name of Date column |
freq |
character, name of a column with a value to display |
cutvar |
character, name of a column with factors |
period |
character, c("hour", "day","week", "month") |
to.period |
character, Convert date period to another period only for aggregated data. If period is "day", to.period can be "week" or "month". If period is "week", to.period can be "month". |
split |
integer, c(1,2,3,4,6,8,12) Value for hourly split |
cutorder |
character vector of factors |
colors |
character vector of colors |
title |
character, title of the plot |
xlabel |
character, label for x axis |
ylabel |
character, label for y axis |
note |
character, add a note under the graph |
square |
boolean, If TRUE (default) squares are used to plot the curve, else if the number of cases is too hight please use square = FALSE |
Details
When period is "week" the date MUST be in ISOweek format YYYY-WNN and library ISOweek is needed. When period is "month" the date MUST be formated YYYY-MM.
When period is "hour" the date MUST be in timeDate format (YYYY-mm-dd HH:MM:SS) or (YYYY-mm-dd HH:MM)
Author(s)
<jean.pierre.decorps@gmail.com>
References
<https://rlab-epiconcept.blogspot.fr/2016/09/courbes-epidemiques-avec-ggplot2.html>
<https://fr.wikipedia.org/wiki/Courbe_épidémique>
Examples
# library(EpiCurve)
date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min")
val <- rep(1, length(date))
tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date))
DF <- data.frame(date, val, tri, stringsAsFactors=TRUE)
names(DF) <- c("date","value", "tri")
EpiCurve(DF,
date = "date",
freq = "value",
period = "hour",
split = 4,
cutvar = "tri",
ylabel="Number of cases",
xlabel= "From 2017-05-10 21:35:22 To 2017-05-12 06:15:12",
title = "Epidemic Curve")