mirror of https://github.com/msberends/AMR.git
77 lines
2.6 KiB
R
77 lines
2.6 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/age.R
|
|
\name{age_groups}
|
|
\alias{age_groups}
|
|
\title{Split Ages into Age Groups}
|
|
\usage{
|
|
age_groups(x, split_at = c(12, 25, 55, 75), na.rm = FALSE)
|
|
}
|
|
\arguments{
|
|
\item{x}{age, e.g. calculated with \code{\link[=age]{age()}}}
|
|
|
|
\item{split_at}{values to split \code{x} at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See \emph{Details}.}
|
|
|
|
\item{na.rm}{a \link{logical} to indicate whether missing values should be removed}
|
|
}
|
|
\value{
|
|
Ordered \link{factor}
|
|
}
|
|
\description{
|
|
Split ages into age groups defined by the \code{split} argument. This allows for easier demographic (antimicrobial resistance) analysis.
|
|
}
|
|
\details{
|
|
To split ages, the input for the \code{split_at} argument can be:
|
|
\itemize{
|
|
\item A \link{numeric} vector. A value of e.g. \code{c(10, 20)} will split \code{x} on 0-9, 10-19 and 20+. A value of only \code{50} will split \code{x} on 0-49 and 50+.
|
|
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).
|
|
\item A character:
|
|
\itemize{
|
|
\item \code{"children"} or \code{"kids"}, equivalent of: \code{c(0, 1, 2, 4, 6, 13, 18)}. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.
|
|
\item \code{"elderly"} or \code{"seniors"}, equivalent of: \code{c(65, 75, 85)}. This will split on 0-64, 65-74, 75-84, 85+.
|
|
\item \code{"fives"}, equivalent of: \code{1:20 * 5}. This will split on 0-4, 5-9, ..., 95-99, 100+.
|
|
\item \code{"tens"}, equivalent of: \code{1:10 * 10}. This will split on 0-9, 10-19, ..., 90-99, 100+.
|
|
}
|
|
}
|
|
}
|
|
\examples{
|
|
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
|
|
|
|
# split into 0-49 and 50+
|
|
age_groups(ages, 50)
|
|
|
|
# split into 0-19, 20-49 and 50+
|
|
age_groups(ages, c(20, 50))
|
|
|
|
# split into groups of ten years
|
|
age_groups(ages, 1:10 * 10)
|
|
age_groups(ages, split_at = "tens")
|
|
|
|
# split into groups of five years
|
|
age_groups(ages, 1:20 * 5)
|
|
age_groups(ages, split_at = "fives")
|
|
|
|
# split specifically for children
|
|
age_groups(ages, c(1, 2, 4, 6, 13, 18))
|
|
age_groups(ages, "children")
|
|
|
|
\donttest{
|
|
# resistance of ciprofloxacin per age group
|
|
if (require("dplyr") && require("ggplot2")) {
|
|
example_isolates \%>\%
|
|
filter_first_isolate() \%>\%
|
|
filter(mo == as.mo("Escherichia coli")) \%>\%
|
|
group_by(age_group = age_groups(age)) \%>\%
|
|
select(age_group, CIP) \%>\%
|
|
ggplot_sir(
|
|
x = "age_group",
|
|
minimum = 0,
|
|
x.title = "Age Group",
|
|
title = "Ciprofloxacin resistance per age group"
|
|
)
|
|
}
|
|
}
|
|
}
|
|
\seealso{
|
|
To determine ages, based on one or more reference dates, use the \code{\link[=age]{age()}} function.
|
|
}
|