age and age_groups

man/age.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/age.R
+\name{age}
+\alias{age}
+\title{Age in years of individuals}
+\usage{
+age(x, y = Sys.Date())
+}
+\arguments{
+\item{x}{date(s) - will be coerced with \code{\link{as.POSIXlt}}}
+
+\item{y}{reference date(s) - defaults to \code{\link{Sys.Date}} - will be coerced with \code{\link{as.POSIXlt}}}
+}
+\value{
+Integer (no decimals)
+}
+\description{
+Calculates age in years based on a reference date, which is the sytem time at default.
+}
+\seealso{
+age_groups
+}

man/age_groups.Rd

@@ -0,0 +1,66 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/age.R
+\name{age_groups}
+\alias{age_groups}
+\title{Split ages in age groups}
+\usage{
+age_groups(x, split_at = c(12, 25, 55, 75))
+}
+\arguments{
+\item{x}{age, e.g. calculated with \code{\link{age}}}
+
+\item{split_at}{values to split \code{x}, defaults to 0-11, 12-24, 26-54, 55-74 and 75+. See Details.}
+}
+\value{
+Ordered \code{\link{factor}}
+}
+\description{
+Splits ages into groups defined by the \code{split} parameter.
+}
+\details{
+To split ages, the input can be:
+\itemize{
+  \item{A numeric vector. A vector of \code{c(10, 20)} will split on 0-9, 10-19 and 20+. A value of only \code{50} will split on 0-49 and 50+.
+        The default is to split on young children (0-11), youth (12-24), young adults (26-54), middle-aged adults (55-74) and elderly (75+).}
+  \item{A character:}
+    \itemize{
+      \item{\code{"children"}, 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, 95)}. This will split on 0-64, 65-74, 75-84, 85-94 and 95+.}
+      \item{\code{"fives"}, equivalent: of \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, 15-19 and so forth.}
+      \item{\code{"tens"}, equivalent: of \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29 and so forth.}
+    }
+}
+}
+\examples{
+ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
+
+# split on 0-49 and 50+
+age_groups(ages, 50)
+
+# split on 0-20, 21-49 and 50+
+age_groups(ages, c(21, 50))
+
+# split on every ten years
+age_groups(ages, 1:10 * 10)
+age_groups(ages, "tens")
+
+# split on every five years
+age_groups(ages, 1:20 * 5)
+age_groups(ages, "fives")
+
+# split on children
+age_groups(ages, "children")
+
+# resistance of ciprofloxacine per age group
+septic_patients \%>\%
+  mutate(first_isolate = first_isolate(.)) \%>\%
+  filter(first_isolate == TRUE,
+         mo == as.mo("E. coli")) \%>\%
+  group_by(age_group = age_groups(age)) \%>\%
+  select(age_group,
+         cipr) \%>\%
+  ggplot_rsi(x = "age_group")
+}
+\seealso{
+age
+}

man/ggplot_rsi.Rd

@@ -114,6 +114,17 @@ septic_patients \%>\%
              size = 1,
              linetype = 2,
              alpha = 0.25)
+
+# resistance of ciprofloxacine per age group
+septic_patients \%>\%
+  mutate(first_isolate = first_isolate(.)) \%>\%
+  filter(first_isolate == TRUE,
+         mo == as.mo("E. coli")) \%>\%
+  # `age_group` is also a function of this package:
+  group_by(age_group = age_groups(age)) \%>\%
+  select(age_group,
+         cipr) \%>\%
+  ggplot_rsi(x = "age_group")
 \donttest{
 
 # for colourblind mode, use divergent colours from the viridis package: