mirror of https://github.com/msberends/AMR.git
74 lines
2.7 KiB
R
Executable File
74 lines
2.7 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/freq.R
|
|
\name{freq}
|
|
\alias{freq}
|
|
\alias{frequency_tbl}
|
|
\title{Frequency table}
|
|
\usage{
|
|
freq(x, sort.count = TRUE, nmax = getOption("max.print.freq"),
|
|
na.rm = TRUE, markdown = FALSE, as.data.frame = FALSE, digits = 2,
|
|
sep = " ")
|
|
|
|
frequency_tbl(x, sort.count = TRUE, nmax = getOption("max.print.freq"),
|
|
na.rm = TRUE, markdown = FALSE, as.data.frame = FALSE, digits = 2,
|
|
sep = " ")
|
|
}
|
|
\arguments{
|
|
\item{x}{data}
|
|
|
|
\item{sort.count}{Sort on count. Use \code{FALSE} to sort alphabetically on item.}
|
|
|
|
\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.}
|
|
|
|
\item{na.rm}{a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of \code{NA}s.}
|
|
|
|
\item{markdown}{print table in markdown format (this forces \code{nmax = NA})}
|
|
|
|
\item{as.data.frame}{return frequency table without header as a \code{data.frame} (e.g. to assign the table to an object)}
|
|
|
|
\item{digits}{how many significant digits are to be used for numeric values (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
|
|
|
|
\item{sep}{a character string to separate the terms when selecting multiple columns}
|
|
}
|
|
\description{
|
|
Create a frequency table of a vector of data, a single column or a maximum of 9 columns of a data frame. Supports markdown for reports.
|
|
}
|
|
\details{
|
|
For numeric values, the next values will be calculated and shown into the header:
|
|
\itemize{
|
|
\item{Mean, using \code{\link[base]{mean}}}
|
|
\item{Standard deviation, using \code{\link[stats]{sd}}}
|
|
\item{Five numbers of Tukey (min, Q1, median, Q3, max), using \code{\link[stats]{fivenum}}}
|
|
\item{Outliers (total count and unique count), using \code{\link{boxplot.stats}}}
|
|
\item{Coefficient of variation (CV), the standard deviation divided by the mean}
|
|
\item{Coefficient of quartile variation (CQV, sometimes called coefficient of dispersion), calculated as \code{(Q3 - Q1) / (Q3 + Q1)} using \code{\link{quantile}} with \code{type = 6} as quantile algorithm to comply with SPSS standards}
|
|
}
|
|
}
|
|
\examples{
|
|
library(dplyr)
|
|
|
|
freq(septic_patients$hospital_id)
|
|
|
|
septic_patients \%>\%
|
|
filter(hospital_id == "A") \%>\%
|
|
select(bactid) \%>\%
|
|
freq()
|
|
|
|
# select multiple columns; they will be pasted together
|
|
septic_patients \%>\%
|
|
left_join_microorganisms \%>\%
|
|
filter(hospital_id == "A") \%>\%
|
|
select(genus, species) \%>\%
|
|
freq()
|
|
|
|
# save frequency table to an object
|
|
years <- septic_patients \%>\%
|
|
mutate(year = format(date, "\%Y")) \%>\%
|
|
select(year) \%>\%
|
|
freq(as.data.frame = TRUE)
|
|
}
|
|
\keyword{freq}
|
|
\keyword{frequency}
|
|
\keyword{summarise}
|
|
\keyword{summary}
|