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include IQR and MAD in freq

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dr. M.S. (Matthijs) Berends
2018-07-03 11:30:40 +02:00
parent 3d0d21f322
commit 10fce8382c
8 changed files with 110 additions and 163 deletions
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50
man/freq.Rd
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@ -4,6 +4,7 @@
\alias{freq}
\alias{frequency_tbl}
\alias{top_freq}
\alias{print.frequency_tbl}
\title{Frequency table}
\usage{
frequency_tbl(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
@ -15,17 +16,20 @@ freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
sep = " ")
top_freq(f, n)
\method{print}{frequency_tbl}(x, nmax = getOption("max.print.freq", default =
15), ...)
}
\arguments{
\item{x}{vector with items, or \code{data.frame}}
\item{x}{vector with items, or a \code{data.frame}}
\item{...}{up to nine different columns of \code{x} to calculate frequencies from, see Examples}
\item{sort.count}{sort on count, i.e. frequencies. Use \code{FALSE} to sort alphabetically on item.}
\item{sort.count}{sort on count, i.e. frequencies. This will be \code{TRUE} at default for everything except for factors.}
\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0}, \code{nmax = NULL} or \code{nmax = NA} to print all rows.}
\item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0}, \code{nmax = Inf}, \code{nmax = NULL} 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{na.rm}{a logical value indicating whether \code{NA} values should be removed from the frequency table. The header will always print the amount of \code{NA}s.}
\item{row.names}{a logical value indicating whether row indices should be printed as \code{1:nrow(x)}}
@ -46,25 +50,28 @@ A \code{data.frame} with an additional class \code{"frequency_tbl"}
Create a frequency table of a vector with items or a data frame. Supports quasiquotation and markdown for reports. \code{top_freq} can be used to get the top/bottom \emph{n} items of a frequency table, with counts as names.
}
\details{
This package also has a vignette available about this function, run: \code{browseVignettes("AMR")} to read it.
Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the `freq` function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. This package also has a vignette available to explain the use of this function further, run \code{browseVignettes("AMR")} to read it.
For numeric values of any class, these additional values will be calculated and shown into the header:
For numeric values of any class, these additional values will all be calculated with \code{na.rm = TRUE} 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}
\item{Standard Deviation, using \code{\link[stats]{sd}}}
\item{Coefficient of Variation (CV), the standard deviation divided by the mean}
\item{Mean Absolute Deviation (MAD), using \code{\link[stats]{mad}}}
\item{Tukey Five-Number Summaries (minimum, Q1, median, Q3, maximum), using \code{\link[stats]{fivenum}}}
\item{Interquartile Range (IQR) calculated as \code{Q3 - Q1} using the Tukey Five-Number Summaries, i.e. \strong{not} using the \code{\link[stats]{quantile}} function}
\item{Coefficient of Quartile Variation (CQV, sometimes called coefficient of dispersion), calculated as \code{(Q3 - Q1) / (Q3 + Q1)} using the Tukey Five-Number Summaries}
\item{Outliers (total count and unique count), using \code{\link[grDevices]{boxplot.stats}}}
}
For dates and times of any class, these additional values will be calculated and shown into the header:
For dates and times of any class, these additional values will be calculated with \code{na.rm = TRUE} and shown into the header:
\itemize{
\item{Oldest, using \code{\link[base]{min}}}
\item{Newest, using \code{\link[base]{max}}, with difference between newest and oldest}
\item{Median, using \code{\link[stats]{median}}, with percentage since oldest}
}
The function \code{top_freq} uses \code{\link[dplyr]{top_n}} internally and will include more than \code{n} rows if there are ties.
}
\examples{
@ -95,17 +102,24 @@ septic_patients \%>\%
filter(hospital_id == "A") \%>\%
freq(genus, species)
# save frequency table to an object
years <- septic_patients \%>\%
mutate(year = format(date, "\%Y")) \%>\%
freq(year)
years \%>\% pull(item)
# get top 10 bugs of hospital A as a vector
septic_patients \%>\%
filter(hospital_id == "A") \%>\%
freq(bactid) \%>\%
top_freq(10)
# save frequency table to an object
years <- septic_patients \%>\%
mutate(year = format(date, "\%Y")) \%>\%
freq(year)
# print only top 5
years \%>\% print(nmax = 5)
# transform to plain data.frame
septic_patients \%>\%
freq(age) \%>\%
as.data.frame()
}
\keyword{freq}
\keyword{frequency}

11
man/print.Rd
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@ -1,15 +1,12 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/freq.R, R/print.R
\name{print.frequency_tbl}
\alias{print.frequency_tbl}
% Please edit documentation in R/print.R
\name{print}
\alias{print}
\alias{print.tbl_df}
\alias{print.tbl}
\alias{print.data.table}
\title{Printing Data Tables and Tibbles}
\usage{
\method{print}{frequency_tbl}(x, ...)
\method{print}{tbl_df}(x, nmax = 10, header = TRUE, row.names = TRUE,
right = FALSE, width = 1, na = "<NA>", ...)
@ -20,8 +17,6 @@
\arguments{
\item{x}{object of class \code{data.frame}.}
\item{...}{optional arguments to \code{print} or \code{plot} methods.}
\item{nmax}{amount of rows to print in total. When the total amount of rows exceeds this limit, the first and last \code{nmax / 2} rows will be printed. Use \code{nmax = NA} to print all rows.}
\item{header}{print header with information about data size and tibble grouping}
@ -36,6 +31,8 @@
\item{na}{value to print instead of NA}
\item{...}{optional arguments to \code{print} or \code{plot} methods.}
\item{print.keys}{print keys for \code{data.table}}
}
\description{