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AMR
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support format.freq

This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-07-16 16:41:48 +02:00
parent 6eaf33baf3
commit 715a7630ca
7 changed files with 113 additions and 18 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.2.0.9011
Date: 2018-07-15
Version: 0.2.0.9012
Date: 2018-07-16
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

6
NAMESPACE
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@ -8,6 +8,7 @@ S3method(as.vector,frequency_tbl)
S3method(as_tibble,frequency_tbl)
S3method(barplot,mic)
S3method(barplot,rsi)
S3method(format,frequency_tbl)
S3method(hist,frequency_tbl)
S3method(kurtosis,data.frame)
S3method(kurtosis,default)
@ -74,6 +75,7 @@ exportMethods(as.vector.frequency_tbl)
exportMethods(as_tibble.frequency_tbl)
exportMethods(barplot.mic)
exportMethods(barplot.rsi)
exportMethods(format.frequency_tbl)
exportMethods(hist.frequency_tbl)
exportMethods(kurtosis)
exportMethods(kurtosis.data.frame)
@ -97,12 +99,15 @@ importFrom(clipr,read_clip_tbl)
importFrom(clipr,write_clip)
importFrom(curl,nslookup)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_vars)
importFrom(dplyr,any_vars)
importFrom(dplyr,arrange)
importFrom(dplyr,arrange_at)
importFrom(dplyr,as_tibble)
importFrom(dplyr,between)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,filter_at)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,if_else)
@ -118,6 +123,7 @@ importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
importFrom(dplyr,top_n)
importFrom(dplyr,vars)
importFrom(grDevices,boxplot.stats)
importFrom(graphics,axis)
importFrom(graphics,barplot)

2
NEWS.md
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@ -14,7 +14,7 @@ ratio(c(772, 1611, 737), ratio = "1:2:1")
* A vignette to explain its usage
* Support for `table` to use as input: `freq(table(x, y))`
* Support for existing functions `hist` and `plot` to use a frequency table as input: `hist(freq(df$age))`
* Support for `as.vector`, `as.data.frame` and `as_tibble`
* Support for `as.vector`, `as.data.frame`, `as_tibble` and `format`
* Support for quasiquotation: `freq(mydata, mycolumn)` is the same as `mydata %>% freq(mycolumn)`
* Function `top_freq` function to return the top/below *n* items as vector
* Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)

27
R/clipboard.R
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@ -7,6 +7,7 @@
#' This also supports automatic column type transformation, with AMR classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
#' @rdname clipboard
#' @name clipboard
#' @inheritParams base::data.frame
#' @inheritParams utils::read.table
#' @inheritParams utils::write.table
#' @inheritParams readr::locale
@ -20,6 +21,10 @@
#' @importFrom utils read.delim write.table object.size
#' @importFrom readr parse_guess locale
#' @details
#' The parameter \code{stringsAsFactors} defaults to \code{FALSE}, as opposed to most base \R methods.
#'
#' The parameters \code{date_format} and \code{time_format} also support generic date and time formats like \code{"dd-mm-yyyy"} like Excel.
#'
#' \if{html}{
#' \strong{Example for copying from Excel:}
#' \out{<div style="text-align: left">}\figure{clipboard_copy.png}\out{</div>}
@ -36,10 +41,27 @@
#' \out{<div style="text-align: left">}\figure{clipboard_rsi.png}\out{</div>}
#' }
#' @export
#' @examples
#' \dontrun{
#'
#' df1 <- data.frame(a = letters[1:12],
#' b = runif(n = 12, min = 1000, max = 2000),
#' stringsAsFactors = FALSE)
#' clipboard_export(df1)
#' df2 <- clipboard_import()
#' identical(df1, df2)
#'
#' # send frequency table to clipboard (e.g. for pasting in Excel)
#' septic_patients %>%
#' freq(age) %>%
#' format() %>% # this will format the percentages
#' clipboard_export()
#' }
clipboard_import <- function(sep = '\t',
header = TRUE,
dec = ".",
na = c("", "NA", "NULL"),
stringsAsFactors = FALSE,
startrow = 1,
as_vector = TRUE,
guess_col_types = TRUE,
@ -58,7 +80,7 @@ clipboard_import <- function(sep = '\t',
dec = dec,
na.strings = na,
encoding = 'UTF-8',
stringsAsFactors = FALSE)
stringsAsFactors = stringsAsFactors)
# use tibble, so column types will be translated correctly
import_tbl <- as_tibble(import_tbl)
@ -91,6 +113,9 @@ clipboard_import <- function(sep = '\t',
import_tbl <- import_tbl %>% pull(1)
}
# and transform back to data.frame
import_tbl <- as.data.frame(import_tbl, stringsAsFactors = stringsAsFactors)
if (info == TRUE) {
cat("Successfully imported from clipboard:", NROW(import_tbl), "obs. of", NCOL(import_tbl), "variables.\n")
}

37
R/freq.R
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@ -100,10 +100,13 @@
#' # show only the top 5
#' years %>% print(nmax = 5)
#'
#' # save to an object with formatted percentages
#' years <- format(years)
#'
#' # print a histogram of numeric values
#' septic_patients %>%
#' freq(age) %>%
#' hist() # prettier: ggplot(septic_patients, aes(age)) + geom_histogram()
#' hist() # prettier: ggplot(septic_patients, aes(age)) + geom_histogram()
#'
#' # or print all points to a regular plot
#' septic_patients %>%
@ -124,13 +127,20 @@
#' freq(age) %>%
#' as.vector() %>%
#' sort(),
#' sort(septic_patients$age)
#' ) # TRUE
#' sort(septic_patients$age)) # TRUE
#'
#' # also supports table:
#' # it also supports `table` objects:
#' table(septic_patients$sex,
#' septic_patients$age) %>%
#' freq()
#' freq(sep = " **sep** ")
#'
#' \dontrun{
#' # send frequency table to clipboard (e.g. for pasting in Excel)
#' septic_patients %>%
#' freq(age) %>%
#' format() %>% # this will format the percentages
#' clipboard_export()
#' }
frequency_tbl <- function(x,
...,
sort.count = TRUE,
@ -603,3 +613,20 @@ plot.frequency_tbl <- function(x, y, ...) {
as.vector.frequency_tbl <- function(x, mode = "any") {
as.vector(rep(x$item, x$count), mode = mode)
}
#' @noRd
#' @exportMethod format.frequency_tbl
#' @export
format.frequency_tbl <- function(x, digits = 1, ...) {
opt <- attr(x, 'opt')
if (opt$nmax.set == TRUE) {
nmax <- opt$nmax
} else {
nmax <- getOption("max.print.freq", default = 15)
}
x <- x[1:nmax,]
x$percent <- percent(x$percent, round = digits, force_zero = TRUE)
x$cum_percent <- percent(x$cum_percent, round = digits, force_zero = TRUE)
base::format.data.frame(x, ...)
}

35
man/clipboard.Rd
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@ -7,9 +7,10 @@
\title{Import/export from clipboard}
\usage{
clipboard_import(sep = "\\t", header = TRUE, dec = ".", na = c("", "NA",
"NULL"), startrow = 1, as_vector = TRUE, guess_col_types = TRUE,
date_names = "en", date_format = "\%Y-\%m-\%d", time_format = "\%H:\%M",
tz = Sys.timezone(), encoding = "UTF-8", info = TRUE)
"NULL"), stringsAsFactors = FALSE, startrow = 1, as_vector = TRUE,
guess_col_types = TRUE, date_names = "en", date_format = "\%Y-\%m-\%d",
time_format = "\%H:\%M", tz = Sys.timezone(), encoding = "UTF-8",
info = TRUE)
clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
info = TRUE)
@ -30,6 +31,11 @@ clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
\item{na}{the string to use for missing values in the data.}
\item{stringsAsFactors}{logical: should character vectors be converted
to factors? The \sQuote{factory-fresh} default is \code{TRUE}, but
this can be changed by setting \code{\link{options}(stringsAsFactors
= FALSE)}.}
\item{startrow}{\emph{n}th row to start importing from. When \code{header = TRUE}, the import will start on row \code{startrow} \emph{below} the header.}
\item{as_vector}{a logical value indicating whether data consisting of only one column should be imported as vector using \code{\link[dplyr]{pull}}. This will strip off the header.}
@ -80,7 +86,11 @@ The data will be read and written as tab-separated by default, which makes it po
This also supports automatic column type transformation, with AMR classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
}
\details{
\if{html}{
The parameter \code{stringsAsFactors} defaults to \code{FALSE}, as opposed to most base \R methods.
The parameters \code{date_format} and \code{time_format} also support generic date and time formats like \code{"dd-mm-yyyy"} like Excel.
\if{html}{
\strong{Example for copying from Excel:}
\out{<div style="text-align: left">}\figure{clipboard_copy.png}\out{</div>}
\cr
@ -96,6 +106,23 @@ This also supports automatic column type transformation, with AMR classes \code{
\out{<div style="text-align: left">}\figure{clipboard_rsi.png}\out{</div>}
}
}
\examples{
\dontrun{
df1 <- data.frame(a = letters[1:12],
b = runif(n = 12, min = 1000, max = 2000),
stringsAsFactors = FALSE)
clipboard_export(df1)
df2 <- clipboard_import()
identical(df1, df2)
# send frequency table to clipboard (e.g. for pasting in Excel)
septic_patients \%>\%
freq(age) \%>\%
format() \%>\% # this will format the percentages
clipboard_export()
}
}
\keyword{clipboard}
\keyword{clipboard_export}
\keyword{clipboard_import}

20
man/freq.Rd
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@ -111,10 +111,13 @@ years <- septic_patients \%>\%
# show only the top 5
years \%>\% print(nmax = 5)
# save to an object with formatted percentages
years <- format(years)
# print a histogram of numeric values
septic_patients \%>\%
freq(age) \%>\%
hist() # prettier: ggplot(septic_patients, aes(age)) + geom_histogram()
hist() # prettier: ggplot(septic_patients, aes(age)) + geom_histogram()
# or print all points to a regular plot
septic_patients \%>\%
@ -135,13 +138,20 @@ identical(septic_patients \%>\%
freq(age) \%>\%
as.vector() \%>\%
sort(),
sort(septic_patients$age)
) # TRUE
sort(septic_patients$age)) # TRUE
# also supports table:
# it also supports `table` objects:
table(septic_patients$sex,
septic_patients$age) \%>\%
freq()
freq(sep = " **sep** ")
\dontrun{
# send frequency table to clipboard (e.g. for pasting in Excel)
septic_patients \%>\%
freq(age) \%>\%
format() \%>\% # this will format the percentages
clipboard_export()
}
}
\keyword{freq}
\keyword{frequency}