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breaks param, tidyr dep change, freq markdown

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dr. M.S. (Matthijs) Berends
2018-10-22 12:32:59 +02:00
parent ec15b82fd6
commit c2a93b46db
11 changed files with 86 additions and 146 deletions
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1
man/as.atc.Rd
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@ -33,6 +33,7 @@ In the ATC classification system, the active substances are classified in a hier
as.atc("J01FA01")
as.atc("Erythromycin")
as.atc("eryt")
as.atc(" eryt 123")
as.atc("ERYT")
as.atc("ERY")
as.atc("Erythrocin") # Trade name

26
man/freq.Rd
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@ -9,12 +9,12 @@
\usage{
frequency_tbl(x, ..., sort.count = TRUE,
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
markdown = FALSE, digits = 2, quote = FALSE, header = !markdown,
sep = " ")
markdown = !interactive(), digits = 2, quote = FALSE,
header = !markdown, sep = " ")
freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
na.rm = TRUE, row.names = TRUE, markdown = FALSE, digits = 2,
quote = FALSE, header = !markdown, sep = " ")
na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
digits = 2, quote = FALSE, header = !markdown, sep = " ")
top_freq(f, n)
@ -30,13 +30,13 @@ top_freq(f, n)
\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 \code{NA} values should be removed from the frequency table. The header_txt 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)}}
\item{markdown}{print table in markdown format (this forces \code{nmax = NA})}
\item{markdown}{a logical value indicating whether the frequency table should be printed in markdown format. This will print all rows and is default behaviour in non-interactive R sessions (like when knitting RMarkdown files).}
\item{digits}{how many significant digits are to be used for numeric values in the header_txt (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
\item{digits}{how many significant digits are to be used for numeric values in the header (not for the items themselves, that depends on \code{\link{getOption}("digits")})}
\item{quote}{a logical value indicating whether or not strings should be printed with surrounding quotes}
@ -57,7 +57,7 @@ Create a frequency table of a vector with items or a data frame. Supports quasiq
\details{
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 all be calculated with \code{na.rm = TRUE} and shown into the header_txt:
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}}}
@ -69,7 +69,7 @@ For numeric values of any class, these additional values will all be calculated
\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 with \code{na.rm = TRUE} and shown into the header_txt:
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{min}}}
\item{Newest, using \code{\link{max}}, with difference between newest and oldest}
@ -153,14 +153,6 @@ table(septic_patients$gender,
# check differences between frequency tables
diff(freq(septic_patients$trim),
freq(septic_patients$trsu))
\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}

11
man/ggplot_rsi.Rd
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@ -11,9 +11,10 @@
\title{AMR bar plots with \code{ggplot}}
\usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, translate_ab = "official",
fun = count_df, nrow = NULL, datalabels = TRUE,
datalabels.size = 3, datalabels.colour = "grey15", ...)
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
translate_ab = "official", fun = count_df, nrow = NULL,
datalabels = TRUE, datalabels.size = 3,
datalabels.colour = "grey15", ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
fill = "Interpretation", translate_ab = "official", fun = count_df,
@ -21,7 +22,7 @@ geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
scale_y_percent()
scale_y_percent(breaks = seq(0, 1, 0.1))
scale_rsi_colours()
@ -41,6 +42,8 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
\item{facet}{variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable}
\item{breaks}{numeric vector of positions}
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.}
\item{fun}{function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}}