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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 18:46:11 +01:00

breaks param, tidyr dep change, freq markdown

This commit is contained in:
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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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.4.0.9005 Version: 0.4.0.9006
Date: 2018-10-19 Date: 2018-10-22
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(
@ -38,10 +38,9 @@ Authors@R: c(
email = "b.sinha@umcg.nl", email = "b.sinha@umcg.nl",
role = "ths", role = "ths",
comment = c(ORCID = "0000-0003-1634-0010"))) comment = c(ORCID = "0000-0003-1634-0010")))
Description: Functions to simplify the analysis of Antimicrobial Resistance (AMR) Description: Functions to simplify the analysis and prediction of Antimicrobial
of microbial isolates, by using new S3 classes and applying EUCAST expert rules Resistance (AMR) and work with microbial and antimicrobial properties by using
on antibiograms according to Leclercq (2013) evidence-based methods.
<doi:10.1111/j.1469-0691.2011.03703.x>.
Depends: Depends:
R (>= 3.1.0) R (>= 3.1.0)
Imports: Imports:
@ -54,14 +53,14 @@ Imports:
knitr (>= 1.0.0), knitr (>= 1.0.0),
rlang (>= 0.2.0), rlang (>= 0.2.0),
rvest (>= 0.3.2), rvest (>= 0.3.2),
tidyr (>= 0.7.0),
xml2 (>= 1.0.0) xml2 (>= 1.0.0)
Suggests: Suggests:
covr (>= 3.0.1), covr (>= 3.0.1),
ggplot2, ggplot2,
rmarkdown, rmarkdown,
rstudioapi, rstudioapi,
testthat (>= 1.0.2), testthat (>= 1.0.2)
tidyr
VignetteBuilder: knitr VignetteBuilder: knitr
URL: https://github.com/msberends/AMR URL: https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues BugReports: https://github.com/msberends/AMR/issues

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@ -17,25 +17,29 @@
* Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met * Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met
* Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion` * Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion`
* Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum` * Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum`
* Functions `as.mo`, `as.rsi` and `as.mic` will not set package name as attribute anymore * Functions `as.mo`, `as.rsi`, `as.mic` and `as.atc` will not set package name as attribute anymore
* Data set `septic_patients` is now a `data.frame`, not a tibble anymore * Data set `septic_patients` is now a `data.frame`, not a tibble anymore
* Check for `hms::is.hms` in frequency tables (`freq()`) * Check for `hms::is.hms` in frequency tables (`freq()`)
* New parameter `header` for frequency tables to turn them off (default when `markdown = TRUE`) * New parameter `header` for frequency tables to turn them off (default when `markdown = TRUE`)
* Freq now prints in markdown at default in non-interactive sessions
* Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters * Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
* Fix for `mo_property` not working properly * Fix for `mo_property` not working properly
* Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5 * Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
* Support for class `difftime` in frequency tables * Support for class `difftime` in frequency tables
* Support for named vectors of class `mo`, useful for `top_freq()` * Support for named vectors of class `mo`, useful for `top_freq()`
* `ggplot_rsi` and `scale_y_percent` have `breaks` parameter
* AI improvements for `as.mo`: * AI improvements for `as.mo`:
* `"CRS"` -> *Stenotrophomonas maltophilia* * `"CRS"` -> *Stenotrophomonas maltophilia*
* `"CRSM"` -> *Stenotrophomonas maltophilia* * `"CRSM"` -> *Stenotrophomonas maltophilia*
* `"MSSA"` -> *Staphylococcus aureus* * `"MSSA"` -> *Staphylococcus aureus*
* `"MSSE"` -> *Staphylococcus epidermidis* * `"MSSE"` -> *Staphylococcus epidermidis*
* Fix for `join` functions * Fix for `join` functions
* In `g.test`, when `sum(x)` is below 1000, suggest Fisher's Exact Test * In `g.test`, when `sum(x)` is below 1000 or any of the expected values is below 5, Fisher's Exact Test will be suggested
* `ab_name` will try to fall back on `as.atc` when no results are found
#### Other #### Other
* New dependency on package `crayon`, to support formatted text in the console * New dependency on package `crayon`, to support formatted text in the console
* Dependency `tidyr` is now mandatory (went to `Import` field) since `portion_df` and `count_df` rely on it
* Updated vignettes to comply with README * Updated vignettes to comply with README

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@ -133,18 +133,19 @@ abname <- function(abcode,
abcode[i] <- abx[which(abx[,from] == abcode[i]),] %>% pull(to) %>% .[1] abcode[i] <- abx[which(abx[,from] == abcode[i]),] %>% pull(to) %>% .[1]
} }
# when nothing found, try first chars of official name
# if (is.na(abcode[i])) {
# abcode[i] <- antibiotics %>%
# filter(official %like% paste0('^', abcode.bak[i])) %>%
# pull(to) %>%
# .[1]
# next
# }
if (is.na(abcode[i]) | length(abcode[i] == 0)) { if (is.na(abcode[i]) | length(abcode[i] == 0)) {
abcode[i] <- abcode.bak[i] # try as.atc
warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE) try(suppressWarnings(
abcode[i] <- as.atc(abcode[i])
), silent = TRUE)
if (is.na(abcode[i])) {
# still not found
abcode[i] <- abcode.bak[i]
warning('Code "', abcode.bak[i], '" not found in antibiotics list.', call. = FALSE)
} else {
# fill in the found ATC code
abcode[i] <- abname(abcode[i], from = "atc", to = to)
}
} }
} }

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@ -37,6 +37,7 @@
#' as.atc("J01FA01") #' as.atc("J01FA01")
#' as.atc("Erythromycin") #' as.atc("Erythromycin")
#' as.atc("eryt") #' as.atc("eryt")
#' as.atc(" eryt 123")
#' as.atc("ERYT") #' as.atc("ERYT")
#' as.atc("ERY") #' as.atc("ERY")
#' as.atc("Erythrocin") # Trade name #' as.atc("Erythrocin") # Trade name
@ -50,6 +51,10 @@
as.atc <- function(x) { as.atc <- function(x) {
x.new <- rep(NA_character_, length(x)) x.new <- rep(NA_character_, length(x))
x <- trimws(x, which = "both")
# keep only a-z when it's not an ATC code
x[!x %like% "[A-Z][0-9]{2}[A-Z]{2}[0-9]{2}"] <- gsub("[^a-zA-Z]+", "", x[!x %like% "[A-Z][0-9]{2}[A-Z]{2}[0-9]{2}"])
x.bak <- x x.bak <- x
x <- unique(x[!is.na(x)]) x <- unique(x[!is.na(x)])
failures <- character(0) failures <- character(0)
@ -64,7 +69,7 @@ as.atc <- function(x) {
x.new[is.na(x.new) & x.bak == x[i]] <- found[1L] x.new[is.na(x.new) & x.bak == x[i]] <- found[1L]
} }
# try ATC in code form, even if it does not exist in the antibiotics data set YET # try ATC in ATC code form, even if it does not exist in the antibiotics data set YET
if (length(found) == 0 & x[i] %like% '[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]') { if (length(found) == 0 & x[i] %like% '[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]') {
warning("ATC code ", x[i], " is not yet in the `antibiotics` data set.") warning("ATC code ", x[i], " is not yet in the `antibiotics` data set.")
fail <- FALSE fail <- FALSE
@ -134,7 +139,6 @@ as.atc <- function(x) {
call. = FALSE) call. = FALSE)
} }
class(x.new) <- "atc" class(x.new) <- "atc"
attr(x.new, 'package') <- 'AMR'
x.new x.new
} }

111
R/freq.R
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@ -23,10 +23,10 @@
#' @param ... up to nine different columns of \code{x} when \code{x} is a \code{data.frame} or \code{tibble}, to calculate frequencies from - see Examples #' @param ... up to nine different columns of \code{x} when \code{x} is a \code{data.frame} or \code{tibble}, to calculate frequencies from - see Examples
#' @param sort.count sort on count, i.e. frequencies. This will be \code{TRUE} at default for everything except for factors. #' @param sort.count sort on count, i.e. frequencies. This will be \code{TRUE} at default for everything except for factors.
#' @param 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. #' @param 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.
#' @param 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. #' @param 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.
#' @param row.names a logical value indicating whether row indices should be printed as \code{1:nrow(x)} #' @param row.names a logical value indicating whether row indices should be printed as \code{1:nrow(x)}
#' @param markdown print table in markdown format (this forces \code{nmax = NA}) #' @param 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).
#' @param 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")}) #' @param 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")})
#' @param quote a logical value indicating whether or not strings should be printed with surrounding quotes #' @param quote a logical value indicating whether or not strings should be printed with surrounding quotes
#' @param header a logical value indicating whether an informative header should be printed #' @param header a logical value indicating whether an informative header should be printed
#' @param sep a character string to separate the terms when selecting multiple columns #' @param sep a character string to separate the terms when selecting multiple columns
@ -34,7 +34,7 @@
#' @param n number of top \emph{n} items to return, use -n for the bottom \emph{n} items. It will include more than \code{n} rows if there are ties. #' @param n number of top \emph{n} items to return, use -n for the bottom \emph{n} items. It will include more than \code{n} rows if there are ties.
#' @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. #' @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{ #' \itemize{
#' \item{Mean, using \code{\link[base]{mean}}} #' \item{Mean, using \code{\link[base]{mean}}}
#' \item{Standard Deviation, using \code{\link[stats]{sd}}} #' \item{Standard Deviation, using \code{\link[stats]{sd}}}
@ -46,7 +46,7 @@
#' \item{Outliers (total count and unique count), using \code{\link[grDevices]{boxplot.stats}}} #' \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{ #' \itemize{
#' \item{Oldest, using \code{\link{min}}} #' \item{Oldest, using \code{\link{min}}}
#' \item{Newest, using \code{\link{max}}, with difference between newest and oldest} #' \item{Newest, using \code{\link{max}}, with difference between newest and oldest}
@ -140,21 +140,13 @@
#' # check differences between frequency tables #' # check differences between frequency tables
#' diff(freq(septic_patients$trim), #' diff(freq(septic_patients$trim),
#' freq(septic_patients$trsu)) #' freq(septic_patients$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()
#' }
frequency_tbl <- function(x, frequency_tbl <- function(x,
..., ...,
sort.count = TRUE, sort.count = TRUE,
nmax = getOption("max.print.freq"), nmax = getOption("max.print.freq"),
na.rm = TRUE, na.rm = TRUE,
row.names = TRUE, row.names = TRUE,
markdown = FALSE, markdown = !interactive(),
digits = 2, digits = 2,
quote = FALSE, quote = FALSE,
header = !markdown, header = !markdown,
@ -201,17 +193,14 @@ frequency_tbl <- function(x,
cols <- NULL cols <- NULL
} }
} else if (any(class(x) == 'table')) { } else if (any(class(x) == 'table')) {
if (!"tidyr" %in% rownames(installed.packages())) { x <- as.data.frame(x, stringsAsFactors = FALSE)
stop('transformation from `table` to frequency table requires the tidyr package.', call. = FALSE) # now this DF contains 3 columns: the 2 vars and a Freq column
} # paste the first 2 cols and repeat them Freq times:
x <- x %>% x <- rep(x = do.call(paste, c(x[colnames(x)[1:2]], sep = sep)),
as.data.frame(stringsAsFactors = FALSE) %>% times = x$Freq)
# paste first two columns
tidyr::unite(col = "Pasted", 1:2, sep = sep, remove = TRUE)
x <- rep(x %>% pull(Pasted), x %>% pull(Freq))
x.name <- "a `table` object" x.name <- "a `table` object"
cols <- NULL cols <- NULL
mult.columns <- 2 #mult.columns <- 2
} else { } else {
x.name <- NULL x.name <- NULL
cols <- NULL cols <- NULL
@ -221,74 +210,8 @@ frequency_tbl <- function(x,
if (ncol(x) == 1 & any(class(x) == 'data.frame')) { if (ncol(x) == 1 & any(class(x) == 'data.frame')) {
x <- x %>% pull(1) x <- x %>% pull(1)
} else if (ncol(x) < 10) { } else if (ncol(x) < 10) {
mult.columns <- ncol(x) mult.columns <- ncol(x)
x <- do.call(paste, c(x[colnames(x)], sep = sep))
colnames(x) <- LETTERS[1:ncol(x)]
if (ncol(x) == 2) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
sep = sep)
} else if (ncol(x) == 3) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
sep = sep)
} else if (ncol(x) == 4) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
x$D %>% as.character(),
sep = sep)
} else if (ncol(x) == 5) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
x$D %>% as.character(),
x$E %>% as.character(),
sep = sep)
} else if (ncol(x) == 6) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
x$D %>% as.character(),
x$E %>% as.character(),
x$F %>% as.character(),
sep = sep)
} else if (ncol(x) == 7) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
x$D %>% as.character(),
x$E %>% as.character(),
x$F %>% as.character(),
x$G %>% as.character(),
sep = sep)
} else if (ncol(x) == 8) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
x$D %>% as.character(),
x$E %>% as.character(),
x$F %>% as.character(),
x$G %>% as.character(),
x$H %>% as.character(),
sep = sep)
} else if (ncol(x) == 9) {
x$total <- paste(x$A %>% as.character(),
x$B %>% as.character(),
x$C %>% as.character(),
x$D %>% as.character(),
x$E %>% as.character(),
x$F %>% as.character(),
x$G %>% as.character(),
x$H %>% as.character(),
x$I %>% as.character(),
sep = sep)
}
x <- x$total
} else { } else {
stop('A maximum of 9 columns can be analysed at the same time.', call. = FALSE) stop('A maximum of 9 columns can be analysed at the same time.', call. = FALSE)
} }
@ -585,7 +508,7 @@ diff.frequency_tbl <- function(x, y, ...) {
#' @exportMethod print.frequency_tbl #' @exportMethod print.frequency_tbl
#' @importFrom knitr kable #' @importFrom knitr kable
#' @importFrom dplyr n_distinct #' @importFrom dplyr n_distinct
#' @importFrom crayon bold #' @importFrom crayon bold silver
#' @export #' @export
print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default = 15), ...) { print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default = 15), ...) {
@ -629,6 +552,9 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
if (!is.null(opt$header_txt)) { if (!is.null(opt$header_txt)) {
cat(opt$header_txt) cat(opt$header_txt)
} }
} else if (opt$tbl_format == "markdown") {
# do print title as caption in markdown
cat("\n", title, sep = "")
} }
if (NROW(x) == 0) { if (NROW(x) == 0) {
@ -671,6 +597,9 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
' (', ' (',
(x.unprinted / (x.unprinted + x.printed)) %>% percent(force_zero = TRUE), (x.unprinted / (x.unprinted + x.printed)) %>% percent(force_zero = TRUE),
') ]\n', sep = '') ') ]\n', sep = '')
if (opt$tbl_format == "pandoc") {
footer <- silver(footer) # only silver in regular printing
}
} else { } else {
footer <- NULL footer <- NULL
} }

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@ -23,6 +23,7 @@
#' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} #' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable #' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable #' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
#' @param breaks numeric vector of positions
#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable #' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
#' @param 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. #' @param 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.
#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}} #' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
@ -136,6 +137,7 @@ ggplot_rsi <- function(data,
fill = "Interpretation", fill = "Interpretation",
# params = list(), # params = list(),
facet = NULL, facet = NULL,
breaks = seq(0, 1, 0.1),
translate_ab = "official", translate_ab = "official",
fun = count_df, fun = count_df,
nrow = NULL, nrow = NULL,
@ -189,7 +191,7 @@ ggplot_rsi <- function(data,
if (fun_name == "portion_df" if (fun_name == "portion_df"
| (fun_name == "count_df" & position == "fill")) { | (fun_name == "count_df" & position == "fill")) {
# portions, so use y scale with percentage # portions, so use y scale with percentage
p <- p + scale_y_percent() p <- p + scale_y_percent(breaks = breaks)
} }
if (fun_name == "count_df" & datalabels == TRUE) { if (fun_name == "count_df" & datalabels == TRUE) {
@ -281,9 +283,9 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @export #' @export
scale_y_percent <- function() { scale_y_percent <- function(breaks = seq(0, 1, 0.1)) {
ggplot2::scale_y_continuous(breaks = seq(0, 1, 0.1), ggplot2::scale_y_continuous(breaks = breaks,
labels = percent(seq(0, 1, 0.1))) labels = percent(breaks))
} }
#' @rdname ggplot_rsi #' @rdname ggplot_rsi

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@ -3,15 +3,17 @@
This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl). This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl).
:arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities. Read all changes and new functions in **[NEWS.md](https://github.com/msberends/AMR/blob/master/NEWS.md)**. :arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities.
:arrow_forward: Read the [changelog here](https://github.com/msberends/AMR/blob/master/NEWS.md).
## Authors ## Authors
<a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Matthijs S. Berends<sup>1,2,a</sup>, Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
<a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Christian F. Luz<sup>1,a</sup>, Christian F. Luz <a href="https://orcid.org/0000-0001-5809-5995"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,a</sup>,
Erwin E.A. Hassing<sup>2</sup>, Erwin E.A. Hassing<sup>2</sup>,
<a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Corinna Glasner<sup>1,b</sup>, Corinna Glasner <a href="https://orcid.org/0000-0003-1241-1328"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
<a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Alex W. Friedrich<sup>1,b</sup>, Alex W. Friedrich <a href="https://orcid.org/0000-0003-4881-038X"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>,
<a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> Bhanu Sinha<sup>1,b</sup> Bhanu Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,b</sup>
<sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br> <sup>1</sup> Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - [rug.nl](http://www.rug.nl) [umcg.nl](http://www.umcg.nl)<br>
<sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br> <sup>2</sup> Certe Medical Diagnostics & Advice, Groningen, the Netherlands - [certe.nl](http://www.certe.nl)<br>

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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("J01FA01")
as.atc("Erythromycin") as.atc("Erythromycin")
as.atc("eryt") as.atc("eryt")
as.atc(" eryt 123")
as.atc("ERYT") as.atc("ERYT")
as.atc("ERY") as.atc("ERY")
as.atc("Erythrocin") # Trade name as.atc("Erythrocin") # Trade name

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@ -9,12 +9,12 @@
\usage{ \usage{
frequency_tbl(x, ..., sort.count = TRUE, frequency_tbl(x, ..., sort.count = TRUE,
nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE, nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
markdown = FALSE, digits = 2, quote = FALSE, header = !markdown, markdown = !interactive(), digits = 2, quote = FALSE,
sep = " ") header = !markdown, sep = " ")
freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"), freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
na.rm = TRUE, row.names = TRUE, markdown = FALSE, digits = 2, na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
quote = FALSE, header = !markdown, sep = " ") digits = 2, quote = FALSE, header = !markdown, sep = " ")
top_freq(f, n) 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{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{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} \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{ \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. 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{ \itemize{
\item{Mean, using \code{\link[base]{mean}}} \item{Mean, using \code{\link[base]{mean}}}
\item{Standard Deviation, using \code{\link[stats]{sd}}} \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}}} \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{ \itemize{
\item{Oldest, using \code{\link{min}}} \item{Oldest, using \code{\link{min}}}
\item{Newest, using \code{\link{max}}, with difference between newest and oldest} \item{Newest, using \code{\link{max}}, with difference between newest and oldest}
@ -153,14 +153,6 @@ table(septic_patients$gender,
# check differences between frequency tables # check differences between frequency tables
diff(freq(septic_patients$trim), diff(freq(septic_patients$trim),
freq(septic_patients$trsu)) 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{freq}
\keyword{frequency} \keyword{frequency}

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@ -11,9 +11,10 @@
\title{AMR bar plots with \code{ggplot}} \title{AMR bar plots with \code{ggplot}}
\usage{ \usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic", ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, translate_ab = "official", fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
fun = count_df, nrow = NULL, datalabels = TRUE, translate_ab = "official", fun = count_df, nrow = NULL,
datalabels.size = 3, datalabels.colour = "grey15", ...) datalabels = TRUE, datalabels.size = 3,
datalabels.colour = "grey15", ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"), geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
fill = "Interpretation", translate_ab = "official", fun = count_df, 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) facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
scale_y_percent() scale_y_percent(breaks = seq(0, 1, 0.1))
scale_rsi_colours() 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{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{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}}} \item{fun}{function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}}

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@ -13,7 +13,10 @@ test_that("abname works", {
expect_error(abname("AMOX", to = c(1:3))) expect_error(abname("AMOX", to = c(1:3)))
expect_error(abname("AMOX", to = "test")) expect_error(abname("AMOX", to = "test"))
expect_warning(abname("TEST expect_warning(abname("NOTEXISTING
")) "))
expect_warning(abname("AMOX or GENT")) expect_warning(abname("AMOX or GENT"))
# this one is being found with as.atc internally
expect_equal(abname("flu_clox123"), "Flucloxacillin")
}) })