mirror of
https://github.com/msberends/AMR.git
synced 2024-12-24 18:46:14 +01:00
italicise antibiogram
This commit is contained in:
parent
db2830124f
commit
714a048fa9
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.8.2.9131
|
||||
Date: 2023-02-15
|
||||
Version: 1.8.2.9132
|
||||
Date: 2023-02-17
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
|
||||
2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
|
||||
# AMR 1.8.2.9131
|
||||
# AMR 1.8.2.9132
|
||||
|
||||
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
|
||||
|
||||
|
||||
@ -44,7 +44,7 @@
|
||||
#' @param combine_SI a [logical] to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to `TRUE`)
|
||||
#' @param sep a separating character for antibiotic columns in combination antibiograms
|
||||
#' @param object an [antibiogram()] object
|
||||
#' @param ... method extensions
|
||||
#' @param ... when used in [print()]: arguments passed on to [knitr::kable()] (otherwise, has no use)
|
||||
#' @details This function returns a table with values between 0 and 100 for *susceptibility*, not resistance.
|
||||
#'
|
||||
#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
|
||||
@ -208,7 +208,16 @@
|
||||
#' )
|
||||
#' )
|
||||
#'
|
||||
#'
|
||||
#' # Print the output for R Markdown / Quarto -----------------------------
|
||||
#'
|
||||
#' ureido <- antibiogram(example_isolates,
|
||||
#' antibiotics = ureidopenicillins(),
|
||||
#' ab_transform = "name")
|
||||
#'
|
||||
#' # in an Rmd file, you would just need print(ureido), but to be explicit:
|
||||
#' print(ureido, as_kable = TRUE, format = "markdown", italicise = TRUE)
|
||||
#'
|
||||
#'
|
||||
#' # Generate plots with ggplot2 or base R --------------------------------
|
||||
#'
|
||||
#' ab1 <- antibiogram(example_isolates,
|
||||
@ -221,17 +230,16 @@
|
||||
#' syndromic_group = "ward"
|
||||
#' )
|
||||
#'
|
||||
#' plot(ab1)
|
||||
#'
|
||||
#' if (requireNamespace("ggplot2")) {
|
||||
#' ggplot2::autoplot(ab1)
|
||||
#' }
|
||||
#'
|
||||
#' plot(ab2)
|
||||
#'
|
||||
#' if (requireNamespace("ggplot2")) {
|
||||
#' ggplot2::autoplot(ab2)
|
||||
#' }
|
||||
#'
|
||||
#' plot(ab1)
|
||||
#' plot(ab2)
|
||||
#'
|
||||
#' }
|
||||
antibiogram <- function(x,
|
||||
antibiotics = where(is.sir),
|
||||
@ -540,18 +548,37 @@ autoplot.antibiogram <- function(object, ...) {
|
||||
|
||||
#' @export
|
||||
#' @param as_kable a [logical] to indicate whether the printing should be done using [knitr::kable()] (which is the default in non-interactive sessions)
|
||||
#' @param italicise a [logical] to indicate whether the microorganism names in the output table should be made italic, using [italicise_taxonomy()]. This only works when the output format is markdown, such as in HTML output.
|
||||
#' @details Printing the antibiogram in non-interactive sessions will be done by [knitr::kable()], with support for [all their implemented formats][knitr::kable()], such as "markdown". The knitr format will be automatically determined if printed inside a knitr document (LaTeX, HTML, etc.).
|
||||
#' @rdname antibiogram
|
||||
print.antibiogram <- function(x, as_kable = !interactive(), ...) {
|
||||
print.antibiogram <- function(x, as_kable = !interactive(), italicise = TRUE, ...) {
|
||||
meet_criteria(as_kable, allow_class = "logical", has_length = 1)
|
||||
|
||||
kable <- import_fn("kable", "knitr", error_on_fail = FALSE)
|
||||
if (!is.null(kable) &&
|
||||
isTRUE(as_kable) &&
|
||||
meet_criteria(italicise, allow_class = "logical", has_length = 1)
|
||||
|
||||
if (isTRUE(as_kable) &&
|
||||
# be sure not to run kable in pkgdown for our website generation
|
||||
!identical(Sys.getenv("IN_PKGDOWN"), "true")) {
|
||||
kable(x, ...)
|
||||
|
||||
!(missing(as_kable) && identical(Sys.getenv("IN_PKGDOWN"), "true"))) {
|
||||
out <- knitr::kable(x, ...)
|
||||
format <- attributes(out)$format
|
||||
if (!is.null(format) && format %in% c("markdown", "pipe")) {
|
||||
# try to italicise the output
|
||||
rows_with_txt <- which(out %like% "[a-z]")
|
||||
rows_without_txt <- setdiff(seq_len(length(out)), rows_with_txt)
|
||||
out[rows_with_txt] <- gsub("^[|]", "| ", out[rows_with_txt])
|
||||
# put hyphen directly after second character
|
||||
out[rows_without_txt] <- gsub("^[|](.)", "|\\1-", out[rows_without_txt])
|
||||
out_ita <- italicise_taxonomy(as.character(out), type = "markdown")
|
||||
if (length(unique(nchar(out_ita))) != 1) {
|
||||
# so there has been alterations done by italicise_taxonomy()
|
||||
to_fill <- which(nchar(out_ita) < max(nchar(out_ita)))
|
||||
out_ita[intersect(to_fill, rows_with_txt)] <- gsub("(^[|].*?)([|])(.*)", "\\1 \\2\\3", out_ita[intersect(to_fill, rows_with_txt)], perl = TRUE)
|
||||
out_ita[intersect(to_fill, rows_without_txt)] <- gsub("(^[|].*?)([|])(.*)", "\\1--\\2\\3", out_ita[intersect(to_fill, rows_without_txt)], perl = TRUE)
|
||||
}
|
||||
attributes(out_ita) <- attributes(out)
|
||||
out <- out_ita
|
||||
}
|
||||
out
|
||||
|
||||
} else {
|
||||
# remove 'antibiogram' class and print with default method
|
||||
class(x) <- class(x)[class(x) != "antibiogram"]
|
||||
|
||||
34
index.md
34
index.md
@ -85,18 +85,18 @@ antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()))
|
||||
```
|
||||
|
||||
|Pathogen (N min-max) | AMK| GEN| IPM| KAN| MEM| TOB|
|
||||
|:----------------------|---:|---:|---:|---:|---:|---:|
|
||||
|CoNS (43-309) | 0| 86| 52| 0| 52| 22|
|
||||
|E. coli (0-462) | 100| 98| 100| NA| 100| 97|
|
||||
|E. faecalis (0-39) | 0| 0| 100| 0| NA| 0|
|
||||
|K. pneumoniae (0-58) | NA| 90| 100| NA| 100| 90|
|
||||
|P. aeruginosa (17-30) | NA| 100| NA| 0| NA| 100|
|
||||
|P. mirabilis (0-34) | NA| 94| 94| NA| NA| 94|
|
||||
|S. aureus (2-233) | NA| 99| NA| NA| NA| 98|
|
||||
|S. epidermidis (8-163) | 0| 79| NA| 0| NA| 51|
|
||||
|S. hominis (3-80) | NA| 92| NA| NA| NA| 85|
|
||||
|S. pneumoniae (11-117) | 0| 0| NA| 0| NA| 0|
|
||||
|Pathogen (N min-max) | AMK| GEN| IPM| KAN| MEM| TOB|
|
||||
|:------------------------|---:|---:|---:|---:|---:|---:|
|
||||
|CoNS (43-309) | 0| 86| 52| 0| 52| 22|
|
||||
|*E. coli* (0-462) | 100| 98| 100| | 100| 97|
|
||||
|*E. faecalis* (0-39) | 0| 0| 100| 0| | 0|
|
||||
|*K. pneumoniae* (0-58) | | 90| 100| | 100| 90|
|
||||
|*P. aeruginosa* (17-30) | | 100| | 0| | 100|
|
||||
|*P. mirabilis* (0-34) | | 94| 94| | | 94|
|
||||
|*S. aureus* (2-233) | | 99| | | | 98|
|
||||
|*S. epidermidis* (8-163) | 0| 79| | 0| | 51|
|
||||
|*S. hominis* (3-80) | | 92| | | | 85|
|
||||
|*S. pneumoniae* (11-117) | 0| 0| | 0| | 0|
|
||||
|
||||
In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:
|
||||
|
||||
@ -111,7 +111,7 @@ antibiogram(example_isolates,
|
||||
|Gram-negative (641-693) | 88| 99| 98|
|
||||
|Gram-positive (345-1044) | 86| 98| 95|
|
||||
|
||||
Like many other functions in this package, `antibiograms()` comes with support for 20 languages that are often detected automatically based on system language:
|
||||
Like many other functions in this package, `antibiogram()` comes with support for 20 languages that are often detected automatically based on system language:
|
||||
|
||||
```r
|
||||
antibiogram(example_isolates,
|
||||
@ -129,6 +129,8 @@ antibiogram(example_isolates,
|
||||
|
||||
#### Calculating resistance per group
|
||||
|
||||
For a manual approach, you can use the `resistance` or `susceptibility()` function:
|
||||
|
||||
```r
|
||||
library(AMR)
|
||||
library(dplyr)
|
||||
@ -147,7 +149,7 @@ out
|
||||
|:-----------|------:|------:|------:|------:|------:|
|
||||
| Clinical | 0.229 | 0.315 | 0.626 | 1 | 0.780 |
|
||||
| ICU | 0.290 | 0.400 | 0.662 | 1 | 0.857 |
|
||||
| Outpatient | 0.200 | 0.368 | 0.605 | NA | 0.889 |
|
||||
| Outpatient | 0.200 | 0.368 | 0.605 | | 0.889 |
|
||||
|
||||
```r
|
||||
# transform the antibiotic columns to names:
|
||||
@ -158,7 +160,7 @@ out %>% set_ab_names()
|
||||
|:-----------|-----------:|-----------:|----------|----------:|----------:|
|
||||
| Clinical | 0.229 | 0.315 | 0.626 | 1 | 0.780 |
|
||||
| ICU | 0.290 | 0.400 | 0.662 | 1 | 0.857 |
|
||||
| Outpatient | 0.200 | 0.368 | 0.605 | NA | 0.889 |
|
||||
| Outpatient | 0.200 | 0.368 | 0.605 | | 0.889 |
|
||||
|
||||
```r
|
||||
# transform the antibiotic column to ATC codes:
|
||||
@ -169,7 +171,7 @@ out %>% set_ab_names(property = "atc")
|
||||
|:-----------|-----------:|-----------:|----------|----------:|----------:|
|
||||
| Clinical | 0.229 | 0.315 | 0.626 | 1 | 0.780 |
|
||||
| ICU | 0.290 | 0.400 | 0.662 | 1 | 0.857 |
|
||||
| Outpatient | 0.200 | 0.368 | 0.605 | NA | 0.889 |
|
||||
| Outpatient | 0.200 | 0.368 | 0.605 | | 0.889 |
|
||||
|
||||
### What else can you do with this package?
|
||||
|
||||
|
||||
@ -34,7 +34,7 @@ antibiogram(
|
||||
|
||||
\method{autoplot}{antibiogram}(object, ...)
|
||||
|
||||
\method{print}{antibiogram}(x, as_kable = !interactive(), ...)
|
||||
\method{print}{antibiogram}(x, as_kable = !interactive(), italicise = TRUE, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{a \link{data.frame} containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see \code{\link[=as.sir]{as.sir()}})}
|
||||
@ -63,11 +63,13 @@ antibiogram(
|
||||
|
||||
\item{sep}{a separating character for antibiotic columns in combination antibiograms}
|
||||
|
||||
\item{...}{method extensions}
|
||||
\item{...}{when used in \code{\link[=print]{print()}}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)}
|
||||
|
||||
\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}
|
||||
|
||||
\item{as_kable}{a \link{logical} to indicate whether the printing should be done using \code{\link[knitr:kable]{knitr::kable()}} (which is the default in non-interactive sessions)}
|
||||
|
||||
\item{italicise}{a \link{logical} to indicate whether the microorganism names in the output table should be made italic, using \code{\link[=italicise_taxonomy]{italicise_taxonomy()}}. This only works when the output format is markdown, such as in HTML output.}
|
||||
}
|
||||
\description{
|
||||
Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker \emph{et al.} and Barbieri \emph{et al.} (see \emph{Source}), and allow reporting in e.g. R Markdown and Quarto as well.
|
||||
@ -225,6 +227,15 @@ antibiogram(example_isolates,
|
||||
)
|
||||
)
|
||||
|
||||
# Print the output for R Markdown / Quarto -----------------------------
|
||||
|
||||
ureido <- antibiogram(example_isolates,
|
||||
antibiotics = ureidopenicillins(),
|
||||
ab_transform = "name")
|
||||
|
||||
# in an Rmd file, you would just need print(ureido), but to be explicit:
|
||||
print(ureido, as_kable = TRUE, format = "markdown", italicise = TRUE)
|
||||
|
||||
|
||||
# Generate plots with ggplot2 or base R --------------------------------
|
||||
|
||||
@ -238,16 +249,15 @@ ab2 <- antibiogram(example_isolates,
|
||||
syndromic_group = "ward"
|
||||
)
|
||||
|
||||
plot(ab1)
|
||||
|
||||
if (requireNamespace("ggplot2")) {
|
||||
ggplot2::autoplot(ab1)
|
||||
}
|
||||
|
||||
plot(ab2)
|
||||
|
||||
if (requireNamespace("ggplot2")) {
|
||||
ggplot2::autoplot(ab2)
|
||||
}
|
||||
|
||||
plot(ab1)
|
||||
plot(ab2)
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user