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