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fix for antibiograms on R < 3.5
This commit is contained in:
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.8.2.9142
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Date: 2023-02-23
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Version: 1.8.2.9143
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Date: 2023-02-24
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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
@ -1,4 +1,4 @@
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# AMR 1.8.2.9142
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# AMR 1.8.2.9143
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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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@ -988,7 +988,7 @@ pm_summarise.default <- function(.data, ...) {
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if (is.list(x_res)) I(x_res) else x_res
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}
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)
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res <- as.data.frame(res)
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res <- as.data.frame(res, stringsAsFactors = FALSE)
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fn_names <- names(fns)
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colnames(res) <- if (is.null(fn_names)) fns else fn_names
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if (pm_groups_exist) res <- cbind(group, res, row.names = NULL)
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@ -49,7 +49,11 @@
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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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#'
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#' All types of antibiograms as listed below can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]). The `antibiogram` object can also be used directly in R Markdown / Quarto (i.e., `knitr`) for reports. In this case, [knitr::kable()] will be applied automatically and microorganism names will even be printed in italics at default (see argument `italicise`). You can also use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. with [`as_flextable()`][flextable::as_flextable()] or [`gt()`][gt::gt()].
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#'
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#' ### Antibiogram Types
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#'
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#' There are four antibiogram types, as proposed by Klinker *et al.* (2021, \doi{10.1177/20499361211011373}), and they are all supported by [antibiogram()]:
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#'
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#' 1. **Traditional Antibiogram**
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@ -103,8 +107,6 @@
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#' "Study Group", "Control Group"))
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#' ```
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#'
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#' All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using [ggplot2::autoplot()] or base \R [plot()]/[barplot()]) or directly used into R Markdown / Quarto formats for reports (in the last case, [knitr::kable()] will be applied automatically). Use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. `flextable::as_flextable()` or `gt::gt()`.
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#'
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#' Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the `only_all_tested` argument (default is `FALSE`). See this example for two antibiotics, Drug A and Drug B, about how [antibiogram()] works to calculate the %SI:
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#'
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#' ```
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@ -125,6 +127,7 @@
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#' <NA> <NA> - - - -
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#' --------------------------------------------------------------------
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#' ```
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#'
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#' @source
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#' * Klinker KP *et al.* (2021). **Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms**. *Therapeutic Advances in Infectious Disease*, May 5;8:20499361211011373; \doi{10.1177/20499361211011373}
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#' * Barbieri E *et al.* (2021). **Development of a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) to guide the choice of the empiric antibiotic treatment for urinary tract infection in paediatric patients: a Bayesian approach** *Antimicrobial Resistance & Infection Control* May 1;10(1):74; \doi{10.1186/s13756-021-00939-2}
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@ -208,6 +211,7 @@
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#' "WISCA Group 1", "WISCA Group 2"
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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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@ -504,6 +508,7 @@ antibiogram <- function(x,
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out <- as_original_data_class(new_df, class(x), extra_class = "antibiogram")
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rownames(out) <- NULL
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structure(out,
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has_syndromic_group = has_syndromic_group,
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long = long,
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combine_SI = combine_SI
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)
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@ -578,39 +583,25 @@ autoplot.antibiogram <- function(object, ...) {
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}
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# will be exported in zzz.R
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#' @param italicise a [logical] to indicate whether the microorganism names in the [knitr][knitr::kable()] 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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#' @method knit_print antibiogram
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#' @param italicise a [logical] to indicate whether the microorganism names in the [knitr][knitr::kable()] table should be made italic, using [italicise_taxonomy()].
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#' @param na character to use for showing `NA` values
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#' @rdname antibiogram
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knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) {
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stop_ifnot_installed("knitr")
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meet_criteria(italicise, allow_class = "logical", has_length = 1)
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meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE)
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if (isTRUE(italicise)) {
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# make all microorganism names italic, according to nomenclature
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names_col <- ifelse(isTRUE(attributes(x)$has_syndromic_group), 2, 1)
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x[[names_col]] <- italicise_taxonomy(x[[names_col]], type = "markdown")
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}
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old_option <- getOption("knitr.kable.NA")
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options(knitr.kable.NA = na)
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on.exit(options(knitr.kable.NA = old_option))
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out <- knitr::kable(x, ..., output = FALSE)
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format <- attributes(out)$format
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if (isTRUE(italicise) &&
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!is.null(format) &&
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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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res <- paste(c("", "", out), collapse = "\n")
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knitr::asis_output(res)
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out <- paste(c("", "", knitr::kable(x, ..., output = FALSE)), collapse = "\n")
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knitr::asis_output(out)
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}
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@ -39,7 +39,7 @@
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#' @param ... arguments passed on to `FUN`
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#' @inheritParams sir_df
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#' @inheritParams base::formatC
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#' @details The function [format()] calculates the resistance per bug-drug combination. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S.
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#' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
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#' @export
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#' @rdname bug_drug_combinations
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#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
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@ -327,7 +327,15 @@ format.bug_drug_combinations <- function(x,
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}
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rownames(y) <- NULL
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as_original_data_class(y, class(x.bak)) # will remove tibble groups
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as_original_data_class(y, class(x.bak), extra_class = "formatted_bug_drug_combinations") # will remove tibble groups
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}
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# will be exported in zzz.R
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knit_print.formatted_bug_drug_combinations <- function(x, ...) {
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stop_ifnot_installed("knitr")
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# make columns with MO names italic according to nomenclature
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colnames(x)[3:NCOL(x)] <- italicise_taxonomy(colnames(x)[3:NCOL(x)], type = "markdown")
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knitr::asis_output(paste("", "", knitr::kable(x, ...), collapse = "\n"))
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}
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#' @method print bug_drug_combinations
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R/sysdata.rda
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R/sysdata.rda
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3
R/zzz.R
3
R/zzz.R
@ -128,8 +128,9 @@ if (utf8_supported && !is_latex) {
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s3_register("ggplot2::fortify", "sir")
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s3_register("ggplot2::fortify", "mic")
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s3_register("ggplot2::fortify", "disk")
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# Support for knitr / R Markdown
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# Support for knitr (R Markdown/Quarto)
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s3_register("knitr::knit_print", "antibiogram")
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s3_register("knitr::knit_print", "formatted_bug_drug_combinations")
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# Support vctrs package for use in e.g. dplyr verbs
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# S3: ab_selector
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s3_register("vctrs::vec_ptype2", "character.ab_selector")
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@ -2,7 +2,7 @@
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title: "Generating antibiograms with the AMR package"
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author: "AMR package developers"
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date: "`r Sys.Date()`"
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output: html_document
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output: pdf_document
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---
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```{r setup, include=FALSE}
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@ -11,7 +11,7 @@
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<meta name="author" content="AMR package developers" />
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<meta name="date" content="2023-02-23" />
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<meta name="date" content="2023-02-24" />
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<title>Generating antibiograms with the AMR package</title>
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@ -299,23 +299,17 @@ overflow-y: auto;
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border: 1px solid #ddd;
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border-radius: 4px;
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}
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.tabset-dropdown > .nav-tabs > li.active:before {
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content: "";
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.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "\e259";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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content: "";
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border: none;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "";
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content: "\e258";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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border: none;
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}
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.tabset-dropdown > .nav-tabs > li.active {
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display: block;
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@ -359,7 +353,7 @@ display: none;
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<h1 class="title toc-ignore">Generating antibiograms with the AMR
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package</h1>
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<h4 class="author">AMR package developers</h4>
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<h4 class="date">2023-02-23</h4>
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<h4 class="date">2023-02-24</h4>
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</div>
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@ -370,26 +364,25 @@ package</h1>
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looks like:</p>
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<pre class="r"><code>example_isolates</code></pre>
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<pre><code>## # A tibble: 2,000 × 46
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## date patient age gender ward mo PEN
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## <date> <chr> <dbl> <chr> <chr> <mo> <sir>
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## 1 2002-01-02 A77334 65 F Clini… B_ESCHR_COLI R
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## 2 2002-01-03 A77334 65 F Clini… B_ESCHR_COLI R
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## 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R
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## 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R
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## 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R
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## 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R
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## 7 2002-01-14 462729 78 M Clini… B_STPHY_AURS R
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## 8 2002-01-14 462729 78 M Clini… B_STPHY_AURS R
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## 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R
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## 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R
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## # … with 1,990 more rows, and 39 more variables: OXA <sir>,
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## # FLC <sir>, AMX <sir>, AMC <sir>, AMP <sir>, TZP <sir>,
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## # CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>,
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## # CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>,
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## # KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>,
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## # LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
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## # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, …
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## # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</code></pre>
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## date patient age gender ward mo PEN OXA FLC AMX
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## <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
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## 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
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## 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
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## 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
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## 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
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## 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
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## 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
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## 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
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## 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
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## 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
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## 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
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## # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>,
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## # TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>,
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## # CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>,
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## # TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>,
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## # MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>,
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## # ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,
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## # CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></code></pre>
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<div id="traditional-antibiogram" class="section level3">
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<h3>Traditional Antibiogram</h3>
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<pre class="r"><code>antibiogram(example_isolates,
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@ -397,7 +390,7 @@ looks like:</p>
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<table>
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<thead>
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<tr class="header">
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<th align="left">Pathogeen (N min-max)</th>
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<th align="left">Pathogen (N min-max)</th>
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<th align="right">AMK</th>
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<th align="right">GEN</th>
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<th align="right">IPM</th>
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@ -408,7 +401,7 @@ looks like:</p>
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</thead>
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<tbody>
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<tr class="odd">
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<td align="left">CNS (43-309)</td>
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<td align="left">CoNS (43-309)</td>
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<td align="right">0</td>
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<td align="right">86</td>
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<td align="right">52</td>
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@ -507,7 +500,7 @@ looks like:</p>
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<table>
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<thead>
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<tr class="header">
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<th align="left">Pathogeen (N min-max)</th>
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<th align="left">Pathogen (N min-max)</th>
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<th align="right">TZP</th>
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<th align="right">TZP + GEN</th>
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<th align="right">TZP + TOB</th>
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@ -515,7 +508,7 @@ looks like:</p>
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</thead>
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<tbody>
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<tr class="odd">
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<td align="left">CNS (29-274)</td>
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<td align="left">CoNS (29-274)</td>
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<td align="right">30</td>
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<td align="right">97</td>
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<td align="right"></td>
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@ -577,10 +570,20 @@ looks like:</p>
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antibiotics = c(aminoglycosides(), carbapenems()),
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syndromic_group = "ward")</code></pre>
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<table>
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<colgroup>
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<col width="25%" />
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<col width="37%" />
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<col width="6%" />
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<col width="6%" />
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<col width="6%" />
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<col width="6%" />
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<col width="6%" />
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<col width="6%" />
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</colgroup>
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<thead>
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<tr class="header">
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<th align="left">Syndroomgroep</th>
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<th align="left">Pathogeen (N min-max)</th>
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<th align="left">Syndromic Group</th>
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<th align="left">Pathogen (N min-max)</th>
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<th align="right">AMK</th>
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<th align="right">GEN</th>
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<th align="right">IPM</th>
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@ -592,7 +595,7 @@ looks like:</p>
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<tbody>
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<tr class="odd">
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<td align="left">Clinical</td>
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<td align="left">CNS (23-205)</td>
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<td align="left">CoNS (23-205)</td>
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<td align="right"></td>
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<td align="right">89</td>
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<td align="right">57</td>
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@ -602,7 +605,7 @@ looks like:</p>
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</tr>
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<tr class="even">
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<td align="left">ICU</td>
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<td align="left">CNS (10-73)</td>
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<td align="left">CoNS (10-73)</td>
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<td align="right"></td>
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<td align="right">79</td>
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<td align="right"></td>
|
||||
@ -612,7 +615,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Outpatient</td>
|
||||
<td align="left">CNS (3-31)</td>
|
||||
<td align="left">CoNS (3-31)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">84</td>
|
||||
<td align="right"></td>
|
||||
@ -622,7 +625,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">E. <em>coli</em> (0-299)</td>
|
||||
<td align="left"><em>E. coli</em> (0-299)</td>
|
||||
<td align="right">100</td>
|
||||
<td align="right">98</td>
|
||||
<td align="right">100</td>
|
||||
@ -632,7 +635,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">ICU</td>
|
||||
<td align="left">E. <em>coli</em> (0-137)</td>
|
||||
<td align="left"><em>E. coli</em> (0-137)</td>
|
||||
<td align="right">100</td>
|
||||
<td align="right">99</td>
|
||||
<td align="right">100</td>
|
||||
@ -642,7 +645,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">K. <em>pneumoniae</em> (0-51)</td>
|
||||
<td align="left"><em>K. pneumoniae</em> (0-51)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">92</td>
|
||||
<td align="right">100</td>
|
||||
@ -652,7 +655,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">P. <em>mirabilis</em> (0-30)</td>
|
||||
<td align="left"><em>P. mirabilis</em> (0-30)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">100</td>
|
||||
<td align="right"></td>
|
||||
@ -662,7 +665,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">S. <em>aureus</em> (2-150)</td>
|
||||
<td align="left"><em>S. aureus</em> (2-150)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">99</td>
|
||||
<td align="right"></td>
|
||||
@ -672,7 +675,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">ICU</td>
|
||||
<td align="left">S. <em>aureus</em> (0-66)</td>
|
||||
<td align="left"><em>S. aureus</em> (0-66)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">100</td>
|
||||
<td align="right"></td>
|
||||
@ -682,7 +685,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">S. <em>epidermidis</em> (4-79)</td>
|
||||
<td align="left"><em>S. epidermidis</em> (4-79)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">82</td>
|
||||
<td align="right"></td>
|
||||
@ -692,7 +695,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">ICU</td>
|
||||
<td align="left">S. <em>epidermidis</em> (4-75)</td>
|
||||
<td align="left"><em>S. epidermidis</em> (4-75)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">72</td>
|
||||
<td align="right"></td>
|
||||
@ -702,7 +705,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">S. <em>hominis</em> (1-45)</td>
|
||||
<td align="left"><em>S. hominis</em> (1-45)</td>
|
||||
<td align="right"></td>
|
||||
<td align="right">96</td>
|
||||
<td align="right"></td>
|
||||
@ -712,7 +715,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Clinical</td>
|
||||
<td align="left">S. <em>pneumoniae</em> (5-78)</td>
|
||||
<td align="left"><em>S. pneumoniae</em> (5-78)</td>
|
||||
<td align="right">0</td>
|
||||
<td align="right">0</td>
|
||||
<td align="right"></td>
|
||||
@ -722,7 +725,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">ICU</td>
|
||||
<td align="left">S. <em>pneumoniae</em> (5-30)</td>
|
||||
<td align="left"><em>S. pneumoniae</em> (5-30)</td>
|
||||
<td align="right">0</td>
|
||||
<td align="right">0</td>
|
||||
<td align="right"></td>
|
||||
@ -742,9 +745,9 @@ looks like:</p>
|
||||
syndromic_group = ifelse(example_isolates$age >= 65 &
|
||||
example_isolates$gender == "M",
|
||||
"WISCA Group 1", "WISCA Group 2"))</code></pre>
|
||||
<table style="width:100%;">
|
||||
<table>
|
||||
<colgroup>
|
||||
<col width="22%" />
|
||||
<col width="23%" />
|
||||
<col width="35%" />
|
||||
<col width="5%" />
|
||||
<col width="14%" />
|
||||
@ -753,8 +756,8 @@ looks like:</p>
|
||||
</colgroup>
|
||||
<thead>
|
||||
<tr class="header">
|
||||
<th align="left">Syndroomgroep</th>
|
||||
<th align="left">Pathogeen (N min-max)</th>
|
||||
<th align="left">Syndromic Group</th>
|
||||
<th align="left">Pathogen (N min-max)</th>
|
||||
<th align="right">AMC</th>
|
||||
<th align="right">AMC + CIP</th>
|
||||
<th align="right">TZP</th>
|
||||
@ -764,7 +767,7 @@ looks like:</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">WISCA Group 1</td>
|
||||
<td align="left">Gram-negatief (261-285)</td>
|
||||
<td align="left">Gram-negative (261-285)</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">95</td>
|
||||
<td align="right">89</td>
|
||||
@ -772,7 +775,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">WISCA Group 2</td>
|
||||
<td align="left">Gram-negatief (380-442)</td>
|
||||
<td align="left">Gram-negative (380-442)</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">98</td>
|
||||
<td align="right">88</td>
|
||||
@ -780,7 +783,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">WISCA Group 1</td>
|
||||
<td align="left">Gram-positief (123-406)</td>
|
||||
<td align="left">Gram-positive (123-406)</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">89</td>
|
||||
<td align="right">81</td>
|
||||
@ -788,7 +791,7 @@ looks like:</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">WISCA Group 2</td>
|
||||
<td align="left">Gram-positief (222-732)</td>
|
||||
<td align="left">Gram-positive (222-732)</td>
|
||||
<td align="right">76</td>
|
||||
<td align="right">89</td>
|
||||
<td align="right">88</td>
|
||||
|
BIN
data-raw/antibiograms.pdf
Normal file
BIN
data-raw/antibiograms.pdf
Normal file
Binary file not shown.
@ -107,3 +107,4 @@ contents <- c(
|
||||
writeLines(contents, "R/aa_helper_pm_functions.R")
|
||||
|
||||
# note: pm_left_join() will be overwritten by aaa_helper_functions.R, which contains a faster implementation
|
||||
# replace `res <- as.data.frame(res)` with `res <- as.data.frame(res, stringsAsFactors = FALSE)`
|
||||
|
@ -35,7 +35,7 @@ antibiogram(
|
||||
|
||||
\method{autoplot}{antibiogram}(object, ...)
|
||||
|
||||
knit_print.antibiogram(
|
||||
\method{knit_print}{antibiogram}(
|
||||
x,
|
||||
italicise = TRUE,
|
||||
na = getOption("knitr.kable.NA", default = ""),
|
||||
@ -75,7 +75,7 @@ knit_print.antibiogram(
|
||||
|
||||
\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}
|
||||
|
||||
\item{italicise}{a \link{logical} to indicate whether the microorganism names in the \link[knitr:kable]{knitr} 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.}
|
||||
\item{italicise}{a \link{logical} to indicate whether the microorganism names in the \link[knitr:kable]{knitr} table should be made italic, using \code{\link[=italicise_taxonomy]{italicise_taxonomy()}}.}
|
||||
|
||||
\item{na}{character to use for showing \code{NA} values}
|
||||
}
|
||||
@ -87,6 +87,9 @@ This function returns a table with values between 0 and 100 for \emph{susceptibi
|
||||
|
||||
\strong{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 \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set with one of the four available algorithms.
|
||||
|
||||
All types of antibiograms as listed below can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}). The \code{antibiogram} object can also be used directly in R Markdown / Quarto (i.e., \code{knitr}) for reports. In this case, \code{\link[knitr:kable]{knitr::kable()}} will be applied automatically and microorganism names will even be printed in italics at default (see argument \code{italicise}). You can also use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. with \code{\link[flextable:as_flextable]{as_flextable()}} or \code{\link[gt:gt]{gt()}}.
|
||||
\subsection{Antibiogram Types}{
|
||||
|
||||
There are four antibiogram types, as proposed by Klinker \emph{et al.} (2021, \doi{10.1177/20499361211011373}), and they are all supported by \code{\link[=antibiogram]{antibiogram()}}:
|
||||
\enumerate{
|
||||
\item \strong{Traditional Antibiogram}
|
||||
@ -134,8 +137,6 @@ your_data \%>\%
|
||||
}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using \code{\link[ggplot2:autoplot]{ggplot2::autoplot()}} or base \R \code{\link[=plot]{plot()}}/\code{\link[=barplot]{barplot()}}) or directly used into R Markdown / Quarto formats for reports (in the last case, \code{\link[knitr:kable]{knitr::kable()}} will be applied automatically). Use functions from specific 'table reporting' packages to transform the output of \code{\link[=antibiogram]{antibiogram()}} to your needs, e.g. \code{flextable::as_flextable()} or \code{gt::gt()}.
|
||||
|
||||
Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the \code{only_all_tested} argument (default is \code{FALSE}). See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=antibiogram]{antibiogram()}} works to calculate the \%SI:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
|
||||
@ -156,6 +157,7 @@ Note that for combination antibiograms, it is important to realise that suscepti
|
||||
--------------------------------------------------------------------
|
||||
}\if{html}{\out{</div>}}
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
# example_isolates is a data set available in the AMR package.
|
||||
# run ?example_isolates for more info.
|
||||
@ -233,6 +235,7 @@ antibiogram(example_isolates,
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
# Print the output for R Markdown / Quarto -----------------------------
|
||||
|
||||
ureido <- antibiogram(example_isolates,
|
||||
|
@ -55,7 +55,7 @@ The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} retur
|
||||
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publishable/printable format, see \emph{Examples}.
|
||||
}
|
||||
\details{
|
||||
The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination. Use \code{combine_SI = TRUE} (default) to test R vs. S+I and \code{combine_SI = FALSE} to test R+I vs. S.
|
||||
The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use \code{combine_SI = TRUE} (default) to test R vs. S+I and \code{combine_SI = FALSE} to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. \code{\link[knitr:kable]{knitr::kable()}}.
|
||||
}
|
||||
\examples{
|
||||
# example_isolates is a data set available in the AMR package.
|
||||
|
Loading…
Reference in New Issue
Block a user