italicise antibiogram

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9131
+Version: 1.8.2.9132
-Date: 2023-02-15
+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

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!)*
 

R/antibiogram.R

@@ -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.
@@ -208,6 +208,15 @@
 #'   )
 #' )
 #'
+#' # 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 --------------------------------
 #'
@@ -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),
@@ -540,17 +548,36 @@ 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)
+  meet_criteria(italicise, allow_class = "logical", has_length = 1)
 
-  kable <- import_fn("kable", "knitr", error_on_fail = FALSE)
+  if (isTRUE(as_kable) &&
-  if (!is.null(kable) &&
-      isTRUE(as_kable) &&
       # be sure not to run kable in pkgdown for our website generation
-      !identical(Sys.getenv("IN_PKGDOWN"), "true")) {
+      !(missing(as_kable) && identical(Sys.getenv("IN_PKGDOWN"), "true"))) {
-    kable(x, ...)
+    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

index.md

@@ -86,17 +86,17 @@ antibiogram(example_isolates,
 ```
 
 |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. coli* (0-462)        | 100|  98| 100|    | 100|  97|
-|E. faecalis (0-39)     |   0|   0| 100|   0|  NA|   0|
+|*E. faecalis* (0-39)     |   0|   0| 100|   0|    |   0|
-|K. pneumoniae (0-58)   |  NA|  90| 100|  NA| 100|  90|
+|*K. pneumoniae* (0-58)   |    |  90| 100|    | 100|  90|
-|P. aeruginosa (17-30)  |  NA| 100|  NA|   0|  NA| 100|
+|*P. aeruginosa* (17-30)  |    | 100|    |   0|    | 100|
-|P. mirabilis (0-34)    |  NA|  94|  94|  NA|  NA|  94|
+|*P. mirabilis* (0-34)    |    |  94|  94|    |    |  94|
-|S. aureus (2-233)      |  NA|  99|  NA|  NA|  NA|  98|
+|*S. aureus* (2-233)      |    |  99|    |    |    |  98|
-|S. epidermidis (8-163) |   0|  79|  NA|   0|  NA|  51|
+|*S. epidermidis* (8-163) |   0|  79|    |   0|    |  51|
-|S. hominis (3-80)      |  NA|  92|  NA|  NA|  NA|  85|
+|*S. hominis* (3-80)      |    |  92|    |    |    |  85|
-|S. pneumoniae (11-117) |   0|   0|  NA|   0|  NA|   0|
+|*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?
 

man/antibiogram.Rd

@@ -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)
+
 }
 }