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knitr format

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dr. M.S. (Matthijs) Berends 2023-02-23 16:27:40 +01:00
parent a84101db08
commit e70f2cd32c
10 changed files with 236 additions and 257 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9141 Version: 1.8.2.9142
Date: 2023-02-22 Date: 2023-02-23
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

1
NAMESPACE
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@ -131,7 +131,6 @@ S3method(plot,resistance_predict)
S3method(plot,rsi) S3method(plot,rsi)
S3method(plot,sir) S3method(plot,sir)
S3method(print,ab) S3method(print,ab)
S3method(print,antibiogram)
S3method(print,av) S3method(print,av)
S3method(print,bug_drug_combinations) S3method(print,bug_drug_combinations)
S3method(print,custom_eucast_rules) S3method(print,custom_eucast_rules)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9141 # AMR 1.8.2.9142
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

45
R/antibiogram.R
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@ -45,7 +45,7 @@
#' @param sep a separating character for antibiotic columns in combination antibiograms #' @param sep a separating character for antibiotic columns in combination antibiograms
#' @param info a [logical] to indicate info should be printed - the default is `TRUE` only in interactive mode #' @param info a [logical] to indicate info should be printed - the default is `TRUE` only in interactive mode
#' @param object an [antibiogram()] object #' @param object an [antibiogram()] object
#' @param ... when used in [print()]: arguments passed on to [knitr::kable()] (otherwise, has no use) #' @param ... when used in [R Markdown or Quarto][knitr::kable()]: 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. #' @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. #' **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.
@ -103,7 +103,7 @@
#' "Study Group", "Control Group")) #' "Study Group", "Control Group"))
#' ``` #' ```
#' #'
#' 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 printed into R Markdown / Quarto formats for reports using `print()`. Use functions from specific 'table reporting' packages to transform the output of [antibiogram()] to your needs, e.g. `flextable::as_flextable()` or `gt::gt()`. #' 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()`.
#' #'
#' 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: #' 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:
#' #'
@ -215,8 +215,11 @@
#' antibiotics = ureidopenicillins(), #' antibiotics = ureidopenicillins(),
#' ab_transform = "name") #' ab_transform = "name")
#' #'
#' # in an Rmd file, you would just need print(ureido), but to be explicit: #' # in an Rmd file, you would just need to return `ureido` in a chunk,
#' print(ureido, as_kable = TRUE, format = "markdown", italicise = TRUE) #' # but to be explicit here:
#' if (requireNamespace("knitr")) {
#' knitr::knit_print(ureido)
#' }
#' #'
#' #'
#' # Generate plots with ggplot2 or base R -------------------------------- #' # Generate plots with ggplot2 or base R --------------------------------
@ -489,7 +492,7 @@ antibiogram <- function(x,
} }
if (NCOL(new_df) == edit_col + 1) { if (NCOL(new_df) == edit_col + 1) {
# only 1 antibiotic # only 1 antibiotic
new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", unlist(lapply(strsplit(count_group, "-"), function(x) x[1])), ")") new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", unlist(lapply(strsplit(x = count_group, split = "-", fixed = TRUE), function(x) x[1])), ")")
colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N)") colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N)")
} else { } else {
# more than 1 antibiotic # more than 1 antibiotic
@ -574,27 +577,24 @@ autoplot.antibiogram <- function(object, ...) {
) )
} }
#' @export # will be exported in zzz.R
#' @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 [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.
#' @param italicise (only when `as_kable = TRUE`) 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. #' @param na character to use for showing `NA` values
#' @param na (only when `as_kable = TRUE`) character to use for showing `NA` values
#' @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 #' @rdname antibiogram
print.antibiogram <- function(x, as_kable = !interactive(), italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) { knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.kable.NA", default = ""), ...) {
meet_criteria(as_kable, allow_class = "logical", has_length = 1) stop_ifnot_installed("knitr")
meet_criteria(italicise, allow_class = "logical", has_length = 1) meet_criteria(italicise, allow_class = "logical", has_length = 1)
meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE) meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE)
if (isTRUE(as_kable) &&
pkg_is_available("knitr") &&
# be sure not to run kable in pkgdown for our website generation
!(missing(as_kable) && identical(Sys.getenv("IN_PKGDOWN"), "true"))) {
old_option <- getOption("knitr.kable.NA") old_option <- getOption("knitr.kable.NA")
options(knitr.kable.NA = na) options(knitr.kable.NA = na)
on.exit(options(knitr.kable.NA = old_option)) on.exit(options(knitr.kable.NA = old_option))
out <- knitr::kable(x, ...) out <- knitr::kable(x, ..., output = FALSE)
format <- attributes(out)$format format <- attributes(out)$format
if (!is.null(format) && format %in% c("markdown", "pipe")) { if (isTRUE(italicise) &&
!is.null(format) &&
format %in% c("markdown", "pipe")) {
# try to italicise the output # try to italicise the output
rows_with_txt <- which(out %like% "[a-z]") rows_with_txt <- which(out %like% "[a-z]")
rows_without_txt <- setdiff(seq_len(length(out)), rows_with_txt) rows_without_txt <- setdiff(seq_len(length(out)), rows_with_txt)
@ -611,11 +611,6 @@ print.antibiogram <- function(x, as_kable = !interactive(), italicise = TRUE, na
attributes(out_ita) <- attributes(out) attributes(out_ita) <- attributes(out)
out <- out_ita out <- out_ita
} }
out res <- paste(c("", "", out), collapse = "\n")
knitr::asis_output(res)
} else {
# remove 'antibiogram' class and print with default method
class(x) <- class(x)[class(x) != "antibiogram"]
print(x, ...)
}
} }

48
R/plot.R
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@ -146,15 +146,15 @@ plot.mic <- function(x,
legend_txt <- character(0) legend_txt <- character(0)
legend_col <- character(0) legend_col <- character(0)
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) { if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- "Susceptible" legend_txt <- c(legend_txt, "(S) Susceptible")
legend_col <- colours_SIR[1] legend_col <- colours_SIR[1]
} }
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) { if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline)) legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
legend_col <- c(legend_col, colours_SIR[2]) legend_col <- c(legend_col, colours_SIR[2])
} }
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) { if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Resistant") legend_txt <- c(legend_txt, "(R) Resistant")
legend_col <- c(legend_col, colours_SIR[3]) legend_col <- c(legend_col, colours_SIR[3])
} }
@ -272,11 +272,13 @@ autoplot.mic <- function(object,
df <- as.data.frame(x, stringsAsFactors = TRUE) df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("mic", "count") colnames(df) <- c("mic", "count")
df$cols <- cols_sub$cols df$cols <- cols_sub$cols
df$cols[df$cols == colours_SIR[1]] <- "Susceptible" df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[2]] <- plot_name_of_I(cols_sub$guideline) df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[3]] <- "Resistant" df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language), df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"), levels = translate_into_language(c("(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"),
language = language language = language
), ),
ordered = TRUE ordered = TRUE
@ -285,10 +287,10 @@ autoplot.mic <- function(object,
if (any(colours_SIR %in% cols_sub$cols)) { if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c( vals <- c(
"Susceptible" = colours_SIR[1], "(S) Susceptible" = colours_SIR[1],
"Susceptible, incr. exp." = colours_SIR[2], "(I) Susceptible, incr. exp." = colours_SIR[2],
"Intermediate" = colours_SIR[2], "(I) Intermediate" = colours_SIR[2],
"Resistant" = colours_SIR[3] "(R) Resistant" = colours_SIR[3]
) )
names(vals) <- translate_into_language(names(vals), language = language) names(vals) <- translate_into_language(names(vals), language = language)
p <- p + p <- p +
@ -386,15 +388,15 @@ plot.disk <- function(x,
legend_txt <- character(0) legend_txt <- character(0)
legend_col <- character(0) legend_col <- character(0)
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) { if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- "Resistant" legend_txt <- "(R) Resistant"
legend_col <- colours_SIR[3] legend_col <- colours_SIR[3]
} }
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) { if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline)) legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
legend_col <- c(legend_col, colours_SIR[2]) legend_col <- c(legend_col, colours_SIR[2])
} }
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) { if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Susceptible") legend_txt <- c(legend_txt, "(S) Susceptible")
legend_col <- c(legend_col, colours_SIR[1]) legend_col <- c(legend_col, colours_SIR[1])
} }
legend("top", legend("top",
@ -512,11 +514,13 @@ autoplot.disk <- function(object,
colnames(df) <- c("disk", "count") colnames(df) <- c("disk", "count")
df$cols <- cols_sub$cols df$cols <- cols_sub$cols
df$cols[df$cols == colours_SIR[1]] <- "Susceptible" df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[2]] <- plot_name_of_I(cols_sub$guideline) df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[3]] <- "Resistant" df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language), df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"), levels = translate_into_language(c("(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant"),
language = language language = language
), ),
ordered = TRUE ordered = TRUE
@ -525,10 +529,10 @@ autoplot.disk <- function(object,
if (any(colours_SIR %in% cols_sub$cols)) { if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c( vals <- c(
"Susceptible" = colours_SIR[1], "(S) Susceptible" = colours_SIR[1],
"Susceptible, incr. exp." = colours_SIR[2], "(I) Susceptible, incr. exp." = colours_SIR[2],
"Intermediate" = colours_SIR[2], "(I) Intermediate" = colours_SIR[2],
"Resistant" = colours_SIR[3] "(R) Resistant" = colours_SIR[3]
) )
names(vals) <- translate_into_language(names(vals), language = language) names(vals) <- translate_into_language(names(vals), language = language)
p <- p + p <- p +

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R/sysdata.rda
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2
R/zzz.R
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@ -128,6 +128,8 @@ if (utf8_supported && !is_latex) {
s3_register("ggplot2::fortify", "sir") s3_register("ggplot2::fortify", "sir")
s3_register("ggplot2::fortify", "mic") s3_register("ggplot2::fortify", "mic")
s3_register("ggplot2::fortify", "disk") s3_register("ggplot2::fortify", "disk")
# Support for knitr / R Markdown
s3_register("knitr::knit_print", "antibiogram")
# Support vctrs package for use in e.g. dplyr verbs # Support vctrs package for use in e.g. dplyr verbs
# S3: ab_selector # S3: ab_selector
s3_register("vctrs::vec_ptype2", "character.ab_selector") s3_register("vctrs::vec_ptype2", "character.ab_selector")

16
data-raw/antibiograms.Rmd
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@ -22,41 +22,33 @@ example_isolates
### Traditional Antibiogram ### Traditional Antibiogram
```{r trad} ```{r trad}
print( antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems())) antibiotics = c(aminoglycosides(), carbapenems()))
)
``` ```
### Combined Antibiogram ### Combined Antibiogram
```{r comb} ```{r comb}
print( antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN")) antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
)
``` ```
### Syndromic Antibiogram ### Syndromic Antibiogram
```{r synd} ```{r synd}
print( antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()), antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward") syndromic_group = "ward")
)
``` ```
### Weighted-Incidence Syndromic Combination Antibiogram (WISCA) ### Weighted-Incidence Syndromic Combination Antibiogram (WISCA)
```{r wisca} ```{r wisca}
print( antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"), antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain", mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 & syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M", example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2")) "WISCA Group 1", "WISCA Group 2"))
)
``` ```

273
data-raw/antibiograms.html
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@ -11,7 +11,7 @@
<meta name="author" content="AMR package developers" /> <meta name="author" content="AMR package developers" />
<meta name="date" content="2023-02-18" /> <meta name="date" content="2023-02-23" />
<title>Generating antibiograms with the AMR package</title> <title>Generating antibiograms with the AMR package</title>
@ -299,18 +299,24 @@ overflow-y: auto;
border: 1px solid #ddd; border: 1px solid #ddd;
border-radius: 4px; border-radius: 4px;
} }
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before { .tabset-dropdown > .nav-tabs > li.active:before {
content: "\e259"; content: "";
font-family: 'Glyphicons Halflings'; font-family: 'Glyphicons Halflings';
display: inline-block; display: inline-block;
padding: 10px; padding: 10px;
border-right: 1px solid #ddd; border-right: 1px solid #ddd;
} }
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258"; content: "";
font-family: 'Glyphicons Halflings';
border: none; border: none;
} }
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active { .tabset-dropdown > .nav-tabs > li.active {
display: block; display: block;
} }
@ -353,7 +359,7 @@ display: none;
<h1 class="title toc-ignore">Generating antibiograms with the AMR <h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1> package</h1>
<h4 class="author">AMR package developers</h4> <h4 class="author">AMR package developers</h4>
<h4 class="date">2023-02-18</h4> <h4 class="date">2023-02-23</h4>
</div> </div>
@ -364,35 +370,34 @@ package</h1>
looks like:</p> looks like:</p>
<pre class="r"><code>example_isolates</code></pre> <pre class="r"><code>example_isolates</code></pre>
<pre><code>## # A tibble: 2,000 × 46 <pre><code>## # A tibble: 2,000 × 46
## date patient age gender ward mo PEN OXA FLC AMX ## date patient age gender ward mo PEN
## &lt;date&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;chr&gt; &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; ## &lt;date&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;chr&gt; &lt;mo&gt; &lt;sir&gt;
## 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA ## 1 2002-01-02 A77334 65 F Clini… B_ESCHR_COLI R
## 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA ## 2 2002-01-03 A77334 65 F Clini… B_ESCHR_COLI R
## 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA ## 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R
## 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA ## 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R
## 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA ## 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R
## 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA ## 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R
## 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R ## 7 2002-01-14 462729 78 M Clini… B_STPHY_AURS R
## 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R ## 8 2002-01-14 462729 78 M Clini… B_STPHY_AURS R
## 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA ## 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R
## 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA ## 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R
## # … with 1,990 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, ## # … with 1,990 more rows, and 39 more variables: OXA &lt;sir&gt;,
## # TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, ## # FLC &lt;sir&gt;, AMX &lt;sir&gt;, AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;,
## # CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, ## # CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,
## # TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;, ## # CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;,
## # MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;, TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ## # KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;,
## # ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;, IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, ## # LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;,
## # CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, RIF &lt;sir&gt;</code></pre> ## # TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, …
## # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</code></pre>
<div id="traditional-antibiogram" class="section level3"> <div id="traditional-antibiogram" class="section level3">
<h3>Traditional Antibiogram</h3> <h3>Traditional Antibiogram</h3>
<pre class="r"><code>print( <pre class="r"><code>antibiogram(example_isolates,
antibiogram(example_isolates, antibiotics = c(aminoglycosides(), carbapenems()))</code></pre>
antibiotics = c(aminoglycosides(), carbapenems()))
)</code></pre>
<table> <table>
<thead> <thead>
<tr class="header"> <tr class="header">
<th align="left">Pathogen (N min-max)</th> <th align="left">Pathogeen (N min-max)</th>
<th align="right">AMK</th> <th align="right">AMK</th>
<th align="right">GEN</th> <th align="right">GEN</th>
<th align="right">IPM</th> <th align="right">IPM</th>
@ -403,7 +408,7 @@ looks like:</p>
</thead> </thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">CoNS (43-309)</td> <td align="left">CNS (43-309)</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">86</td> <td align="right">86</td>
<td align="right">52</td> <td align="right">52</td>
@ -416,7 +421,7 @@ looks like:</p>
<td align="right">100</td> <td align="right">100</td>
<td align="right">98</td> <td align="right">98</td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">97</td> <td align="right">97</td>
</tr> </tr>
@ -426,70 +431,70 @@ looks like:</p>
<td align="right">0</td> <td align="right">0</td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>K. pneumoniae</em> (0-58)</td> <td align="left"><em>K. pneumoniae</em> (0-58)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">90</td> <td align="right">90</td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">90</td> <td align="right">90</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>P. aeruginosa</em> (17-30)</td> <td align="left"><em>P. aeruginosa</em> (17-30)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>P. mirabilis</em> (0-34)</td> <td align="left"><em>P. mirabilis</em> (0-34)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">94</td> <td align="right">94</td>
<td align="right">94</td> <td align="right">94</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">94</td> <td align="right">94</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>S. aureus</em> (2-233)</td> <td align="left"><em>S. aureus</em> (2-233)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">99</td> <td align="right">99</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">98</td> <td align="right">98</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>S. epidermidis</em> (8-163)</td> <td align="left"><em>S. epidermidis</em> (8-163)</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">79</td> <td align="right">79</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">51</td> <td align="right">51</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>S. hominis</em> (3-80)</td> <td align="left"><em>S. hominis</em> (3-80)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">92</td> <td align="right">92</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">85</td> <td align="right">85</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>S. pneumoniae</em> (11-117)</td> <td align="left"><em>S. pneumoniae</em> (11-117)</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
</tr> </tr>
</tbody> </tbody>
@ -497,14 +502,12 @@ looks like:</p>
</div> </div>
<div id="combined-antibiogram" class="section level3"> <div id="combined-antibiogram" class="section level3">
<h3>Combined Antibiogram</h3> <h3>Combined Antibiogram</h3>
<pre class="r"><code>print( <pre class="r"><code>antibiogram(example_isolates,
antibiogram(example_isolates, antibiotics = c(&quot;TZP&quot;, &quot;TZP+TOB&quot;, &quot;TZP+GEN&quot;))</code></pre>
antibiotics = c(&quot;TZP&quot;, &quot;TZP+TOB&quot;, &quot;TZP+GEN&quot;))
)</code></pre>
<table> <table>
<thead> <thead>
<tr class="header"> <tr class="header">
<th align="left">Pathogen (N min-max)</th> <th align="left">Pathogeen (N min-max)</th>
<th align="right">TZP</th> <th align="right">TZP</th>
<th align="right">TZP + GEN</th> <th align="right">TZP + GEN</th>
<th align="right">TZP + TOB</th> <th align="right">TZP + TOB</th>
@ -512,10 +515,10 @@ looks like:</p>
</thead> </thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">CoNS (29-274)</td> <td align="left">CNS (29-274)</td>
<td align="right">30</td> <td align="right">30</td>
<td align="right">97</td> <td align="right">97</td>
<td align="right">NA</td> <td align="right"></td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>E. coli</em> (416-461)</td> <td align="left"><em>E. coli</em> (416-461)</td>
@ -531,31 +534,31 @@ looks like:</p>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>P. aeruginosa</em> (27-30)</td> <td align="left"><em>P. aeruginosa</em> (27-30)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>P. mirabilis</em> (27-34)</td> <td align="left"><em>P. mirabilis</em> (27-34)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>S. aureus</em> (7-231)</td> <td align="left"><em>S. aureus</em> (7-231)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"><em>S. epidermidis</em> (5-128)</td> <td align="left"><em>S. epidermidis</em> (5-128)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"><em>S. hominis</em> (0-74)</td> <td align="left"><em>S. hominis</em> (0-74)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
@ -570,26 +573,14 @@ looks like:</p>
</div> </div>
<div id="syndromic-antibiogram" class="section level3"> <div id="syndromic-antibiogram" class="section level3">
<h3>Syndromic Antibiogram</h3> <h3>Syndromic Antibiogram</h3>
<pre class="r"><code>print( <pre class="r"><code>antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()), antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = &quot;ward&quot;) syndromic_group = &quot;ward&quot;)</code></pre>
)</code></pre>
<table> <table>
<colgroup>
<col width="29%" />
<col width="33%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
</colgroup>
<thead> <thead>
<tr class="header"> <tr class="header">
<th align="left">Syndromic Group</th> <th align="left">Syndroomgroep</th>
<th align="left">Pathogen (N min-max)</th> <th align="left">Pathogeen (N min-max)</th>
<th align="right">AMK</th> <th align="right">AMK</th>
<th align="right">GEN</th> <th align="right">GEN</th>
<th align="right">IPM</th> <th align="right">IPM</th>
@ -601,33 +592,33 @@ looks like:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">CoNS (23-205)</td> <td align="left">CNS (23-205)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">89</td> <td align="right">89</td>
<td align="right">57</td> <td align="right">57</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">57</td> <td align="right">57</td>
<td align="right">26</td> <td align="right">26</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">CoNS (10-73)</td> <td align="left">CNS (10-73)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">79</td> <td align="right">79</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Outpatient</td> <td align="left">Outpatient</td>
<td align="left">CoNS (3-31)</td> <td align="left">CNS (3-31)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">84</td> <td align="right">84</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
@ -635,7 +626,7 @@ looks like:</p>
<td align="right">100</td> <td align="right">100</td>
<td align="right">98</td> <td align="right">98</td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">98</td> <td align="right">98</td>
</tr> </tr>
@ -645,78 +636,78 @@ looks like:</p>
<td align="right">100</td> <td align="right">100</td>
<td align="right">99</td> <td align="right">99</td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">96</td> <td align="right">96</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">K. <em>pneumoniae</em> (0-51)</td> <td align="left">K. <em>pneumoniae</em> (0-51)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">92</td> <td align="right">92</td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">92</td> <td align="right">92</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">P. <em>mirabilis</em> (0-30)</td> <td align="left">P. <em>mirabilis</em> (0-30)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">S. <em>aureus</em> (2-150)</td> <td align="left">S. <em>aureus</em> (2-150)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">99</td> <td align="right">99</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">97</td> <td align="right">97</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">S. <em>aureus</em> (0-66)</td> <td align="left">S. <em>aureus</em> (0-66)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">100</td> <td align="right">100</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">S. <em>epidermidis</em> (4-79)</td> <td align="left">S. <em>epidermidis</em> (4-79)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">82</td> <td align="right">82</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">55</td> <td align="right">55</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">ICU</td> <td align="left">ICU</td>
<td align="left">S. <em>epidermidis</em> (4-75)</td> <td align="left">S. <em>epidermidis</em> (4-75)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">72</td> <td align="right">72</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">41</td> <td align="right">41</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Clinical</td> <td align="left">Clinical</td>
<td align="left">S. <em>hominis</em> (1-45)</td> <td align="left">S. <em>hominis</em> (1-45)</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">96</td> <td align="right">96</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">94</td> <td align="right">94</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
@ -724,9 +715,9 @@ looks like:</p>
<td align="left">S. <em>pneumoniae</em> (5-78)</td> <td align="left">S. <em>pneumoniae</em> (5-78)</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
</tr> </tr>
<tr class="even"> <tr class="even">
@ -734,9 +725,9 @@ looks like:</p>
<td align="left">S. <em>pneumoniae</em> (5-30)</td> <td align="left">S. <em>pneumoniae</em> (5-30)</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
<td align="right">NA</td> <td align="right"></td>
<td align="right">0</td> <td align="right">0</td>
</tr> </tr>
</tbody> </tbody>
@ -744,19 +735,17 @@ looks like:</p>
</div> </div>
<div id="weighted-incidence-syndromic-combination-antibiogram-wisca" class="section level3"> <div id="weighted-incidence-syndromic-combination-antibiogram-wisca" class="section level3">
<h3>Weighted-Incidence Syndromic Combination Antibiogram (WISCA)</h3> <h3>Weighted-Incidence Syndromic Combination Antibiogram (WISCA)</h3>
<pre class="r"><code>print( <pre class="r"><code>antibiogram(example_isolates,
antibiogram(example_isolates,
antibiotics = c(&quot;AMC&quot;, &quot;AMC+CIP&quot;, &quot;TZP&quot;, &quot;TZP+TOB&quot;), antibiotics = c(&quot;AMC&quot;, &quot;AMC+CIP&quot;, &quot;TZP&quot;, &quot;TZP+TOB&quot;),
mo_transform = &quot;gramstain&quot;, mo_transform = &quot;gramstain&quot;,
minimum = 10, # this should be &gt;= 30, but now just as example minimum = 10, # this should be &gt;= 30, but now just as example
syndromic_group = ifelse(example_isolates$age &gt;= 65 &amp; syndromic_group = ifelse(example_isolates$age &gt;= 65 &amp;
example_isolates$gender == &quot;M&quot;, example_isolates$gender == &quot;M&quot;,
&quot;WISCA Group 1&quot;, &quot;WISCA Group 2&quot;)) &quot;WISCA Group 1&quot;, &quot;WISCA Group 2&quot;))</code></pre>
)</code></pre> <table style="width:100%;">
<table>
<colgroup> <colgroup>
<col width="24%" /> <col width="22%" />
<col width="34%" /> <col width="35%" />
<col width="5%" /> <col width="5%" />
<col width="14%" /> <col width="14%" />
<col width="5%" /> <col width="5%" />
@ -764,8 +753,8 @@ looks like:</p>
</colgroup> </colgroup>
<thead> <thead>
<tr class="header"> <tr class="header">
<th align="left">Syndromic Group</th> <th align="left">Syndroomgroep</th>
<th align="left">Pathogen (N min-max)</th> <th align="left">Pathogeen (N min-max)</th>
<th align="right">AMC</th> <th align="right">AMC</th>
<th align="right">AMC + CIP</th> <th align="right">AMC + CIP</th>
<th align="right">TZP</th> <th align="right">TZP</th>
@ -775,7 +764,7 @@ looks like:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">WISCA Group 1</td> <td align="left">WISCA Group 1</td>
<td align="left">Gram-negative (261-285)</td> <td align="left">Gram-negatief (261-285)</td>
<td align="right">76</td> <td align="right">76</td>
<td align="right">95</td> <td align="right">95</td>
<td align="right">89</td> <td align="right">89</td>
@ -783,7 +772,7 @@ looks like:</p>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">WISCA Group 2</td> <td align="left">WISCA Group 2</td>
<td align="left">Gram-negative (380-442)</td> <td align="left">Gram-negatief (380-442)</td>
<td align="right">76</td> <td align="right">76</td>
<td align="right">98</td> <td align="right">98</td>
<td align="right">88</td> <td align="right">88</td>
@ -791,7 +780,7 @@ looks like:</p>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">WISCA Group 1</td> <td align="left">WISCA Group 1</td>
<td align="left">Gram-positive (123-406)</td> <td align="left">Gram-positief (123-406)</td>
<td align="right">76</td> <td align="right">76</td>
<td align="right">89</td> <td align="right">89</td>
<td align="right">81</td> <td align="right">81</td>
@ -799,7 +788,7 @@ looks like:</p>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">WISCA Group 2</td> <td align="left">WISCA Group 2</td>
<td align="left">Gram-positive (222-732)</td> <td align="left">Gram-positief (222-732)</td>
<td align="right">76</td> <td align="right">76</td>
<td align="right">89</td> <td align="right">89</td>
<td align="right">88</td> <td align="right">88</td>

24
man/antibiogram.Rd
View File

@ -4,7 +4,7 @@
\alias{antibiogram} \alias{antibiogram}
\alias{plot.antibiogram} \alias{plot.antibiogram}
\alias{autoplot.antibiogram} \alias{autoplot.antibiogram}
\alias{print.antibiogram} \alias{knit_print.antibiogram}
\title{Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)} \title{Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)}
\source{ \source{
\itemize{ \itemize{
@ -35,9 +35,8 @@ antibiogram(
\method{autoplot}{antibiogram}(object, ...) \method{autoplot}{antibiogram}(object, ...)
\method{print}{antibiogram}( knit_print.antibiogram(
x, x,
as_kable = !interactive(),
italicise = TRUE, italicise = TRUE,
na = getOption("knitr.kable.NA", default = ""), na = getOption("knitr.kable.NA", default = ""),
... ...
@ -72,15 +71,13 @@ antibiogram(
\item{info}{a \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode} \item{info}{a \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode}
\item{...}{when used in \code{\link[=print]{print()}}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)} \item{...}{when used in \link[knitr:kable]{R Markdown or Quarto}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)}
\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object} \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 \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}{(only when \code{as_kable = TRUE}) 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.} \item{na}{character to use for showing \code{NA} values}
\item{na}{(only when \code{as_kable = TRUE}) character to use for showing \code{NA} values}
} }
\description{ \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. 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.
@ -137,7 +134,7 @@ your_data \%>\%
}\if{html}{\out{</div>}} }\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 printed into R Markdown / Quarto formats for reports using \code{print()}. 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()}. 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: 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:
@ -158,8 +155,6 @@ Note that for combination antibiograms, it is important to realise that suscepti
<NA> <NA> - - - - <NA> <NA> - - - -
-------------------------------------------------------------------- --------------------------------------------------------------------
}\if{html}{\out{</div>}} }\if{html}{\out{</div>}}
Printing the antibiogram in non-interactive sessions will be done by \code{\link[knitr:kable]{knitr::kable()}}, with support for \link[knitr:kable]{all their implemented formats}, such as "markdown". The knitr format will be automatically determined if printed inside a knitr document (LaTeX, HTML, etc.).
} }
\examples{ \examples{
# example_isolates is a data set available in the AMR package. # example_isolates is a data set available in the AMR package.
@ -244,8 +239,11 @@ ureido <- antibiogram(example_isolates,
antibiotics = ureidopenicillins(), antibiotics = ureidopenicillins(),
ab_transform = "name") ab_transform = "name")
# in an Rmd file, you would just need print(ureido), but to be explicit: # in an Rmd file, you would just need to return `ureido` in a chunk,
print(ureido, as_kable = TRUE, format = "markdown", italicise = TRUE) # but to be explicit here:
if (requireNamespace("knitr")) {
knitr::knit_print(ureido)
}
# Generate plots with ggplot2 or base R -------------------------------- # Generate plots with ggplot2 or base R --------------------------------