(v1.7.1.9020) autoplot generics

v1.8.2
parent fc946564d1
commit 6838f03bde
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      DESCRIPTION
  2. 7
      NEWS.md
  3. 148
      R/plot.R
  4. 28
      R/resistance_predict.R
  5. 4
      R/zzz.R
  6. BIN
      data-raw/AMR_latest.tar.gz
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      docs/404.html
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      docs/LICENSE-text.html
  9. 4
      docs/articles/datasets.html
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      docs/authors.html
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      docs/news/index.html
  14. 2
      docs/pkgdown.yml
  15. 2
      docs/reference/as.rsi.html
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      inst/tinytest/test-mic.R
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      inst/tinytest/test-resistance_predict.R
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      man/resistance_predict.Rd

@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9019
Version: 1.7.1.9020
Date: 2021-07-12
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

@ -1,22 +1,21 @@
# `AMR` 1.7.1.9019
# `AMR` 1.7.1.9020
## <small>Last updated: 12 July 2021</small>
### Changed
* Previously implemented `ggplot2::gggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` did not follow the `ggplot2` logic, and were replaced with `autoplot()` generics.
* Antibiotic class selectors (see `ab_class()`)
* They now also work in R-3.0 and R-3.1, supporting every version of R since 2013
* Added more selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
* Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
* Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
* Fix for duplicate ATC codes in the `antibiotics` data set
* Added `ggplot2::autoplot()` generic for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>`
* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
* When warnings are throws because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* Taxonomic names now print in italic in tibbles, if created with `mo_name()`, `mo_fullname()`, `mo_shortname()`, `mo_genus()` or `mo_family()`
* When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* `ab_name()` gained argument `snake_case`, which is useful for column renaming
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed)
* Fix for minor translation errors

@ -26,15 +26,14 @@
#' Plotting for Classes `rsi`, `mic` and `disk`
#'
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
#' @inheritSection lifecycle Stable Lifecycle
#' @inheritSection lifecycle Maturing Lifecycle
#' @inheritSection AMR Read more on Our Website!
#' @param x,data MIC values created with [as.mic()] or disk diffusion values created with [as.disk()]
#' @param mapping aesthetic mappings to use for [`ggplot()`][ggplot2::ggplot()]
#' @param main,title title of the plot
#' @param xlab,ylab axis title
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()]
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
#' @param main,title title of the plot
#' @param xlab,ylab axis title
#' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
#' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
@ -46,7 +45,7 @@
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
#' @name plot
#' @rdname plot
#' @return The `ggplot` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
#' @param ... arguments passed on to [as.rsi()]
#' @examples
#' some_mic_values <- random_mic(size = 100)
@ -63,9 +62,9 @@
#'
#' \donttest{
#' if (require("ggplot2")) {
#' ggplot(some_mic_values)
#' ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
#' ggplot(some_rsi_values)
#' autoplot(some_mic_values)
#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
#' autoplot(some_rsi_values)
#' }
#' }
NULL
@ -75,22 +74,22 @@ NULL
#' @export
#' @rdname plot
plot.mic <- function(x,
main = paste("MIC values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -161,12 +160,12 @@ plot.mic <- function(x,
#' @export
#' @noRd
barplot.mic <- function(height,
main = paste("MIC values of", deparse(substitute(height))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(height))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
@ -202,28 +201,27 @@ barplot.mic <- function(height,
...)
}
#' @method ggplot mic
#' @method autplot mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
ggplot.mic <- function(data,
mapping = NULL,
title = paste("MIC values of", deparse(substitute(data))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
autoplot.mic <- function(object,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
title = paste("MIC values of", deparse(substitute(object))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -243,7 +241,7 @@ ggplot.mic <- function(data,
title <- gsub(" +", " ", paste0(title, collapse = " "))
}
x <- plot_prepare_table(data, expand = expand)
x <- plot_prepare_table(object, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo,
ab = ab,
@ -262,11 +260,7 @@ ggplot.mic <- function(data,
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language),
ordered = TRUE)
if (!is.null(mapping)) {
p <- ggplot2::ggplot(df, mapping = mapping)
} else {
p <- ggplot2::ggplot(df)
}
p <- ggplot2::ggplot(df)
if (any(colours_RSI %in% cols_sub$cols)) {
vals <- c("Resistant" = colours_RSI[1],
@ -289,10 +283,6 @@ ggplot.mic <- function(data,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method autoplot mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.mic <- ggplot.mic
#' @method plot disk
#' @export
@ -427,21 +417,20 @@ barplot.disk <- function(height,
...)
}
#' @method ggplot disk
#' @method autoplot disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
ggplot.disk <- function(data,
mapping = NULL,
title = paste("Disk zones of", deparse(substitute(data))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
autoplot.disk <- function(object,
mo = NULL,
ab = NULL,
title = paste("Disk zones of", deparse(substitute(object))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
@ -468,7 +457,7 @@ ggplot.disk <- function(data,
title <- gsub(" +", " ", paste0(title, collapse = " "))
}
x <- plot_prepare_table(data, expand = expand)
x <- plot_prepare_table(object, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(x = x,
mo = mo,
ab = ab,
@ -488,11 +477,7 @@ ggplot.disk <- function(data,
levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language),
ordered = TRUE)
if (!is.null(mapping)) {
p <- ggplot2::ggplot(df, mapping = mapping)
} else {
p <- ggplot2::ggplot(df)
}
p <- ggplot2::ggplot(df)
if (any(colours_RSI %in% cols_sub$cols)) {
vals <- c("Resistant" = colours_RSI[1],
@ -515,11 +500,6 @@ ggplot.disk <- function(data,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method autoplot disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.disk <- ggplot.disk
#' @method plot rsi
#' @export
#' @importFrom graphics plot text axis
@ -618,17 +598,16 @@ barplot.rsi <- function(height,
axis(2, seq(0, max(x)))
}
#' @method ggplot rsi
#' @method autoplot rsi
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
ggplot.rsi <- function(data,
mapping = NULL,
title = paste("Resistance Overview of", deparse(substitute(data))),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
...) {
autoplot.rsi <- function(object,
title = paste("Resistance Overview of", deparse(substitute(object))),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
@ -654,15 +633,9 @@ ggplot.rsi <- function(data,
colours_RSI <- rep(colours_RSI, 3)
}
df <- as.data.frame(table(data), stringsAsFactors = TRUE)
df <- as.data.frame(table(object), stringsAsFactors = TRUE)
colnames(df) <- c("rsi", "count")
if (!is.null(mapping)) {
p <- ggplot2::ggplot(df, mapping = mapping)
} else {
p <- ggplot2::ggplot(df)
}
p +
ggplot2::ggplot(df) +
ggplot2::geom_col(ggplot2::aes(x = rsi, y = count, fill = rsi)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
ggplot2::scale_fill_manual(values = c("R" = colours_RSI[1],
@ -673,11 +646,6 @@ ggplot.rsi <- function(data,
ggplot2::theme(legend.position = "none")
}
#' @method autoplot rsi
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.rsi <- ggplot.rsi
plot_prepare_table <- function(x, expand) {
x <- x[!is.na(x)]
stop_if(length(x) == 0, "no observations to plot", call = FALSE)

@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Predict antimicrobial resistance
#' Predict Antimicrobial Resistance
#'
#' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
#' @inheritSection lifecycle Stable Lifecycle
@ -99,9 +99,9 @@
#' info = FALSE,
#' minimum = 15)
#'
#' ggplot(data)
#' autoplot(data)
#'
#' ggplot(as.data.frame(data),
#' ggplot(data,
#' aes(x = year)) +
#' geom_col(aes(y = value),
#' fill = "grey75") +
@ -394,20 +394,22 @@ ggplot_rsi_predict <- function(x,
p
}
#' @method ggplot resistance_predict
#' @method autoplot resistance_predict
#' @rdname resistance_predict
# will be exported using s3_register() in R/zzz.R
ggplot.resistance_predict <- function(x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...) {
x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
autoplot.resistance_predict <- function(object,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...) {
x_name <- paste0(ab_name(attributes(object)$ab), " (", attributes(object)$ab, ")")
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ribbon, allow_class = "logical", has_length = 1)
ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
ggplot_rsi_predict(x = object, main = main, ribbon = ribbon, ...)
}
#' @method autoplot resistance_predict
#' @rdname resistance_predict
#' @method fortify resistance_predict
#' @noRd
# will be exported using s3_register() in R/zzz.R
autoplot.resistance_predict <- ggplot.resistance_predict
fortify.resistance_predict <- function(model, data, ...) {
as.data.frame(model)
}

@ -61,10 +61,6 @@ if (utf8_supported && !is_latex) {
s3_register("skimr::get_skimmers", "rsi")
s3_register("skimr::get_skimmers", "mic")
s3_register("skimr::get_skimmers", "disk")
s3_register("ggplot2::ggplot", "rsi")
s3_register("ggplot2::ggplot", "mic")
s3_register("ggplot2::ggplot", "disk")
s3_register("ggplot2::ggplot", "resistance_predict")
s3_register("ggplot2::autoplot", "rsi")
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")

Binary file not shown.

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>
@ -1007,7 +1007,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 12 July 2021 10:10:26 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 12 July 2021 10:54:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>

@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719019" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9019">
<a href="#amr-1719019" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9019</h1>
<div id="amr-1719020" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9020">
<a href="#amr-1719020" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9020</h1>
<div id="last-updated-12-july-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-12-july-2021" class="anchor"></a><small>Last updated: 12 July 2021</small>
@ -247,6 +247,7 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Previously implemented <code>ggplot2::gggplot()</code> generics for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code> did not follow the <code>ggplot2</code> logic, and were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">autoplot()</a></code> generics.</li>
<li>Antibiotic class selectors (see <code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code>)
<ul>
<li>They now also work in R-3.0 and R-3.1, supporting every version of R since 2013</li>
@ -257,8 +258,6 @@
</ul>
</li>
<li>Fix for duplicate ATC codes in the <code>antibiotics</code> data set</li>
<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generic for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code>
</li>
<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
<li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
<li>When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using <code><a href="../reference/as.mo.html">as.mo()</a></code>
@ -268,9 +267,7 @@
<li>The right input types for <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> are now enforced</li>
<li>
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now correct for textual input (such as “Susceptible”, “Resistant”) in Dutch, English, French, German, Italian, Portuguese and Spanish</li>
<li>When warnings are throws because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
<li>Taxonomic names now print in italic in tibbles, if created with <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, <code><a href="../reference/mo_property.html">mo_shortname()</a></code>, <code><a href="../reference/mo_property.html">mo_genus()</a></code> or <code><a href="../reference/mo_property.html">mo_family()</a></code>
</li>
<li>When warnings are thrown because of too few isolates in any <code>count_*()</code>, <code>proportion_*()</code> function (or <code>resistant()</code> or <code>susceptible()</code>), the <code>dplyr</code> group will be shown, if available</li>
<li>
<code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li>
<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
@ -329,7 +326,7 @@
</ul>
</li>
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -430,7 +427,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@ -487,7 +484,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-07-12T10:28Z
last_built: 2021-07-12T18:24Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>
@ -508,7 +508,7 @@
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
</tr><tr>
@ -532,9 +532,9 @@
</tr><tr>
<td>
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">autoplot(<i>&lt;resistance_predict&gt;</i>)</a></code> </p>
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">autoplot(<i>&lt;resistance_predict&gt;</i>)</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
<td><p>Predict Antimicrobial Resistance</p></td>
</tr><tr>
<td>

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>
@ -245,28 +245,12 @@
<pre class="usage"><span class='co'># S3 method for mic</span>
<span class='fu'>plot</span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
@ -274,15 +258,14 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
<span class='fu'>autplot</span><span class='op'>(</span>
<span class='va'>object</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
@ -305,30 +288,13 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>object</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
@ -345,23 +311,10 @@
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
<span class='va'>object</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
@ -373,16 +326,8 @@
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x, data</th>
<td><p>MIC values created with <code><a href='as.mic.html'>as.mic()</a></code> or disk diffusion values created with <code><a href='as.disk.html'>as.disk()</a></code></p></td>
</tr>
<tr>
<th>main, title</th>
<td><p>title of the plot</p></td>
</tr>
<tr>
<th>xlab, ylab</th>
<td><p>axis title</p></td>
<th>x, object</th>
<td><p>values created with <code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code> or <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
</tr>
<tr>
<th>mo</th>
@ -396,6 +341,14 @@
<th>guideline</th>
<td><p>interpretation guideline to use, defaults to the latest included EUCAST guideline, see <em>Details</em></p></td>
</tr>
<tr>
<th>main, title</th>
<td><p>title of the plot</p></td>
</tr>
<tr>
<th>xlab, ylab</th>
<td><p>axis title</p></td>
</tr>
<tr>
<th>colours_RSI</th>
<td><p>colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.</p></td>
@ -412,27 +365,22 @@
<th>...</th>
<td><p>arguments passed on to <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
</tr>
<tr>
<th>mapping</th>
<td><p>aesthetic mappings to use for <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot()</a></code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The <code>ggplot</code> functions return a <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p>
<p>The <code><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot()</a></code> functions return a <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -454,9 +402,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Predict antimicrobial resistance — resistance_predict • AMR (for R)</title>
<title>Predict Antimicrobial Resistance — resistance_predict • AMR (for R)</title>
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@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Predict antimicrobial resistance — resistance_predict" />
<meta property="og:title" content="Predict Antimicrobial Resistance — resistance_predict" />
<meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
</span>
</div>
@ -90,14 +90,14 @@
<ul class="nav navbar-nav">
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@ -106,77 +106,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Get properties of a microorganism
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Get properties of an antibiotic
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@ -185,14 +185,14 @@
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