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7
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.0.9004 Version: 1.8.0.9002
Date: 2022-03-03 Date: 2022-03-02
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
@ -71,8 +71,7 @@ Depends: R (>= 3.0.0)
Enhances: Enhances:
cleaner, cleaner,
skimr, skimr,
ggplot2, ggplot2
tidyselect
Suggests: Suggests:
curl, curl,
dplyr, dplyr,

6
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.8.0.9004 # `AMR` 1.8.0.9002
## <small>Last updated: 3 March 2022</small> ## <small>Last updated: 2 March 2022</small>
All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months. All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
@ -11,8 +11,6 @@ All functions in this package are considered to be stable. Updates to the AMR in
#> [1] "Staphylococcus aureus" #> [1] "Staphylococcus aureus"
``` ```
* More informative warning messages * More informative warning messages
* Added 192 as valid MIC
* Updated MIC printing in tibbles
### Other ### Other
* Fix for unit testing on R 3.3 * Fix for unit testing on R 3.3

6
R/mic.R
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@ -37,8 +37,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
function(x) paste0(x, sort(c(1:9, 1.5)))))), function(x) paste0(x, sort(c(1:9, 1.5)))))),
c(t(vapply(FUN.VALUE = character(45), ops, c(t(vapply(FUN.VALUE = character(45), ops,
function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))), function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
c(t(vapply(FUN.VALUE = character(17), ops, c(t(vapply(FUN.VALUE = character(16), ops,
function(x) paste0(x, sort(c(2 ^ c(7:11), 192, 80 * c(2:12)))))))) function(x) paste0(x, sort(c(2 ^ c(7:11), 80 * c(2:12))))))))
#' Transform Input to Minimum Inhibitory Concentrations (MIC) #' Transform Input to Minimum Inhibitory Concentrations (MIC)
#' #'
@ -247,9 +247,7 @@ pillar_shaft.mic <- function(x, ...) {
out <- pasted out <- pasted
out[is.na(x)] <- font_na(NA) out[is.na(x)] <- font_na(NA)
out <- gsub("(<|=|>)", font_silver("\\1"), out) out <- gsub("(<|=|>)", font_silver("\\1"), out)
if (any(out %like% "[.]", na.rm = TRUE)) {
out <- gsub("([.]?0+)$", font_white("\\1"), out) out <- gsub("([.]?0+)$", font_white("\\1"), out)
}
create_pillar_column(out, align = "right", width = max(nchar(pasted))) create_pillar_column(out, align = "right", width = max(nchar(pasted)))
} }

2
R/rsi.R
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@ -67,7 +67,7 @@
#' #'
#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). #' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
#' #'
#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored. #' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
#' #'
#' ## After Interpretation #' ## After Interpretation
#' #'

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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <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="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span> </span>
</div> </div>

4
docs/articles/datasets.html
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@ -44,7 +44,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span> </span>
</div> </div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">03 March 2022</h4> <h4 data-toc-skip class="date">02 March 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div> <div class="hidden name"><code>datasets.Rmd</code></div>

15
docs/articles/datasets_files/accessible-code-block-0.0.1/empty-anchor.js
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@ -1,15 +0,0 @@
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
// v0.0.1
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
document.addEventListener('DOMContentLoaded', function() {
const codeList = document.getElementsByClassName("sourceCode");
for (var i = 0; i < codeList.length; i++) {
var linkList = codeList[i].getElementsByTagName('a');
for (var j = 0; j < linkList.length; j++) {
if (linkList[j].innerHTML === "") {
linkList[j].setAttribute('aria-hidden', 'true');
}
}
}
});

2
docs/authors.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -47,7 +47,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span> </span>
</div> </div>

14
docs/news/index.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span> </span>
</div> </div>
@ -157,13 +157,13 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="page-header" data-toc-text="1.8.0.9004" id="amr-1809004"> <h2 class="page-header" data-toc-text="1.8.0.9002" id="amr-1809002">
<code>AMR</code> 1.8.0.9004<a class="anchor" aria-label="anchor" href="#amr-1809004"></a></h2> <code>AMR</code> 1.8.0.9002<a class="anchor" aria-label="anchor" href="#amr-1809002"></a></h2>
<div class="section level3"> <div class="section level3">
<h3 id="last-updated-march-1-8-0-9004"><small>Last updated: 3 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9004"></a></h3> <h3 id="last-updated-march-1-8-0-9002"><small>Last updated: 2 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9002"></a></h3>
<p>All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p> <p>All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
<div class="section level4"> <div class="section level4">
<h4 id="changed-1-8-0-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9004"></a></h4> <h4 id="changed-1-8-0-9002">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9002"></a></h4>
<ul><li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li> <ul><li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
<li> <li>
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p> <p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p>
@ -173,11 +173,9 @@
<span class="co">#&gt; [1] "Staphylococcus aureus"</span></code></pre></div> <span class="co">#&gt; [1] "Staphylococcus aureus"</span></code></pre></div>
</li> </li>
<li><p>More informative warning messages</p></li> <li><p>More informative warning messages</p></li>
<li><p>Added 192 as valid MIC</p></li>
<li><p>Updated MIC printing in tibbles</p></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="other-1-8-0-9004">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9004"></a></h4> <h4 id="other-1-8-0-9002">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9002"></a></h4>
<ul><li>Fix for unit testing on R 3.3</li> <ul><li>Fix for unit testing on R 3.3</li>
<li>Fix for size of some image elements, as requested by CRAN</li> <li>Fix for size of some image elements, as requested by CRAN</li>
</ul></div> </ul></div>

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docs/reference/AMR-deprecated.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

2
docs/reference/WHOCC.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

2
docs/reference/ab_from_text.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

2
docs/reference/ab_property.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/age.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/age_groups.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/antibiotic_class_selectors.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/antibiotics.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

2
docs/reference/as.ab.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/as.disk.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/as.mic.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/as.mo.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
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</span> </span>
</div> </div>

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docs/reference/as.rsi.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>
@ -264,7 +264,7 @@
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).</p> <p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2021"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p> <p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2021"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
</div> </div>
<div class="section"> <div class="section">

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
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docs/reference/count.html
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@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -18,7 +18,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/kurtosis.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -19,7 +19,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/microorganisms.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/microorganisms.old.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/mo_matching_score.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/mo_property.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/mo_source.html
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@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/proportion.html
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@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/random.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/resistance_predict.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
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docs/reference/skewness.html
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@ -18,7 +18,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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docs/reference/translate.html
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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
</span> </span>
</div> </div>

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@ -17,7 +17,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9004</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
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man/as.rsi.Rd
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@ -113,7 +113,7 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2021"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored. Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2021"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
} }
\subsection{After Interpretation}{ \subsection{After Interpretation}{