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dr. M.S. (Matthijs) Berends 2022-05-16 09:29:46 +02:00
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DESCRIPTION
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Package: AMR
Version: 1.8.1.9008
Date: 2022-05-11
Version: 1.8.1.9009
Date: 2022-05-16
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

5
NEWS.md
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# `AMR` 1.8.1.9008
## <small>Last updated: 11 mei 2022</small>
# `AMR` 1.8.1.9009
## <small>Last updated: 16 May 2022</small>
### New
* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
@ -10,6 +10,7 @@
* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class.
* Small fix for using `ab_from_text()`
* Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
* Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
# `AMR` 1.8.1

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R/data.R
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#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
#' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
#' @details
#' Overview of the data set:
#'
#' ```{r}
#' head(rsi_translation)
#' ```
#'
#' The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @seealso [intrinsic_resistant]

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R/random.R
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#' @param ... ignored, only in place to allow future extensions
#' @details The base \R function [sample()] is used for generating values.
#'
#' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
#' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
#' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
#' @name random
#' @rdname random
@ -89,6 +89,7 @@ random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
}
random_exec <- function(type, size, mo = NULL, ab = NULL) {
check_dataset_integrity()
df <- rsi_translation %pm>%
pm_filter(guideline %like% "EUCAST") %pm>%
pm_arrange(pm_desc(guideline)) %pm>%

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R/rsi.R
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@ -33,7 +33,7 @@
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate
#' @param guideline defaults to the latest included EUCAST guideline, supports 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)))`), see *Details*
#' @param guideline defaults to EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [rsi_translation] data set), supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$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)))`), see *Details*
#' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.

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docs/404.html
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</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

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docs/LICENSE-text.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

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docs/articles/datasets.html
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@ -44,7 +44,7 @@
</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">11 mei 2022</h4>
<h4 data-toc-skip class="date">16 May 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>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -224,8 +224,8 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</e
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R
@ -466,8 +466,8 @@ i.e. of column <em>‘fullname_new’</em>, see the
<code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R
@ -553,8 +553,8 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R
@ -740,8 +740,8 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
<em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R
@ -883,13 +883,13 @@ Dipivoxil, …</td>
<div class="section level2">
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</h2>
<p>A data set with 20,369 rows and 11 columns, containing the following
<p>A data set with 20,318 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</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 11 mei 2022 08:14:33 UTC. Find more info about
<p>It was last updated on 10 May 2022 19:42:39 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>
@ -915,8 +915,8 @@ file</a> (3.8 MB)</li>
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
(2011-2022).</p>
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
(2011-2021).</p>
</div>
<div class="section level3">
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@ -954,7 +954,7 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_MGTS</td>
@ -965,11 +965,11 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">4</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_NIGR</td>
@ -980,11 +980,11 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">4</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD</td>
@ -995,11 +995,11 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_ALBC</td>
@ -1010,26 +1010,11 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2022</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_DBLN</td>
<td align="center">Candida dubliniensis</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_KRUS</td>
@ -1040,7 +1025,22 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_PRPS</td>
<td align="center">Candida parapsilosis</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
</tbody>
@ -1054,8 +1054,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R
@ -1335,8 +1335,8 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R

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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

2
docs/index.html
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@ -47,7 +47,7 @@
</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

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docs/news/index.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>
@ -157,16 +157,16 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.1.9008" id="amr-1819008">
<code>AMR</code> 1.8.1.9008<a class="anchor" aria-label="anchor" href="#amr-1819008"></a></h2>
<h2 class="page-header" data-toc-text="1.8.1.9009" id="amr-1819009">
<code>AMR</code> 1.8.1.9009<a class="anchor" aria-label="anchor" href="#amr-1819009"></a></h2>
<div class="section level3">
<h3 id="last-updated-mei-1-8-1-9008"><small>Last updated: 11 mei 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-mei-1-8-1-9008"></a></h3>
<h3 id="last-updated-may-1-8-1-9009"><small>Last updated: 16 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9009"></a></h3>
<div class="section level4">
<h4 id="new-1-8-1-9008">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9008"></a></h4>
<h4 id="new-1-8-1-9009">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9009"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9008"></a></h4>
<h4 id="changed-1-8-1-9009">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9009"></a></h4>
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>
@ -174,6 +174,8 @@
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
</li>
<li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
<li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
</li>
</ul></div>
</div>
</div>
@ -1693,7 +1695,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
<span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu">microbenchmark</span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
<span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
<span class="co"># Unit: seconds</span>
<span class="co"># min median max neval</span>
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span></code></pre></div>

2
docs/reference/antibiotic_class_selectors.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

4
docs/reference/as.rsi.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>
@ -225,7 +225,7 @@
<dt>ab</dt>
<dd><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>guideline</dt>
<dd><p>defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see <em>Details</em></p></dd>
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see <em>Details</em></p></dd>
<dt>uti</dt>
<dd><p>(Urinary Tract Infection) A vector with <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, this can also be a column containing <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
<dt>conserve_capped_values</dt>

4
docs/reference/g.test.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>
@ -180,7 +180,7 @@
<dd><p>a numeric vector; ignored if <code>x</code> is a matrix. If
<code>x</code> is a factor, <code>y</code> should be a factor of the same length.</p></dd>
<dt>p</dt>
<dd><p>a vector of probabilities of the same length of <code>x</code>.
<dd><p>a vector of probabilities of the same length as <code>x</code>.
An error is given if any entry of <code>p</code> is negative.</p></dd>
<dt>rescale.p</dt>
<dd><p>a logical scalar; if TRUE then <code>p</code> is rescaled

2
docs/reference/index.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

2
docs/reference/intrinsic_resistant.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

2
docs/reference/mdro.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

2
docs/reference/mo_source.html
View File

@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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="Released version">1.8.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

4
docs/reference/random.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>
@ -189,7 +189,7 @@
<div id="details">
<h2>Details</h2>
<p>The base <span style="R">R</span> function <code><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample()</a></code> is used for generating values.</p>
<p>Generated values are based on the latest EUCAST guideline implemented in the <a href="rsi_translation.html">rsi_translation</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
<p>Generated values are based on the EUCAST 2022 guideline as implemented in the <a href="rsi_translation.html">rsi_translation</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>

19
docs/reference/rsi_translation.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>
@ -181,7 +181,22 @@
</ul></div>
<div id="details">
<h2>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
<p>Overview of the data set:</p><div class="sourceCode r"><pre><code><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></code></pre><p></p></div><div class="sourceCode"><pre><code><span class="co">## guideline method site mo rank_index ab ref_tbl disk_dose</span>
<span class="co">## 1 EUCAST 2022 MIC &lt;NA&gt; F_ASPRG_MGTS 2 AMB Aspergillus &lt;NA&gt;</span>
<span class="co">## 2 EUCAST 2022 MIC &lt;NA&gt; F_ASPRG_NIGR 2 AMB Aspergillus &lt;NA&gt;</span>
<span class="co">## 3 EUCAST 2022 MIC &lt;NA&gt; F_CANDD 3 AMB Candida &lt;NA&gt;</span>
<span class="co">## 4 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_ALBC 2 AMB Candida &lt;NA&gt;</span>
<span class="co">## 5 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_DBLN 2 AMB Candida &lt;NA&gt;</span>
<span class="co">## 6 EUCAST 2022 MIC &lt;NA&gt; F_CANDD_KRUS 2 AMB Candida &lt;NA&gt;</span>
<span class="co">## breakpoint_S breakpoint_R uti</span>
<span class="co">## 1 1 1 FALSE</span>
<span class="co">## 2 1 1 FALSE</span>
<span class="co">## 3 1 1 FALSE</span>
<span class="co">## 4 1 1 FALSE</span>
<span class="co">## 5 1 1 FALSE</span>
<span class="co">## 6 1 1 FALSE</span></code></pre></div>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
</div>
<div id="reference-data-publicly-available">
<h2>Reference Data Publicly Available</h2>

2
docs/survey.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9009</span>
</span>
</div>

2
man/as.rsi.Rd
View File

@ -68,7 +68,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}

2
man/g.test.Rd
View File

@ -21,7 +21,7 @@ g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)
\item{y}{a numeric vector; ignored if \code{x} is a matrix. If
\code{x} is a factor, \code{y} should be a factor of the same length.}
\item{p}{a vector of probabilities of the same length of \code{x}.
\item{p}{a vector of probabilities of the same length as \code{x}.
An error is given if any entry of \code{p} is negative.}
\item{rescale.p}{a logical scalar; if TRUE then \code{p} is rescaled

2
man/random.Rd
View File

@ -33,7 +33,7 @@ These functions can be used for generating random MIC values and disk diffusion
\details{
The base \R function \code{\link[=sample]{sample()}} is used for generating values.
Generated values are based on the latest EUCAST guideline implemented in the \link{rsi_translation} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
Generated values are based on the EUCAST 2022 guideline as implemented in the \link{rsi_translation} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
}
\section{Stable Lifecycle}{

17
man/rsi_translation.Rd
View File

@ -27,6 +27,23 @@ rsi_translation
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
Overview of the data set:\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
}\if{html}{\out{</div>}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
## 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
## 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
## 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
## 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
## 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
## 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
## breakpoint_S breakpoint_R uti
## 1 1 1 FALSE
## 2 1 1 FALSE
## 3 1 1 FALSE
## 4 1 1 FALSE
## 5 1 1 FALSE
## 6 1 1 FALSE
}
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.
}
\section{Reference Data Publicly Available}{