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(v0.7.1.9065) bug-drug fix

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dr. M.S. (Matthijs) Berends 2019-08-27 22:41:09 +02:00
parent f3276592b7
commit 248638ad91
23 changed files with 62 additions and 45 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9064 Version: 0.7.1.9065
Date: 2019-08-27 Date: 2019-08-27
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

8
NAMESPACE
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@ -23,7 +23,7 @@ S3method(c,ab)
S3method(c,mo) S3method(c,mo)
S3method(droplevels,mic) S3method(droplevels,mic)
S3method(droplevels,rsi) S3method(droplevels,rsi)
S3method(format,bugdrug) S3method(format,bug_drug_combinations)
S3method(freq,mo) S3method(freq,mo)
S3method(freq,rsi) S3method(freq,rsi)
S3method(kurtosis,data.frame) S3method(kurtosis,data.frame)
@ -38,7 +38,7 @@ S3method(plot,mic)
S3method(plot,resistance_predict) S3method(plot,resistance_predict)
S3method(plot,rsi) S3method(plot,rsi)
S3method(print,ab) S3method(print,ab)
S3method(print,bugdrug) S3method(print,bug_drug_combinations)
S3method(print,catalogue_of_life_version) S3method(print,catalogue_of_life_version)
S3method(print,disk) S3method(print,disk)
S3method(print,mic) S3method(print,mic)
@ -201,7 +201,7 @@ exportMethods(c.ab)
exportMethods(c.mo) exportMethods(c.mo)
exportMethods(droplevels.mic) exportMethods(droplevels.mic)
exportMethods(droplevels.rsi) exportMethods(droplevels.rsi)
exportMethods(format.bugdrug) exportMethods(format.bug_drug_combinations)
exportMethods(freq.mo) exportMethods(freq.mo)
exportMethods(freq.rsi) exportMethods(freq.rsi)
exportMethods(kurtosis) exportMethods(kurtosis)
@ -211,7 +211,7 @@ exportMethods(kurtosis.matrix)
exportMethods(plot.mic) exportMethods(plot.mic)
exportMethods(plot.rsi) exportMethods(plot.rsi)
exportMethods(print.ab) exportMethods(print.ab)
exportMethods(print.bugdrug) exportMethods(print.bug_drug_combinations)
exportMethods(print.catalogue_of_life_version) exportMethods(print.catalogue_of_life_version)
exportMethods(print.disk) exportMethods(print.disk)
exportMethods(print.mic) exportMethods(print.mic)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9064 # AMR 0.7.1.9065
### Breaking ### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`: * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:

15
R/bug_drug_combinations.R
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@ -24,12 +24,14 @@
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples. #' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
#' @inheritParams eucast_rules #' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed #' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @inheritParams rsi_df #' @inheritParams rsi_df
#' @importFrom dplyr rename #' @importFrom dplyr rename
#' @importFrom tidyr spread #' @importFrom tidyr spread
#' @importFrom clean freq #' @importFrom clean freq
#' @details The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S. #' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
#' @export #' @export
#' @rdname bug_drug_combinations
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. #' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
@ -65,14 +67,15 @@ bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
filter(total >= minimum) %>% filter(total >= minimum) %>%
rename(ab = antibiotic) rename(ab = antibiotic)
structure(.Data = x, class = c("bugdrug", class(x))) structure(.Data = x, class = c("bug_drug_combinations", class(x)))
} }
#' @importFrom dplyr everything rename #' @importFrom dplyr everything rename
#' @importFrom tidyr spread #' @importFrom tidyr spread
#' @exportMethod format.bugdrug #' @exportMethod format.bug_drug_combinations
#' @export #' @export
format.bugdrug <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) { #' @rdname bug_drug_combinations
format.bug_drug_combinations <- function(x, combine_IR = FALSE, add_ab_group = TRUE) {
if (combine_IR == FALSE) { if (combine_IR == FALSE) {
x$isolates <- x$R x$isolates <- x$R
} else { } else {
@ -100,10 +103,10 @@ format.bugdrug <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) {
y y
} }
#' @exportMethod print.bugdrug #' @exportMethod print.bug_drug_combinations
#' @export #' @export
#' @importFrom crayon blue #' @importFrom crayon blue
print.bugdrug <- function(x, ...) { print.bug_drug_combinations <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE)) print(as.data.frame(x, stringsAsFactors = FALSE))
message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing.")) message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing."))
} }

2
R/first_isolate.R
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@ -25,7 +25,7 @@
#' @param x a \code{data.frame} containing isolates. #' @param x a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive) #' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}. #' @param col_mo column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. #' @param col_testcode column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.
#' @param col_specimen column name of the specimen type or group #' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU) #' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9064" class="section level1"> <div id="amr-0-7-1-9065" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9064" class="anchor"></a>AMR 0.7.1.9064<small> Unreleased </small> <a href="#amr-0-7-1-9065" class="anchor"></a>AMR 0.7.1.9065<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -1258,7 +1258,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9064">0.7.1.9064</a></li> <li><a href="#amr-0-7-1-9065">0.7.1.9065</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

4
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -275,7 +275,7 @@
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>threshold</th> <th>threshold</th>

16
docs/reference/bug_drug_combinations.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -234,7 +234,11 @@
</div> </div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>)</pre> <pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>)
<span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments"> <table class="ref-arguments">
@ -245,7 +249,7 @@
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>minimum</th> <th>minimum</th>
@ -255,6 +259,10 @@
<th>combine_IR</th> <th>combine_IR</th>
<td><p>logical to indicate whether values R and I should be summed</p></td> <td><p>logical to indicate whether values R and I should be summed</p></td>
</tr> </tr>
<tr>
<th>add_ab_group</th>
<td><p>logical to indicate where the group of the antimicrobials must be included as a first column</p></td>
</tr>
</table> </table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@ -263,7 +271,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>format</code> calculated the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</p> <p>The function <code>format</code> calculates the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</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> <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>

6
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -246,7 +246,7 @@
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>info</th> <th>info</th>
@ -438,7 +438,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">

4
docs/reference/first_isolate.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -265,7 +265,7 @@
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>col_testcode</th> <th>col_testcode</th>

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@ -78,7 +78,7 @@
</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="Latest development version">0.7.1.9064</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -416,7 +416,7 @@
</tr><tr> </tr><tr>
<td> <td>
<p><code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> </p> <p><code><a href="bug_drug_combinations.html">bug_drug_combinations()</a></code> <code><a href="bug_drug_combinations.html">format(<i>&lt;bug_drug_combinations&gt;</i>)</a></code> </p>
</td> </td>
<td><p>Determine bug-drug combinations</p></td> <td><p>Determine bug-drug combinations</p></td>
</tr><tr> </tr><tr>

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docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -263,7 +263,7 @@
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th> <th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th>

4
docs/reference/mdro.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9065</span>
</span> </span>
</div> </div>
@ -258,7 +258,7 @@
</tr> </tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
</tr> </tr>
<tr> <tr>
<th>info</th> <th>info</th>

2
man/as.rsi.Rd
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@ -33,7 +33,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options} \item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see Examples} \item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see Examples}
} }

10
man/bug_drug_combinations.Rd
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@ -2,27 +2,33 @@
% Please edit documentation in R/bug_drug_combinations.R % Please edit documentation in R/bug_drug_combinations.R
\name{bug_drug_combinations} \name{bug_drug_combinations}
\alias{bug_drug_combinations} \alias{bug_drug_combinations}
\alias{format.bug_drug_combinations}
\title{Determine bug-drug combinations} \title{Determine bug-drug combinations}
\source{ \source{
\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
} }
\usage{ \usage{
bug_drug_combinations(x, col_mo = NULL, minimum = 30) bug_drug_combinations(x, col_mo = NULL, minimum = 30)
\method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
add_ab_group = TRUE)
} }
\arguments{ \arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}} \item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.} \item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
\item{combine_IR}{logical to indicate whether values R and I should be summed} \item{combine_IR}{logical to indicate whether values R and I should be summed}
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
} }
\description{ \description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples. Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
} }
\details{ \details{
The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S. The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
} }
\section{Read more on our website!}{ \section{Read more on our website!}{

2
man/eucast_rules.Rd
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@ -27,7 +27,7 @@ eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
\arguments{ \arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}} \item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress} \item{info}{print progress}

2
man/first_isolate.Rd
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@ -30,7 +30,7 @@ filter_first_weighted_isolate(x, col_date = NULL,
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)} \item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.} \item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.}

2
man/key_antibiotics.Rd
View File

@ -28,7 +28,7 @@ key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
\arguments{ \arguments{
\item{x}{table with antibiotics coloms, like \code{AMX} or \code{amox}} \item{x}{table with antibiotics coloms, like \code{AMX} or \code{amox}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.} \item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}

2
man/mdro.Rd
View File

@ -31,7 +31,7 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{guideline}{a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.} \item{guideline}{a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress} \item{info}{print progress}