(v1.0.0.9007) small doc fix

v1.8.2
parent 0595af2801
commit 0d5e78b2cf
  1. 4
      DESCRIPTION
  2. 4
      NEWS.md
  3. 2
      R/data.R
  4. 2
      R/filter_ab_class.R
  5. 1
      R/first_isolate.R
  6. 2
      docs/404.html
  7. 2
      docs/LICENSE-text.html
  8. 2
      docs/articles/index.html
  9. 2
      docs/authors.html
  10. 2
      docs/index.html
  11. 12
      docs/news/index.html
  12. 2
      docs/reference/eucast_rules.html
  13. 6
      docs/reference/example_isolates_unclean.html
  14. 37
      docs/reference/filter_ab_class.html
  15. 10
      docs/reference/first_isolate.html
  16. 2
      docs/reference/index.html
  17. 2
      docs/reference/mdro.html
  18. 2
      docs/reference/resistance_predict.html
  19. 2
      man/example_isolates_unclean.Rd
  20. 2
      man/filter_ab_class.Rd
  21. 8
      man/first_isolate.Rd

@ -1,6 +1,6 @@
Package: AMR
Version: 1.0.0.9006
Date: 2020-02-21
Version: 1.0.0.9007
Date: 2020-02-22
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

@ -1,5 +1,5 @@
# AMR 1.0.0.9006
## <small>Last updated: 21-Feb-2020</small>
# AMR 1.0.0.9007
## <small>Last updated: 22-Feb-2020</small>
### Changed
* Fixed floating point error for some MIC compa in EUCAST 2020 guideline

@ -163,7 +163,7 @@ catalogue_of_life <- list(
#' Data set with unclean data
#'
#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
#' @format A [`data.frame`] with 3,000 observations and 8 variables:
#' - `patient_id`\cr ID of the patient
#' - `date`\cr date of receipt at the laboratory

@ -21,7 +21,7 @@
#' Filter isolates on result in antibiotic class
#'
#' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
#' Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a data set
#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]

@ -22,6 +22,7 @@
#' Determine first (weighted) isolates
#'
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a [`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_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>
@ -219,13 +219,13 @@
</div>
<div id="amr-1009006" class="section level1">
<div id="amr-1009007" class="section level1">
<h1 class="page-header">
<a href="#amr-1009006" class="anchor"></a>AMR 1.0.0.9006<small> Unreleased </small>
<a href="#amr-1009007" class="anchor"></a>AMR 1.0.0.9007<small> Unreleased </small>
</h1>
<div id="last-updated-21-feb-2020" class="section level2">
<div id="last-updated-22-feb-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-21-feb-2020" class="anchor"></a><small>Last updated: 21-Feb-2020</small>
<a href="#last-updated-22-feb-2020" class="anchor"></a><small>Last updated: 22-Feb-2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
@ -1474,7 +1474,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-1009006">1.0.0.9006</a></li>
<li><a href="#amr-1009007">1.0.0.9007</a></li>
<li><a href="#amr-100">1.0.0</a></li>
<li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li>

@ -80,7 +80,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -45,7 +45,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice." />
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -79,7 +79,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>
@ -222,7 +222,7 @@
</div>
<div class="ref-description">
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.</p>
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.</p>
</div>
<pre class="usage"><span class='no'>example_isolates_unclean</span></pre>

@ -40,18 +40,12 @@
<script src="../pkgdown.js"></script>
<!-- docsearch -->
<script src="../docsearch.js"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Filter isolates on result in antibiotic class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -85,7 +79,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
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@ -211,12 +205,6 @@
</li>
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@ -234,7 +222,7 @@
</div>
<div class="ref-description">
<p>Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.</p>
<p>Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.</p>
</div>
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>x</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
@ -344,7 +332,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<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/'>Alexander 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>, Stichting Certe Medische Diagnostiek en Advies.</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/'>Alexander 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 class="pkgdown">
@ -355,23 +343,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
<script>
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
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transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
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}
});
</script>
</body>

@ -79,7 +79,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>
@ -377,6 +377,13 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which default to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
</ol>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<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>
@ -446,6 +453,7 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -79,7 +79,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -79,7 +79,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
</span>
</div>

@ -16,7 +16,7 @@
example_isolates_unclean
}
\description{
A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
}
\section{Read more on our website!}{

@ -54,7 +54,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
}
\description{
Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
}
\details{
The \code{group} column in \link{antibiotics} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \link{antibiotics} data set.

@ -125,6 +125,14 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
}
}
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.

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