mirror of
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(v1.4.0.9000) more extensive unit tests
This commit is contained in:
34
.github/workflows/check.yaml
vendored
34
.github/workflows/check.yaml
vendored
@@ -48,24 +48,22 @@ jobs:
|
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fail-fast: false
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matrix:
|
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config:
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- {os: windows-latest, r: 'release'}
|
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- {os: macOS-latest, r: 'devel'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: windows-latest, r: 'oldrel'}
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# - {os: macOS-latest, r: 'oldrel'}
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# - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: macOS-latest, r: 'oldrel'}
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- {os: windows-latest, r: 'devel'}
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# - {os: macOS-latest, r: 'devel'}
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# - {os: ubuntu-16.04, r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: windows-latest, r: '3.6'}
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# - {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: windows-latest, r: 'release'}
|
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- {os: windows-latest, r: 'oldrel'}
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- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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@@ -80,7 +78,6 @@ jobs:
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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@@ -88,8 +85,8 @@ jobs:
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uses: actions/cache@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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@@ -100,6 +97,11 @@ jobs:
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sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
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sudo -s eval "$sysreqs"
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|
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- name: Install macOS dependencies
|
||||
if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'devel'
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run: |
|
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brew install mariadb-connector-c
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|
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- name: Install dependencies
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run: |
|
||||
remotes::install_deps(dependencies = TRUE)
|
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@@ -126,7 +128,7 @@ jobs:
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||||
|
||||
- name: Upload check results
|
||||
if: failure()
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uses: actions/upload-artifact@main
|
||||
uses: actions/upload-artifact@master
|
||||
with:
|
||||
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
|
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path: check
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|
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@@ -1,6 +1,6 @@
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Package: AMR
|
||||
Version: 1.4.0
|
||||
Date: 2020-10-08
|
||||
Version: 1.4.0.9000
|
||||
Date: 2020-10-15
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
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|
||||
7
NEWS.md
7
NEWS.md
@@ -1,5 +1,10 @@
|
||||
# AMR 1.4.0
|
||||
# AMR 1.4.0.9000
|
||||
## <small>Last updated: 15 October 2020</small>
|
||||
|
||||
### Other
|
||||
* More extensive unit tests
|
||||
|
||||
# AMR 1.4.0
|
||||
|
||||
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt about this package to. We are those reviewers very grateful for going through our code so thoroughly!
|
||||
|
||||
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -255,7 +255,7 @@ Content not found. Please use links in the navbar.
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -503,7 +503,7 @@ END OF TERMS AND CONDITIONS
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
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12
docs/articles/AMR_files/header-attrs-2.4/header-attrs.js
Normal file
12
docs/articles/AMR_files/header-attrs-2.4/header-attrs.js
Normal file
@@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -187,7 +187,7 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="EUCAST_files/header-attrs-2.3/header-attrs.js"></script><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
</header><script src="EUCAST_files/header-attrs-2.4/header-attrs.js"></script><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to apply EUCAST rules</h1>
|
||||
@@ -216,38 +216,35 @@
|
||||
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
|
||||
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="kw">oops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(mo = <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>,
|
||||
<span class="st">"Escherichia"</span>),
|
||||
ampicillin = <span class="st">"S"</span>)
|
||||
<span class="kw">oops</span>
|
||||
<span class="va">oops</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
|
||||
<span class="st">"Escherichia"</span><span class="op">)</span>,
|
||||
ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
|
||||
<span class="va">oops</span>
|
||||
<span class="co"># mo ampicillin</span>
|
||||
<span class="co"># 1 Klebsiella S</span>
|
||||
<span class="co"># 2 Escherichia S</span>
|
||||
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">oops</span>, info = <span class="fl">FALSE</span>)
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
|
||||
<span class="co"># mo ampicillin</span>
|
||||
<span class="co"># 1 Klebsiella R</span>
|
||||
<span class="co"># 2 Escherichia S</span>
|
||||
</pre></div>
|
||||
<span class="co"># 2 Escherichia S</span></pre></div>
|
||||
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit">
|
||||
<span class="kw">data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(mo = <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,
|
||||
<span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
|
||||
<span class="st">"Enterococcus faecalis"</span>,
|
||||
<span class="st">"Escherichia coli"</span>,
|
||||
<span class="st">"Klebsiella pneumoniae"</span>,
|
||||
<span class="st">"Pseudomonas aeruginosa"</span>),
|
||||
VAN = <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
|
||||
AMX = <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
|
||||
COL = <span class="st">"-"</span>, <span class="co"># Colistin</span>
|
||||
CAZ = <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
|
||||
CXM = <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
|
||||
PEN = <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span>
|
||||
FOX = <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
|
||||
stringsAsFactors = <span class="fl">FALSE</span>)
|
||||
</pre></div>
|
||||
<span class="st">"Pseudomonas aeruginosa"</span><span class="op">)</span>,
|
||||
VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span>
|
||||
AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span>
|
||||
COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span>
|
||||
CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span>
|
||||
CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span>
|
||||
PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylenicillin</span>
|
||||
FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span>
|
||||
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit">
|
||||
<span class="kw">data</span>
|
||||
</pre></div>
|
||||
<span class="va">data</span></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">mo</th>
|
||||
@@ -313,8 +310,7 @@
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">data</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">mo</th>
|
||||
@@ -397,7 +393,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
12
docs/articles/EUCAST_files/header-attrs-2.4/header-attrs.js
Normal file
12
docs/articles/EUCAST_files/header-attrs-2.4/header-attrs.js
Normal file
@@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -187,7 +187,7 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="MDR_files/header-attrs-2.3/header-attrs.js"></script><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
</header><script src="MDR_files/header-attrs-2.4/header-attrs.js"></script><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
|
||||
@@ -240,16 +240,14 @@
|
||||
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
|
||||
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>) <span class="co"># to support pipes: %>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://github.com/msberends/cleaner">cleaner</a></span>) <span class="co"># to create frequency tables</span>
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span> <span class="co"># to support pipes: %>%</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit">
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>() <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>() <span class="co"># show frequency table of the result</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
|
||||
<span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span>
|
||||
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span>
|
||||
</pre></div>
|
||||
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 2,000<br>
|
||||
@@ -288,62 +286,56 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit">
|
||||
<span class="co"># a helper function to get a random vector with values S, I and R</span>
|
||||
<span class="co"># with the probabilities 50% - 10% - 40%</span>
|
||||
<span class="kw">sample_rsi</span> <span class="op"><-</span> <span class="fu">function</span>() {
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),
|
||||
size = <span class="fl">5000</span>,
|
||||
prob = <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),
|
||||
replace = <span class="fl">TRUE</span>)
|
||||
}
|
||||
<span class="va">sample_rsi</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span><span class="op">)</span>,
|
||||
size <span class="op">=</span> <span class="fl">5000</span>,
|
||||
prob <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span><span class="op">)</span>,
|
||||
replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
|
||||
<span class="op">}</span>
|
||||
|
||||
<span class="kw">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(rifampicin = <span class="fu">sample_rsi</span>(),
|
||||
isoniazid = <span class="fu">sample_rsi</span>(),
|
||||
gatifloxacin = <span class="fu">sample_rsi</span>(),
|
||||
ethambutol = <span class="fu">sample_rsi</span>(),
|
||||
pyrazinamide = <span class="fu">sample_rsi</span>(),
|
||||
moxifloxacin = <span class="fu">sample_rsi</span>(),
|
||||
kanamycin = <span class="fu">sample_rsi</span>())
|
||||
</pre></div>
|
||||
<span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
isoniazid <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
gatifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
ethambutol <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
pyrazinamide <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
moxifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
kanamycin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit">
|
||||
<span class="kw">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(RIF = <span class="fu">sample_rsi</span>(),
|
||||
INH = <span class="fu">sample_rsi</span>(),
|
||||
GAT = <span class="fu">sample_rsi</span>(),
|
||||
ETH = <span class="fu">sample_rsi</span>(),
|
||||
PZA = <span class="fu">sample_rsi</span>(),
|
||||
MFX = <span class="fu">sample_rsi</span>(),
|
||||
KAN = <span class="fu">sample_rsi</span>())
|
||||
</pre></div>
|
||||
<span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
INH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
GAT <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
ETH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
PZA <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
MFX <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
KAN <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 R S S R S I</span>
|
||||
<span class="co"># 2 I S S S I R</span>
|
||||
<span class="co"># 3 R R R R R R</span>
|
||||
<span class="co"># 4 R I S R S S</span>
|
||||
<span class="co"># 5 S S I S S R</span>
|
||||
<span class="co"># 1 R S S R R S</span>
|
||||
<span class="co"># 2 I R S R S I</span>
|
||||
<span class="co"># 3 R R S S S S</span>
|
||||
<span class="co"># 4 R R S I S S</span>
|
||||
<span class="co"># 5 S I R S R S</span>
|
||||
<span class="co"># 6 S S S R S S</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 R</span>
|
||||
<span class="co"># 1 S</span>
|
||||
<span class="co"># 2 S</span>
|
||||
<span class="co"># 3 R</span>
|
||||
<span class="co"># 4 R</span>
|
||||
<span class="co"># 3 S</span>
|
||||
<span class="co"># 4 S</span>
|
||||
<span class="co"># 5 S</span>
|
||||
<span class="co"># 6 R</span>
|
||||
</pre></div>
|
||||
<span class="co"># 6 R</span></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="kw">my_TB_data</span>, guideline = <span class="st">"TB"</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></pre></div>
|
||||
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit">
|
||||
<span class="kw">my_TB_data</span><span class="op">$</span><span class="kw">mdr</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span>(<span class="kw">my_TB_data</span>)
|
||||
<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span>
|
||||
</pre></div>
|
||||
<span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></pre></div>
|
||||
<p>Create a frequency table of the results:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_TB_data</span><span class="op">$</span><span class="kw">mdr</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 5,000<br>
|
||||
@@ -363,40 +355,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3225</td>
|
||||
<td align="right">64.50%</td>
|
||||
<td align="right">3225</td>
|
||||
<td align="right">64.50%</td>
|
||||
<td align="right">3262</td>
|
||||
<td align="right">65.24%</td>
|
||||
<td align="right">3262</td>
|
||||
<td align="right">65.24%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">698</td>
|
||||
<td align="right">13.96%</td>
|
||||
<td align="right">3923</td>
|
||||
<td align="right">78.46%</td>
|
||||
<td align="right">664</td>
|
||||
<td align="right">13.28%</td>
|
||||
<td align="right">3926</td>
|
||||
<td align="right">78.52%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">581</td>
|
||||
<td align="right">11.62%</td>
|
||||
<td align="right">4504</td>
|
||||
<td align="right">90.08%</td>
|
||||
<td align="right">609</td>
|
||||
<td align="right">12.18%</td>
|
||||
<td align="right">4535</td>
|
||||
<td align="right">90.70%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">298</td>
|
||||
<td align="right">5.96%</td>
|
||||
<td align="right">4802</td>
|
||||
<td align="right">96.04%</td>
|
||||
<td align="right">283</td>
|
||||
<td align="right">5.66%</td>
|
||||
<td align="right">4818</td>
|
||||
<td align="right">96.36%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">198</td>
|
||||
<td align="right">3.96%</td>
|
||||
<td align="right">182</td>
|
||||
<td align="right">3.64%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -418,7 +410,7 @@ Unique: 5</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
12
docs/articles/MDR_files/header-attrs-2.4/header-attrs.js
Normal file
12
docs/articles/MDR_files/header-attrs-2.4/header-attrs.js
Normal file
@@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -187,7 +187,7 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="benchmarks_files/header-attrs-2.3/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
</header><script src="benchmarks_files/header-attrs-2.4/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
@@ -203,106 +203,44 @@
|
||||
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
|
||||
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code>microbenchmark()</code> runs different input expressions independently of each other and measures their time-to-result.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="kw">microbenchmark</span> <span class="op"><-</span> <span class="kw">microbenchmark</span>::<span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
</pre></div>
|
||||
<span class="va">microbenchmark</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="fu">::</span><span class="va"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span></pre></div>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
|
||||
<p>But the calculation time differs a lot:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit">
|
||||
<span class="kw">S.aureus</span> <span class="op"><-</span> <span class="fu">microbenchmark</span>(
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
|
||||
times = <span class="fl">10</span>)
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">2</span>)
|
||||
<span class="va">S.aureus</span> <span class="op"><-</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="st">"sau"</span><span class="op">)</span>, <span class="co"># WHONET code</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"staaur"</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S aureus"</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>, <span class="co"># official taxonomic name</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus (MRSA)"</span><span class="op">)</span>, <span class="co"># additional text</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Sthafilokkockus aaureuz"</span><span class="op">)</span>, <span class="co"># incorrect spelling</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span>, <span class="co"># Vancomycin Resistant S. aureus</span>
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 11.0 12.0 25.0 13.0 14.0 130 10</span>
|
||||
<span class="co"># as.mo("stau") 210.0 230.0 240.0 250.0 250.0 260 10</span>
|
||||
<span class="co"># as.mo("STAU") 210.0 210.0 240.0 240.0 260.0 270 10</span>
|
||||
<span class="co"># as.mo("staaur") 12.0 14.0 22.0 14.0 41.0 43 10</span>
|
||||
<span class="co"># as.mo("STAAUR") 12.0 12.0 19.0 13.0 14.0 47 10</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 28.0 38.0 30.0 58.0 62 10</span>
|
||||
<span class="co"># as.mo("S aureus") 28.0 29.0 45.0 52.0 56.0 60 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 2.1 2.2 7.9 2.4 2.6 32 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 840.0 880.0 890.0 890.0 890.0 930 10</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 340.0 370.0 390.0 390.0 410.0 490 10</span>
|
||||
<span class="co"># as.mo("MRSA") 11.0 12.0 16.0 13.0 14.0 44 10</span>
|
||||
<span class="co"># as.mo("VISA") 19.0 20.0 32.0 22.0 50.0 51 10</span>
|
||||
<span class="co"># as.mo("VRSA") 18.0 22.0 24.0 22.0 23.0 46 10</span>
|
||||
</pre></div>
|
||||
<span class="co"># as.mo("sau") 12.0 13.0 25.0 15.0 40.0 43 10</span>
|
||||
<span class="co"># as.mo("stau") 210.0 220.0 230.0 230.0 250.0 260 10</span>
|
||||
<span class="co"># as.mo("STAU") 210.0 210.0 230.0 250.0 250.0 260 10</span>
|
||||
<span class="co"># as.mo("staaur") 12.0 13.0 24.0 14.0 41.0 42 10</span>
|
||||
<span class="co"># as.mo("STAAUR") 13.0 13.0 22.0 14.0 39.0 42 10</span>
|
||||
<span class="co"># as.mo("S. aureus") 27.0 30.0 42.0 41.0 54.0 61 10</span>
|
||||
<span class="co"># as.mo("S aureus") 24.0 29.0 45.0 43.0 60.0 66 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 2.1 2.5 4.9 2.5 2.9 26 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 820.0 860.0 880.0 880.0 900.0 970 10</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 330.0 340.0 370.0 370.0 390.0 420 10</span>
|
||||
<span class="co"># as.mo("MRSA") 11.0 13.0 22.0 14.0 41.0 44 10</span>
|
||||
<span class="co"># as.mo("VISA") 21.0 22.0 48.0 47.0 51.0 140 10</span>
|
||||
<span class="co"># as.mo("VRSA") 19.0 20.0 23.0 21.0 22.0 47 10</span></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
|
||||
<p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
@@ -312,79 +250,66 @@
|
||||
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit">
|
||||
<span class="co"># take all MO codes from the example_isolates data set</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="kw">example_isolates</span><span class="op">$</span><span class="kw">mo</span> <span class="op">%>%</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span> <span class="op">%>%</span>
|
||||
<span class="co"># and copy them a thousand times</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">1000</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="co"># then scramble them</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>()
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span><span class="op">(</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># as the example_isolates has 2,000 rows, we should have 2 million items</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="kw">x</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># [1] 2000000</span>
|
||||
|
||||
<span class="co"># and how many unique values do we have?</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="kw">x</span>)
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># [1] 90</span>
|
||||
|
||||
<span class="co"># now let's see:</span>
|
||||
<span class="kw">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">x</span>),
|
||||
times = <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 131 161 200 168 187 341 10</span>
|
||||
</pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.168 seconds. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 150 154 195 179 197 301 10</span></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
|
||||
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit">
|
||||
<span class="kw">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"STAAUR"</span>),
|
||||
B = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
|
||||
C = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
|
||||
times = <span class="fl">10</span>)
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
||||
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 6.85 7.05 7.57 7.51 8.05 8.52 10</span>
|
||||
<span class="co"># B 21.50 21.70 27.40 23.80 25.00 64.70 10</span>
|
||||
<span class="co"># C 1.75 1.86 1.99 1.93 2.08 2.27 10</span>
|
||||
</pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># A 7.11 7.23 7.79 7.74 8.46 8.54 10</span>
|
||||
<span class="co"># B 21.40 21.90 30.40 24.00 25.50 60.00 10</span>
|
||||
<span class="co"># C 1.97 1.98 2.12 2.05 2.34 2.43 10</span></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.002 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit">
|
||||
<span class="kw">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
|
||||
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
|
||||
C = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
|
||||
D = <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),
|
||||
E = <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),
|
||||
F = <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),
|
||||
G = <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),
|
||||
H = <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),
|
||||
times = <span class="fl">10</span>)
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
||||
D <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Staphylococcaceae"</span><span class="op">)</span>,
|
||||
E <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="st">"Bacillales"</span><span class="op">)</span>,
|
||||
F <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span><span class="op">(</span><span class="st">"Bacilli"</span><span class="op">)</span>,
|
||||
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
|
||||
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.38 1.57 1.60 1.61 1.67 1.71 10</span>
|
||||
<span class="co"># B 1.55 1.60 1.73 1.63 1.92 2.05 10</span>
|
||||
<span class="co"># C 1.39 1.50 1.70 1.62 1.84 2.39 10</span>
|
||||
<span class="co"># D 1.32 1.51 1.59 1.57 1.61 2.04 10</span>
|
||||
<span class="co"># E 1.34 1.40 1.52 1.53 1.65 1.66 10</span>
|
||||
<span class="co"># F 1.28 1.53 1.56 1.60 1.66 1.72 10</span>
|
||||
<span class="co"># G 1.30 1.33 1.59 1.61 1.74 1.98 10</span>
|
||||
<span class="co"># H 1.31 1.45 1.62 1.55 1.70 2.46 10</span>
|
||||
</pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.33 1.57 1.70 1.69 1.83 2.18 10</span>
|
||||
<span class="co"># B 1.62 1.67 5.34 1.70 2.15 36.90 10</span>
|
||||
<span class="co"># C 1.43 1.55 1.64 1.59 1.70 2.06 10</span>
|
||||
<span class="co"># D 1.29 1.44 1.53 1.55 1.66 1.70 10</span>
|
||||
<span class="co"># E 1.31 1.58 1.68 1.65 1.71 2.11 10</span>
|
||||
<span class="co"># F 1.54 1.61 1.80 1.67 1.86 2.57 10</span>
|
||||
<span class="co"># G 1.52 1.62 1.73 1.71 1.77 2.04 10</span>
|
||||
<span class="co"># H 1.40 1.55 1.70 1.65 1.92 2.03 10</span></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
@@ -392,34 +317,33 @@
|
||||
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
|
||||
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on an English system</span>
|
||||
<span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
|
||||
<span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
|
||||
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
|
||||
|
||||
<span class="kw">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span>(en = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"en"</span>),
|
||||
de = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"de"</span>),
|
||||
nl = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"nl"</span>),
|
||||
es = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"es"</span>),
|
||||
it = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"it"</span>),
|
||||
fr = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"fr"</span>),
|
||||
pt = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, language = <span class="st">"pt"</span>),
|
||||
times = <span class="fl">100</span>)
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span>en <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span>,
|
||||
de <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>,
|
||||
nl <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>,
|
||||
es <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>,
|
||||
it <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"it"</span><span class="op">)</span>,
|
||||
fr <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"fr"</span><span class="op">)</span>,
|
||||
pt <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 14.00 14.36 18.52 14.64 15.18 57.58 100</span>
|
||||
<span class="co"># de 17.04 17.33 20.94 17.63 18.49 56.23 100</span>
|
||||
<span class="co"># nl 28.21 29.20 32.15 30.06 31.02 72.91 100</span>
|
||||
<span class="co"># es 16.85 17.26 19.83 17.44 17.95 152.20 100</span>
|
||||
<span class="co"># it 16.58 17.10 19.03 17.43 18.24 54.28 100</span>
|
||||
<span class="co"># fr 16.71 17.20 21.24 17.52 19.02 63.25 100</span>
|
||||
<span class="co"># pt 16.76 17.29 23.27 17.62 19.14 65.28 100</span>
|
||||
</pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 14.20 14.66 20.04 15.14 16.90 58.67 100</span>
|
||||
<span class="co"># de 17.15 17.85 24.30 18.27 20.00 59.17 100</span>
|
||||
<span class="co"># nl 29.13 30.50 34.60 31.26 32.86 72.63 100</span>
|
||||
<span class="co"># es 16.95 17.70 22.61 18.35 20.54 59.42 100</span>
|
||||
<span class="co"># it 17.04 17.60 21.72 18.14 19.60 59.19 100</span>
|
||||
<span class="co"># fr 16.82 17.52 21.71 18.05 19.63 61.06 100</span>
|
||||
<span class="co"># pt 16.92 17.58 19.92 18.23 19.19 54.61 100</span></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
@@ -437,7 +361,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 88 KiB After Width: | Height: | Size: 69 KiB |
@@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -187,7 +187,7 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="datasets_files/header-attrs-2.3/header-attrs.js"></script><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
</header><script src="datasets_files/header-attrs-2.4/header-attrs.js"></script><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
@@ -1146,7 +1146,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -272,7 +272,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -325,7 +325,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -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">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -282,8 +282,7 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
<p><img src="https://www.r-pkg.org/badges/version-ago/AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR"></p>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></pre></div>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
|
||||
</div>
|
||||
@@ -292,9 +291,8 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
|
||||
<p>The latest and unpublished development version can be installed from GitHub using:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
|
||||
<span class="kw">remotes</span>::<span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span>(<span class="st">"msberends/AMR"</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span>
|
||||
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="get-started" class="section level3">
|
||||
@@ -458,7 +456,7 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,6 +236,23 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1409000" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9000">
|
||||
<a href="#amr-1409000" class="anchor"></a>AMR 1.4.0.9000<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-15-october-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-15-october-2020" class="anchor"></a><small>Last updated: 15 October 2020</small>
|
||||
</h2>
|
||||
<div id="other" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>More extensive unit tests</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-140" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0">
|
||||
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small>
|
||||
@@ -251,13 +268,12 @@
|
||||
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
|
||||
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw">intrinsic_resistant</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="kw">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(<span class="kw">microorganism</span>)
|
||||
<span class="co">#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span>
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">intrinsic_resistant</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span></pre></div>
|
||||
</li>
|
||||
<li><p>Support for veterinary ATC codes</p></li>
|
||||
<li><p>Support for skimming classes <code><rsi></code>, <code><mic></code>, <code><disk></code> and <code><mo></code> with the <code>skimr</code> package</p></li>
|
||||
@@ -275,13 +291,12 @@
|
||||
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit">
|
||||
<span class="co"># until dplyr 1.0.0</span>
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.mic</span>, <span class="kw">as.rsi</span>)
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.disk</span>, <span class="kw">as.rsi</span>)
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># since dplyr 1.0.0</span>
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.mic</span>), <span class="kw">as.rsi</span>))
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.disk</span>), <span class="kw">as.rsi</span>))
|
||||
</pre></div>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g. <code><a href="../reference/as.rsi.html">as.rsi(df, col1:col9)</a></code></p></li>
|
||||
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
|
||||
@@ -292,10 +307,9 @@
|
||||
<li>
|
||||
<p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span>))
|
||||
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Class <disk></span>
|
||||
<span class="co">#> [1] 24 24</span>
|
||||
</pre></div>
|
||||
<span class="co">#> [1] 24 24</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</p>
|
||||
@@ -330,9 +344,9 @@
|
||||
<li><p>Added parameter <code>excess</code> to the <code><a href="../reference/kurtosis.html">kurtosis()</a></code> function (defaults to <code>FALSE</code>), to return the <em>excess kurtosis</em>, defined as the kurtosis minus three.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level3">
|
||||
<div id="other-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h3>
|
||||
<a href="#other-1" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Removed functions <code>portion_R()</code>, <code>portion_S()</code> and <code>portion_I()</code> that were deprecated since version 0.9.0 (November 2019) and were replaced with <code><a href="../reference/proportion.html">proportion_R()</a></code>, <code><a href="../reference/proportion.html">proportion_S()</a></code> and <code><a href="../reference/proportion.html">proportion_I()</a></code>
|
||||
</li>
|
||||
@@ -353,13 +367,12 @@
|
||||
<li>
|
||||
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span>())
|
||||
<span class="co">#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span>
|
||||
</pre></div>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added <code><a href="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><a href="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
|
||||
<li><p>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</p></li>
|
||||
@@ -416,9 +429,9 @@
|
||||
<li><p>Fixed a bug where <code><a href="../reference/as.mic.html">as.mic()</a></code> could not handle dots without a leading zero (like <code>"<=.25</code>)</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-1" class="section level3">
|
||||
<div id="other-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-1" class="anchor"></a>Other</h3>
|
||||
<a href="#other-2" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
|
||||
</ul>
|
||||
@@ -478,9 +491,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-2" class="section level3">
|
||||
<div id="other-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-2" class="anchor"></a>Other</h3>
|
||||
<a href="#other-3" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="../reference/p_symbol.html">p_symbol()</a></code>
|
||||
</li>
|
||||
@@ -520,9 +533,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-3" class="section level3">
|
||||
<div id="other-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-3" class="anchor"></a>Other</h3>
|
||||
<a href="#other-4" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
|
||||
<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
|
||||
@@ -542,12 +555,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit">
|
||||
<span class="kw">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="st">"E. coli"</span>)
|
||||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
|
||||
|
||||
<span class="kw">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="kw">.</span><span class="op">$</span><span class="kw">mybacteria</span>)
|
||||
</pre></div>
|
||||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">mybacteria</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
|
||||
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
|
||||
@@ -571,24 +583,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Ampicillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)
|
||||
<span class="co">#> [1] "J01CA01"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "J01CA01"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] 115329001 3092008 113961008</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="fl">115329001</span>)
|
||||
<span class="co">#> [1] "Gram-positive"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Gram-positive"</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -624,9 +634,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-4" class="section level3">
|
||||
<div id="other-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-4" class="anchor"></a>Other</h3>
|
||||
<a href="#other-5" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Add a <code>CITATION</code> file</li>
|
||||
<li>Full support for the upcoming R 4.0</li>
|
||||
@@ -647,12 +657,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit">
|
||||
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="kw">...</span>
|
||||
</pre></div>
|
||||
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span><span class="op">)</span> <span class="va">...</span></pre></div>
|
||||
<p>then please adjust this to:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit">
|
||||
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacterales"</span>) <span class="kw">...</span>
|
||||
</pre></div>
|
||||
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacterales"</span><span class="op">)</span> <span class="va">...</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -665,13 +673,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(bug = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">mo</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(amoxicillin = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>),
|
||||
amox_clav = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMC</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amoxicillin</span>) <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amox_clav</span>))
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>bug <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>,
|
||||
amox_clav <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">)</span> <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amox_clav</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
|
||||
@@ -694,17 +701,16 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
|
||||
<span class="st">"staphylokok aureuz"</span>))
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Stafylococcus aureus"</span>,
|
||||
<span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Warning: </span>
|
||||
<span class="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
|
||||
<span class="co">#> Class 'mo'</span>
|
||||
<span class="co">#> [1] B_STPHY_AURS B_STPHY_AURS</span>
|
||||
|
||||
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()
|
||||
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co">#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span>
|
||||
<span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span>
|
||||
</pre></div>
|
||||
<span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -732,9 +738,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-5" class="section level3">
|
||||
<div id="other-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-5" class="anchor"></a>Other</h3>
|
||||
<a href="#other-6" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great <a href="https://roxygen2.r-lib.org/index.html">Roxygen2</a>, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.</li>
|
||||
<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
|
||||
@@ -753,25 +759,23 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">...</span>, include_unknown = <span class="fl">TRUE</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">...</span>, include_unknown <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></pre></div>
|
||||
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="downlit">
|
||||
<span class="co"># how it works in base R:</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
|
||||
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op"><-</span> <span class="st">"B"</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"B"</span>
|
||||
<span class="co">#> Warning message:</span>
|
||||
<span class="co">#> invalid factor level, NA generated</span>
|
||||
|
||||
<span class="co"># how it now works similarly for classes 'mo' and 'ab':</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op"><-</span> <span class="st">"testvalue"</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"testvalue"</span>
|
||||
<span class="co">#> Warning message:</span>
|
||||
<span class="co">#> invalid microorganism code, NA generated</span>
|
||||
</pre></div>
|
||||
<span class="co">#> invalid microorganism code, NA generated</span></pre></div>
|
||||
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
||||
</li>
|
||||
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
@@ -785,9 +789,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="downlit">
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>)
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="co">#> NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span>
|
||||
<span class="co">#> mo ab S I R total</span>
|
||||
<span class="co">#> 1 A. baumannii AMC 0 0 3 3</span>
|
||||
<span class="co">#> 2 A. baumannii AMK 0 0 0 0</span>
|
||||
@@ -796,20 +800,18 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
|
||||
|
||||
<span class="co"># change the transformation with the FUN argument to anything you like:</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>, FUN = <span class="kw">mo_gramstain</span>)
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span>, FUN <span class="op">=</span> <span class="va">mo_gramstain</span><span class="op">)</span>
|
||||
<span class="co">#> NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span>
|
||||
<span class="co">#> mo ab S I R total</span>
|
||||
<span class="co">#> 1 Gram-negative AMC 469 89 174 732</span>
|
||||
<span class="co">#> 2 Gram-negative AMK 251 0 2 253</span>
|
||||
<span class="co">#> 3 Gram-negative AMP 227 0 405 632</span>
|
||||
<span class="co">#> 4 Gram-negative AMX 227 0 405 632</span>
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
|
||||
</pre></div>
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
|
||||
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="kw">x</span>, combine_IR = <span class="fl">FALSE</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
|
||||
@@ -829,19 +831,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co"># S or I <NA> X X - -</span>
|
||||
<span class="co"># R <NA> - - - -</span>
|
||||
<span class="co"># <NA> <NA> - - - -</span>
|
||||
<span class="co"># --------------------------------------------------------------------</span>
|
||||
</pre></div>
|
||||
<span class="co"># --------------------------------------------------------------------</span></pre></div>
|
||||
<p>Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit">
|
||||
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">mo</span><span class="op">:</span><span class="kw">AMC</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span>()
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span><span class="op">:</span><span class="va">AMC</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -898,9 +898,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
<li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
|
||||
</ul>
|
||||
<div id="other-6" class="section level4">
|
||||
<div id="other-7" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-6" class="anchor"></a>Other</h4>
|
||||
<a href="#other-7" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
|
||||
<li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
|
||||
@@ -919,15 +919,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
|
||||
<div class="sourceCode" id="cb18"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">AMX</span>, <span class="kw">CIP</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># antibiotic interpretation value isolates</span>
|
||||
<span class="co"># 1 Amoxicillin SI 0.4442636 546</span>
|
||||
<span class="co"># 2 Amoxicillin R 0.5557364 683</span>
|
||||
<span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span>
|
||||
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span>
|
||||
</pre></div>
|
||||
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
|
||||
@@ -946,13 +945,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</ul>
|
||||
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
|
||||
<span class="co"># B_ESCHR_COL</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
|
||||
<span class="co"># "Escherichia coli"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)
|
||||
<span class="co"># "Gram-negative"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>
|
||||
<span class="co"># "Gram-negative"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||
@@ -985,9 +983,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-7" class="section level4">
|
||||
<div id="other-8" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-7" class="anchor"></a>Other</h4>
|
||||
<a href="#other-8" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Fixed a note thrown by CRAN tests</li>
|
||||
</ul>
|
||||
@@ -1051,15 +1049,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>support for boxplots:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -1081,9 +1078,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-8" class="section level4">
|
||||
<div id="other-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-8" class="anchor"></a>Other</h4>
|
||||
<a href="#other-9" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
|
||||
</li>
|
||||
@@ -1146,37 +1143,34 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>, scope = <span class="st">"all"</span>)
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span>
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span>, scope <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span>
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit">
|
||||
<span class="kw">ab_property</span> <span class="op">-></span> <span class="fu">atc_property</span>()
|
||||
<span class="kw">ab_name</span> <span class="op">-></span> <span class="fu">atc_name</span>()
|
||||
<span class="kw">ab_official</span> <span class="op">-></span> <span class="fu">atc_official</span>()
|
||||
<span class="kw">ab_trivial_nl</span> <span class="op">-></span> <span class="fu">atc_trivial_nl</span>()
|
||||
<span class="kw">ab_certe</span> <span class="op">-></span> <span class="fu">atc_certe</span>()
|
||||
<span class="kw">ab_umcg</span> <span class="op">-></span> <span class="fu">atc_umcg</span>()
|
||||
<span class="kw">ab_tradenames</span> <span class="op">-></span> <span class="fu">atc_tradenames</span>()
|
||||
</pre></div>
|
||||
<span class="va">ab_property</span> <span class="op">-></span> <span class="fu">atc_property</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_name</span> <span class="op">-></span> <span class="fu">atc_name</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_official</span> <span class="op">-></span> <span class="fu">atc_official</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_trivial_nl</span> <span class="op">-></span> <span class="fu">atc_trivial_nl</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_certe</span> <span class="op">-></span> <span class="fu">atc_certe</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_umcg</span> <span class="op">-></span> <span class="fu">atc_umcg</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_tradenames</span> <span class="op">-></span> <span class="fu">atc_tradenames</span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
<p>These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online_property.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</p>
|
||||
</li>
|
||||
<li><p>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</p></li>
|
||||
@@ -1190,25 +1184,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="../reference/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb24"><pre class="downlit">
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">septic_patients</span>, col_ab = <span class="st">"amox"</span>)
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span>(<span class="kw">x</span>)
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">x</span>)
|
||||
</pre></div>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span><span class="va">septic_patients</span>, col_ab <span class="op">=</span> <span class="st">"amox"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">...</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
|
||||
<span class="co"># or</span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></pre></div>
|
||||
<p>is equal to:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(only_firsts = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">only_firsts</span> <span class="op">==</span> <span class="fl">TRUE</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">only_firsts</span>)
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">only_firsts</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">only_firsts</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code></p></li>
|
||||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
@@ -1239,24 +1230,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit">
|
||||
<span class="co"># mo_fullname() uses as.mo() internally</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"Sthafilokockus aaureuz"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)
|
||||
<span class="co">#> [1] "Staphylococcus kloosii"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. klossi"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Staphylococcus kloosii"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
||||
<div class="sourceCode" id="cb28"><pre class="downlit">
|
||||
<span class="co"># equal:</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">TRUE</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">2</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">TRUE</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">...</span>, allow_uncertain <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># also equal:</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">FALSE</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">0</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">FALSE</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">...</span>, allow_uncertain <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></pre></div>
|
||||
<p>Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</p>
|
||||
</li>
|
||||
<li><p>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em></p></li>
|
||||
@@ -1264,11 +1253,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb29"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, language = <span class="st">"es"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"qwerty"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>
|
||||
<span class="co"># Warning: </span>
|
||||
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
|
||||
<span class="co">#> [1] "(género desconocido)"</span>
|
||||
</pre></div>
|
||||
<span class="co">#> [1] "(género desconocido)"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Fix for vector containing only empty values</p></li>
|
||||
<li><p>Finds better results when input is in other languages</p></li>
|
||||
@@ -1316,18 +1304,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb30"><pre class="downlit">
|
||||
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
|
||||
<span class="co"># OLD WAY</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">genus</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Even supports grouping variables:</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">gender</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
<li><p>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||
@@ -1348,9 +1335,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-9" class="section level4">
|
||||
<div id="other-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-9" class="anchor"></a>Other</h4>
|
||||
<a href="#other-10" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
|
||||
</ul>
|
||||
@@ -1398,11 +1385,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
||||
<div class="sourceCode" id="cb31"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. species"</span><span class="op">)</span> <span class="co"># B_ESCHR</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"E. spp."</span><span class="op">)</span> <span class="co"># "Escherichia species"</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. spp"</span><span class="op">)</span> <span class="co"># B_STPHY</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. species"</span><span class="op">)</span> <span class="co"># "Staphylococcus species"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></li>
|
||||
<li><p>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</p></li>
|
||||
@@ -1415,18 +1401,16 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb32"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb33"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">hospital_id</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">count</span>, <span class="op">-</span><span class="kw">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span>
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
||||
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
|
||||
@@ -1470,9 +1454,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-10" class="section level4">
|
||||
<div id="other-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-10" class="anchor"></a>Other</h4>
|
||||
<a href="#other-11" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
|
||||
<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
|
||||
@@ -1503,21 +1487,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</ul>
|
||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb34"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Gram negative"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"de"</span>) <span class="co"># German</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># German</span>
|
||||
<span class="co"># [1] "Gramnegativ"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"es"</span>) <span class="co"># Spanish</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># Spanish</span>
|
||||
<span class="co"># [1] "Gram negativo"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, language = <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
|
||||
<span class="co"># [1] "Streptococcus grupo A"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. group A"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span> <span class="co"># Portuguese</span>
|
||||
<span class="co"># [1] "Streptococcus grupo A"</span></pre></div>
|
||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||
<div class="sourceCode" id="cb35"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Esc blattae"</span><span class="op">)</span>
|
||||
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
|
||||
<span class="co"># [1] "Gram negative"</span>
|
||||
</pre></div>
|
||||
<span class="co"># [1] "Gram negative"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates</p>
|
||||
@@ -1529,21 +1511,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
||||
<div class="sourceCode" id="cb36"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="co"># [1] B_ESCHR_COL</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>
|
||||
<span class="co"># [1] B_STPHY_AUR</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)
|
||||
<span class="co"># [1] B_STRPTC_GRA</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S group A"</span><span class="op">)</span>
|
||||
<span class="co"># [1] B_STRPTC_GRA</span></pre></div>
|
||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||
<div class="sourceCode" id="cb37"><pre class="downlit">
|
||||
<span class="kw">thousands_of_E_colis</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
|
||||
<span class="kw">microbenchmark</span>::<span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">thousands_of_E_colis</span>), unit = <span class="st">"s"</span>)
|
||||
<span class="va">thousands_of_E_colis</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">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"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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>
|
||||
</pre></div>
|
||||
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</p></li>
|
||||
<li>
|
||||
@@ -1572,13 +1552,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
||||
<div class="sourceCode" id="cb38"><pre class="downlit">
|
||||
<span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
|
||||
<span class="fu">ab_official</span><span class="op">(</span><span class="st">"Bactroban"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Mupirocin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
|
||||
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></pre></div>
|
||||
</li>
|
||||
<li><p>For <code>first_isolate</code>, rows will be ignored when there’s no species available</p></li>
|
||||
<li><p>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</p></li>
|
||||
@@ -1589,14 +1568,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||
<div class="sourceCode" id="cb39"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>) <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># which is the same as:</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span>
|
||||
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span>(<span class="kw">amcl</span>)
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span>(<span class="kw">amcl</span>, <span class="kw">gent</span>)
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span>(<span class="kw">amcl</span>, <span class="kw">gent</span>, <span class="kw">pita</span>)
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span><span class="op">)</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span>, <span class="va">gent</span><span class="op">)</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span>, <span class="va">gent</span>, <span class="va">pita</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</p></li>
|
||||
<li><p>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</p></li>
|
||||
@@ -1609,21 +1587,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb40"><pre class="downlit">
|
||||
<span class="kw">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="kw">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">age</span>, <span class="kw">gender</span>), ncol = <span class="fl">2</span>))
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_matrix</span>)
|
||||
</pre></div>
|
||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb41"><pre class="downlit">
|
||||
<span class="kw">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(age = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">age</span>, gender = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">gender</span>)
|
||||
<span class="kw">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>)
|
||||
<span class="kw">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
|
||||
</pre></div>
|
||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-11" class="section level4">
|
||||
<div id="other-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-11" class="anchor"></a>Other</h4>
|
||||
<a href="#other-12" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>More unit tests to ensure better integrity of functions</li>
|
||||
</ul>
|
||||
@@ -1750,9 +1726,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Other small fixes</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-12" class="section level4">
|
||||
<div id="other-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-12" class="anchor"></a>Other</h4>
|
||||
<a href="#other-13" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
|
||||
<ul>
|
||||
@@ -1812,9 +1788,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-13" class="section level4">
|
||||
<div id="other-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-13" class="anchor"></a>Other</h4>
|
||||
<a href="#other-14" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Expanded <code>README.md</code> with more examples</li>
|
||||
<li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>
|
||||
@@ -1862,7 +1838,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -1,8 +1,18 @@
|
||||
pandoc: 2.9.2.1
|
||||
pkgdown: 1.5.1.9000
|
||||
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
|
||||
articles: []
|
||||
last_built: 2020-10-08T09:09Z
|
||||
pkgdown: 1.6.1
|
||||
pkgdown_sha: ~
|
||||
articles:
|
||||
AMR: AMR.html
|
||||
EUCAST: EUCAST.html
|
||||
MDR: MDR.html
|
||||
PCA: PCA.html
|
||||
SPSS: SPSS.html
|
||||
WHONET: WHONET.html
|
||||
benchmarks: benchmarks.html
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2020-10-15T07:41Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -309,7 +309,7 @@ The Netherlands</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -260,10 +260,10 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01DH02"</span>)
|
||||
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01DH02"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span><span class='op'>(</span><span class='st'>"flucloxacillin"</span><span class='op'>)</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -280,7 +280,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>WHONET</span></pre>
|
||||
<pre class="usage"><span class='va'>WHONET</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -302,7 +302,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,14 +242,14 @@
|
||||
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href='https://rdrr.io/r/base/list.html'>list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_from_text</span>(
|
||||
<span class='kw'>text</span>,
|
||||
type = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
|
||||
collapse = <span class='kw'>NULL</span>,
|
||||
translate_ab = <span class='fl'>FALSE</span>,
|
||||
thorough_search = <span class='kw'>NULL</span>,
|
||||
<span class='kw'>...</span>
|
||||
)</pre>
|
||||
<pre class="usage"><span class='fu'>ab_from_text</span><span class='op'>(</span>
|
||||
<span class='va'>text</span>,
|
||||
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span><span class='op'>)</span>,
|
||||
collapse <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
thorough_search <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -285,14 +285,14 @@
|
||||
<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3>Parameter <code>type</code></h3>
|
||||
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Parameter <code>type</code></h3>
|
||||
|
||||
|
||||
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
|
||||
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
|
||||
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
|
||||
|
||||
<h3>Parameter <code>collapse</code></h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Parameter <code>collapse</code></h3>
|
||||
|
||||
|
||||
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
|
||||
@@ -316,36 +316,36 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
|
||||
<span class='co'># straight from a true health care record:</span>
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span>)
|
||||
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type = <span class='st'>"dose"</span>)
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type = <span class='st'>"admin"</span>)
|
||||
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"500 mg amoxi po and 400mg cipro iv"</span><span class='op'>)</span>
|
||||
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type <span class='op'>=</span> <span class='st'>"dose"</span><span class='op'>)</span>
|
||||
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, type <span class='op'>=</span> <span class='st'>"admin"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, collapse = <span class='st'>", "</span>)
|
||||
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, collapse <span class='op'>=</span> <span class='st'>", "</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># if you want to know which antibiotic groups were administered, do e.g.:</span>
|
||||
<span class='kw'>abx</span> <span class='op'><-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='kw'>abx</span>[[<span class='fl'>1</span>]])
|
||||
<span class='va'>abx</span> <span class='op'><-</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"500 mg amoxi po and 400mg cipro iv"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_group</a></span><span class='op'>(</span><span class='va'>abx</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='fu'><a href='https://tibble.tidyverse.org/reference/tibble.html'>tibble</a></span>(clinical_text = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
|
||||
<span class='st'>"started on doxy iv today"</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(abx_codes = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>),
|
||||
abx_doses = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, type = <span class='st'>"doses"</span>),
|
||||
abx_admin = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, type = <span class='st'>"admin"</span>),
|
||||
abx_coll = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>, collapse = <span class='st'>"|"</span>),
|
||||
abx_coll_names = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
|
||||
collapse = <span class='st'>"|"</span>,
|
||||
translate_ab = <span class='st'>"name"</span>),
|
||||
abx_coll_doses = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
|
||||
type = <span class='st'>"doses"</span>,
|
||||
collapse = <span class='st'>"|"</span>),
|
||||
abx_coll_admin = <span class='fu'>ab_from_text</span>(<span class='kw'>clinical_text</span>,
|
||||
type = <span class='st'>"admin"</span>,
|
||||
collapse = <span class='st'>"|"</span>))
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='fu'><a href='https://tibble.tidyverse.org/reference/tibble.html'>tibble</a></span><span class='op'>(</span>clinical_text <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"given 400mg cipro and 500 mg amox"</span>,
|
||||
<span class='st'>"started on doxy iv today"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>abx_codes <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span><span class='op'>)</span>,
|
||||
abx_doses <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span>, type <span class='op'>=</span> <span class='st'>"doses"</span><span class='op'>)</span>,
|
||||
abx_admin <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span>, type <span class='op'>=</span> <span class='st'>"admin"</span><span class='op'>)</span>,
|
||||
abx_coll <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span>, collapse <span class='op'>=</span> <span class='st'>"|"</span><span class='op'>)</span>,
|
||||
abx_coll_names <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span>,
|
||||
collapse <span class='op'>=</span> <span class='st'>"|"</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span><span class='op'>)</span>,
|
||||
abx_coll_doses <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span>,
|
||||
type <span class='op'>=</span> <span class='st'>"doses"</span>,
|
||||
collapse <span class='op'>=</span> <span class='st'>"|"</span><span class='op'>)</span>,
|
||||
abx_coll_admin <span class='op'>=</span> <span class='fu'>ab_from_text</span><span class='op'>(</span><span class='va'>clinical_text</span>,
|
||||
type <span class='op'>=</span> <span class='st'>"admin"</span>,
|
||||
collapse <span class='op'>=</span> <span class='st'>"|"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
}
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -362,7 +362,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,31 +242,31 @@
|
||||
<p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_name</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), tolower = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
|
||||
<pre class="usage"><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_atc</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_cid</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_synonyms</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_synonyms</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_tradenames</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_tradenames</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_group</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_group</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_atc_group1</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_atc_group2</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_loinc</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_loinc</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_ddd</span>(<span class='kw'>x</span>, administration = <span class='st'>"oral"</span>, units = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_ddd</span><span class='op'>(</span><span class='va'>x</span>, administration <span class='op'>=</span> <span class='st'>"oral"</span>, units <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_info</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_info</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_url</span>(<span class='kw'>x</span>, open = <span class='fl'>FALSE</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>ab_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ab_property</span>(<span class='kw'>x</span>, property = <span class='st'>"name"</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)</pre>
|
||||
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -349,42 +349,42 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># all properties:</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"AMX"</span>) <span class='co'># "Amoxicillin"</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMX"</span>) <span class='co'># J01CA04 (ATC code from the WHO)</span>
|
||||
<span class='fu'>ab_cid</span>(<span class='st'>"AMX"</span>) <span class='co'># 33613 (Compound ID from PubChem)</span>
|
||||
<span class='fu'>ab_synonyms</span>(<span class='st'>"AMX"</span>) <span class='co'># a list with brand names of amoxicillin</span>
|
||||
<span class='fu'>ab_tradenames</span>(<span class='st'>"AMX"</span>) <span class='co'># same</span>
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactams/penicillins"</span>
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='st'>"AMX"</span>) <span class='co'># "Penicillins with extended spectrum"</span>
|
||||
<span class='fu'>ab_url</span>(<span class='st'>"AMX"</span>) <span class='co'># link to the official WHO page</span>
|
||||
<span class='fu'>ab_name</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Amoxicillin"</span>
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># J01CA04 (ATC code from the WHO)</span>
|
||||
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># 33613 (Compound ID from PubChem)</span>
|
||||
<span class='fu'>ab_synonyms</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># a list with brand names of amoxicillin</span>
|
||||
<span class='fu'>ab_tradenames</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># same</span>
|
||||
<span class='fu'>ab_group</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Beta-lactams/penicillins"</span>
|
||||
<span class='fu'>ab_atc_group1</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
|
||||
<span class='fu'>ab_atc_group2</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Penicillins with extended spectrum"</span>
|
||||
<span class='fu'>ab_url</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># link to the official WHO page</span>
|
||||
|
||||
<span class='co'># smart lowercase tranformation</span>
|
||||
<span class='fu'>ab_name</span>(x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
|
||||
<span class='fu'>ab_name</span>(x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
|
||||
tolower = <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
|
||||
<span class='fu'>ab_name</span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"AMC"</span>, <span class='st'>"PLB"</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
|
||||
<span class='fu'>ab_name</span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"AMC"</span>, <span class='st'>"PLB"</span><span class='op'>)</span>,
|
||||
tolower <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
|
||||
|
||||
<span class='co'># defined daily doses (DDD)</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, units = <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, units = <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
<span class='fu'>ab_ddd</span><span class='op'>(</span><span class='st'>"AMX"</span>, <span class='st'>"oral"</span><span class='op'>)</span> <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span><span class='op'>(</span><span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, units <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "g"</span>
|
||||
<span class='fu'>ab_ddd</span><span class='op'>(</span><span class='st'>"AMX"</span>, <span class='st'>"iv"</span><span class='op'>)</span> <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span><span class='op'>(</span><span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, units <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "g"</span>
|
||||
|
||||
<span class='fu'>ab_info</span>(<span class='st'>"AMX"</span>) <span class='co'># all properties as a list</span>
|
||||
<span class='fu'>ab_info</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># all properties as a list</span>
|
||||
|
||||
<span class='co'># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMP"</span>) <span class='co'># ATC code of AMP (ampicillin)</span>
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"J01CA01"</span>) <span class='co'># Drug group of ampicillins ATC code</span>
|
||||
<span class='fu'>ab_loinc</span>(<span class='st'>"ampicillin"</span>) <span class='co'># LOINC codes of ampicillin</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"21066-6"</span>) <span class='co'># "Ampicillin" (using LOINC)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='fl'>6249</span>) <span class='co'># "Ampicillin" (using CID)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"J01CA01"</span>) <span class='co'># "Ampicillin" (using ATC)</span>
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"AMP"</span><span class='op'>)</span> <span class='co'># ATC code of AMP (ampicillin)</span>
|
||||
<span class='fu'>ab_group</span><span class='op'>(</span><span class='st'>"J01CA01"</span><span class='op'>)</span> <span class='co'># Drug group of ampicillins ATC code</span>
|
||||
<span class='fu'>ab_loinc</span><span class='op'>(</span><span class='st'>"ampicillin"</span><span class='op'>)</span> <span class='co'># LOINC codes of ampicillin</span>
|
||||
<span class='fu'>ab_name</span><span class='op'>(</span><span class='st'>"21066-6"</span><span class='op'>)</span> <span class='co'># "Ampicillin" (using LOINC)</span>
|
||||
<span class='fu'>ab_name</span><span class='op'>(</span><span class='fl'>6249</span><span class='op'>)</span> <span class='co'># "Ampicillin" (using CID)</span>
|
||||
<span class='fu'>ab_name</span><span class='op'>(</span><span class='st'>"J01CA01"</span><span class='op'>)</span> <span class='co'># "Ampicillin" (using ATC)</span>
|
||||
|
||||
<span class='co'># spelling from different languages and dyslexia are no problem</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"ceftriaxon"</span><span class='op'>)</span>
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"cephtriaxone"</span><span class='op'>)</span>
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"cephthriaxone"</span><span class='op'>)</span>
|
||||
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"seephthriaaksone"</span><span class='op'>)</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -401,7 +401,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>age</span>(<span class='kw'>x</span>, reference = <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(), exact = <span class='fl'>FALSE</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>age</span><span class='op'>(</span><span class='va'>x</span>, reference <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, exact <span class='op'>=</span> <span class='cn'>FALSE</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -286,13 +286,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># 10 random birth dates</span>
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(birth_date = <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>() <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span>(<span class='fl'>10</span>) <span class='op'>*</span> <span class='fl'>25000</span>)
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>birth_date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span><span class='op'>(</span><span class='fl'>10</span><span class='op'>)</span> <span class='op'>*</span> <span class='fl'>25000</span><span class='op'>)</span>
|
||||
<span class='co'># add ages</span>
|
||||
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>age</span> <span class='op'><-</span> <span class='fu'>age</span>(<span class='kw'>df</span><span class='op'>$</span><span class='kw'>birth_date</span>)
|
||||
<span class='va'>df</span><span class='op'>$</span><span class='va'>age</span> <span class='op'><-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span><span class='op'>)</span>
|
||||
<span class='co'># add exact ages</span>
|
||||
<span class='kw'>df</span><span class='op'>$</span><span class='kw'>age_exact</span> <span class='op'><-</span> <span class='fu'>age</span>(<span class='kw'>df</span><span class='op'>$</span><span class='kw'>birth_date</span>, exact = <span class='fl'>TRUE</span>)
|
||||
<span class='va'>df</span><span class='op'>$</span><span class='va'>age_exact</span> <span class='op'><-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span>, exact <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>df</span>
|
||||
<span class='va'>df</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -309,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>Split ages into age groups defined by the <code>split</code> parameter. This allows for easier demographic (antimicrobial resistance) analysis.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>age_groups</span>(<span class='kw'>x</span>, split_at = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span>), na.rm = <span class='fl'>FALSE</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>x</span>, split_at <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span><span class='op'>)</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -294,36 +294,36 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='kw'>ages</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span>)
|
||||
<pre class="examples"><span class='va'>ages</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># split into 0-49 and 50+</span>
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fl'>50</span>)
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fl'>50</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># split into 0-19, 20-49 and 50+</span>
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>20</span>, <span class='fl'>50</span>))
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>20</span>, <span class='fl'>50</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># split into groups of ten years</span>
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>10</span> <span class='op'>*</span> <span class='fl'>10</span>)
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, split_at = <span class='st'>"tens"</span>)
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>10</span> <span class='op'>*</span> <span class='fl'>10</span><span class='op'>)</span>
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, split_at <span class='op'>=</span> <span class='st'>"tens"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># split into groups of five years</span>
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>20</span> <span class='op'>*</span> <span class='fl'>5</span>)
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, split_at = <span class='st'>"fives"</span>)
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>20</span> <span class='op'>*</span> <span class='fl'>5</span><span class='op'>)</span>
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, split_at <span class='op'>=</span> <span class='st'>"fives"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># split specifically for children</span>
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='st'>"children"</span>)
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='st'>"children"</span><span class='op'>)</span>
|
||||
<span class='co'># same:</span>
|
||||
<span class='fu'>age_groups</span>(<span class='kw'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
|
||||
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'># resistance of ciprofloxacine per age group</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(age_group = <span class='fu'>age_groups</span>(<span class='kw'>age</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>age_group</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(x = <span class='st'>"age_group"</span>, minimum = <span class='fl'>0</span>)
|
||||
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span>, minimum <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -341,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,33 +242,33 @@
|
||||
<p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_class</span>(<span class='kw'>ab_class</span>)
|
||||
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>aminoglycosides</span>()
|
||||
<span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>carbapenems</span>()
|
||||
<span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>cephalosporins</span>()
|
||||
<span class='fu'>cephalosporins</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>cephalosporins_1st</span>()
|
||||
<span class='fu'>cephalosporins_1st</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>cephalosporins_2nd</span>()
|
||||
<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>cephalosporins_3rd</span>()
|
||||
<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>cephalosporins_4th</span>()
|
||||
<span class='fu'>cephalosporins_4th</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>cephalosporins_5th</span>()
|
||||
<span class='fu'>cephalosporins_5th</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>fluoroquinolones</span>()
|
||||
<span class='fu'>fluoroquinolones</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>glycopeptides</span>()
|
||||
<span class='fu'>glycopeptides</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>macrolides</span>()
|
||||
<span class='fu'>macrolides</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>penicillins</span>()
|
||||
<span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>tetracyclines</span>()</pre>
|
||||
<span class='fu'>tetracyclines</span><span class='op'>(</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -298,34 +298,34 @@
|
||||
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<pre class="examples"><span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
|
||||
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>aminoglycosides</span>())
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>mo</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>mo</span>, <span class='fu'>ab_class</span><span class='op'>(</span><span class='st'>"mycobact"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"pos"</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>mo</span>, <span class='fu'>macrolides</span>()) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"pos"</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>mo</span>, <span class='fu'>macrolides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(some_column = <span class='st'>"some_value"</span>,
|
||||
J01CA01 = <span class='st'>"S"</span>) <span class='op'>%>%</span> <span class='co'># ATC code of ampicillin</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>penicillins</span>()) <span class='co'># only the 'J01CA01' column will be selected</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>some_column <span class='op'>=</span> <span class='st'>"some_value"</span>,
|
||||
J01CA01 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span> <span class='op'>%>%</span> <span class='co'># ATC code of ampicillin</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># only the 'J01CA01' column will be selected</span>
|
||||
|
||||
}
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -342,7 +342,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,15 +242,15 @@
|
||||
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_property()</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>antibiotics</span>
|
||||
<pre class="usage"><span class='va'>antibiotics</span>
|
||||
|
||||
<span class='kw'>antivirals</span></pre>
|
||||
<span class='va'>antivirals</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
|
||||
<h3>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 455 observations and 14 variables:</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 455 observations and 14 variables:</h3>
|
||||
|
||||
<ul>
|
||||
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
|
||||
@@ -270,7 +270,7 @@
|
||||
</ul>
|
||||
|
||||
|
||||
<h3>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
|
||||
|
||||
<ul>
|
||||
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
|
||||
@@ -294,7 +294,7 @@
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
|
||||
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3>Direct download</h3>
|
||||
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
|
||||
|
||||
|
||||
<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
|
||||
@@ -346,7 +346,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,9 +242,9 @@
|
||||
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.ab</span>(<span class='kw'>x</span>, flag_multiple_results = <span class='fl'>TRUE</span>, info = <span class='fl'>TRUE</span>, <span class='kw'>...</span>)
|
||||
<pre class="usage"><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is.ab</span>(<span class='kw'>x</span>)</pre>
|
||||
<span class='fu'>is.ab</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -325,27 +325,27 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"eryt"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>" eryt 123"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"ERYT"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"ERY"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"eritromicine"</span>) <span class='co'># spelled wrong, yet works</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"J 01 FA 01"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"Erythromycin"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"eryt"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>" eryt 123"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"ERYT"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"ERY"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"eritromicine"</span><span class='op'>)</span> <span class='co'># spelled wrong, yet works</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"Erythrocin"</span><span class='op'>)</span> <span class='co'># trade name</span>
|
||||
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"Romycin"</span><span class='op'>)</span> <span class='co'># trade name</span>
|
||||
|
||||
<span class='co'># spelling from different languages and dyslexia are no problem</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>)
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>) <span class='co'># small spelling error</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>) <span class='co'># or a bit more severe</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>) <span class='co'># and even this works</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span><span class='op'>(</span><span class='st'>"ceftriaxon"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span><span class='op'>(</span><span class='st'>"cephtriaxone"</span><span class='op'>)</span> <span class='co'># small spelling error</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span><span class='op'>(</span><span class='st'>"cephthriaxone"</span><span class='op'>)</span> <span class='co'># or a bit more severe</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_atc</a></span><span class='op'>(</span><span class='st'>"seephthriaaksone"</span><span class='op'>)</span> <span class='co'># and even this works</span>
|
||||
|
||||
<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
|
||||
<span class='co'># they use as.ab() internally:</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span> <span class='co'># "Erythromycin"</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"eryt"</span><span class='op'>)</span> <span class='co'># "Erythromycin"</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -362,7 +362,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,9 +242,9 @@
|
||||
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.disk</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is.disk</span>(<span class='kw'>x</span>)</pre>
|
||||
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -284,23 +284,23 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='co'># transform existing disk zones to the `disk` class</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(microorganism = <span class='st'>"E. coli"</span>,
|
||||
AMP = <span class='fl'>20</span>,
|
||||
CIP = <span class='fl'>14</span>,
|
||||
GEN = <span class='fl'>18</span>,
|
||||
TOB = <span class='fl'>16</span>)
|
||||
<span class='kw'>df</span>[, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span>] <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='kw'>df</span>[, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span>], <span class='kw'>as.disk</span>)
|
||||
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
|
||||
AMP <span class='op'>=</span> <span class='fl'>20</span>,
|
||||
CIP <span class='op'>=</span> <span class='fl'>14</span>,
|
||||
GEN <span class='op'>=</span> <span class='fl'>18</span>,
|
||||
TOB <span class='op'>=</span> <span class='fl'>16</span><span class='op'>)</span>
|
||||
<span class='va'>df</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>[</span>, <span class='fl'>2</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span>, <span class='va'>as.disk</span><span class='op'>)</span>
|
||||
<span class='co'># same with dplyr:</span>
|
||||
<span class='co'># df %>% mutate(across(AMP:TOB, as.disk))</span>
|
||||
|
||||
<span class='co'># interpret disk values, see ?as.rsi</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.disk</span>(<span class='fl'>18</span>),
|
||||
mo = <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
|
||||
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
|
||||
guideline = <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.disk</span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
|
||||
mo <span class='op'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
|
||||
ab <span class='op'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>df</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,9 +242,9 @@
|
||||
<p>This transforms a vector to a new class <code>mic</code>, which is an ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with valid minimum inhibitory concentrations (MIC) as levels. Invalid MIC values will be translated as <code>NA</code> with a warning.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.mic</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>as.mic</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is.mic</span>(<span class='kw'>x</span>)</pre>
|
||||
<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -282,24 +282,24 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='kw'>mic_data</span> <span class='op'><-</span> <span class='fu'>as.mic</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>">=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"<=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span>))
|
||||
<span class='fu'>is.mic</span>(<span class='kw'>mic_data</span>)
|
||||
<pre class="examples"><span class='va'>mic_data</span> <span class='op'><-</span> <span class='fu'>as.mic</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>">=32"</span>, <span class='st'>"1.0"</span>, <span class='st'>"1"</span>, <span class='st'>"1.00"</span>, <span class='fl'>8</span>, <span class='st'>"<=0.128"</span>, <span class='st'>"8"</span>, <span class='st'>"16"</span>, <span class='st'>"16"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='fu'>is.mic</span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># this can also coerce combined MIC/RSI values:</span>
|
||||
<span class='fu'>as.mic</span>(<span class='st'>"<=0.002; S"</span>) <span class='co'># will return <=0.002</span>
|
||||
<span class='fu'>as.mic</span><span class='op'>(</span><span class='st'>"<=0.002; S"</span><span class='op'>)</span> <span class='co'># will return <=0.002</span>
|
||||
|
||||
<span class='co'># interpret MIC values</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.mic</span>(<span class='fl'>2</span>),
|
||||
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
ab = <span class='st'>"AMX"</span>,
|
||||
guideline = <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(x = <span class='fu'>as.mic</span>(<span class='fl'>4</span>),
|
||||
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
ab = <span class='st'>"AMX"</span>,
|
||||
guideline = <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.mic</span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span>,
|
||||
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,
|
||||
ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'>as.mic</span><span class='op'>(</span><span class='fl'>4</span><span class='op'>)</span>,
|
||||
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,
|
||||
ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>mic_data</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>mic_data</span>)
|
||||
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span><span class='va'>mic_data</span><span class='op'>)</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -316,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,24 +242,24 @@
|
||||
<p>Use this function to determine a valid microorganism ID (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (like <code>"S. aureus"</code>), an abbreviation known in the field (like <code>"MRSA"</code>), or just a genus. Please see <em>Examples</em>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.mo</span>(
|
||||
<span class='kw'>x</span>,
|
||||
Becker = <span class='fl'>FALSE</span>,
|
||||
Lancefield = <span class='fl'>FALSE</span>,
|
||||
allow_uncertain = <span class='fl'>TRUE</span>,
|
||||
reference_df = <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(),
|
||||
ignore_pattern = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_ignore_pattern"</span>),
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
Becker <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
Lancefield <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
allow_uncertain <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
reference_df <span class='op'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
ignore_pattern <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_ignore_pattern"</span><span class='op'>)</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is.mo</span>(<span class='kw'>x</span>)
|
||||
<span class='fu'>is.mo</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_failures</span>()
|
||||
<span class='fu'>mo_failures</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_uncertainties</span>()
|
||||
<span class='fu'>mo_uncertainties</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_renamed</span>()</pre>
|
||||
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -306,7 +306,7 @@
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
|
||||
<h3>General info</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General info</h3>
|
||||
|
||||
|
||||
<p>A microorganism ID from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
|
||||
@@ -334,7 +334,7 @@
|
||||
|
||||
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
|
||||
|
||||
<h3>Coping with uncertain results</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Coping with uncertain results</h3>
|
||||
|
||||
|
||||
<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul>
|
||||
@@ -358,7 +358,7 @@
|
||||
</ul>
|
||||
|
||||
|
||||
<h3>Microbial prevalence of pathogens in humans</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Microbial prevalence of pathogens in humans</h3>
|
||||
|
||||
|
||||
<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into human pathogenic prevalence is explained in the section <em>Matching score for microorganisms</em> below.</p>
|
||||
@@ -423,39 +423,39 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"sau"</span>) <span class='co'># WHONET code</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"stau"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"STAU"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"staaur"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. aureus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S aureus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Zthafilokkoockus oureuz"</span>) <span class='co'># handles incorrect spelling</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
|
||||
<span class='fu'>as.mo</span>(<span class='fl'>115329001</span>) <span class='co'># SNOMED CT code</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"sau"</span><span class='op'>)</span> <span class='co'># WHONET code</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"stau"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"STAU"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"staaur"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. aureus"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S aureus"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Staphylococcus aureus (MRSA)"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Zthafilokkoockus oureuz"</span><span class='op'>)</span> <span class='co'># handles incorrect spelling</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"MRSA"</span><span class='op'>)</span> <span class='co'># Methicillin Resistant S. aureus</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"VISA"</span><span class='op'>)</span> <span class='co'># Vancomycin Intermediate S. aureus</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"VRSA"</span><span class='op'>)</span> <span class='co'># Vancomycin Resistant S. aureus</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='fl'>115329001</span><span class='op'>)</span> <span class='co'># SNOMED CT code</span>
|
||||
|
||||
<span class='co'># Dyslexia is no problem - these all work:</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticum"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticus"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasmium urealytica"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplazma urealitycium"</span>)
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplasma urealyticum"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplasma urealyticus"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplasmium urealytica"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Ureaplazma urealitycium"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"GBS"</span>) <span class='co'># Group B Streptococci</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"Streptococcus group A"</span><span class='op'>)</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"GAS"</span><span class='op'>)</span> <span class='co'># Group A Streptococci</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"GBS"</span><span class='op'>)</span> <span class='co'># Group B Streptococci</span>
|
||||
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPDR</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CONS</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. epidermidis"</span><span class='op'>)</span> <span class='co'># will remain species: B_STPHY_EPDR</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. epidermidis"</span>, Becker <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># will not remain species: B_STPHY_CONS</span>
|
||||
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYGN</span>
|
||||
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRPA</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span><span class='op'>)</span> <span class='co'># will remain species: B_STRPT_PYGN</span>
|
||||
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span>, Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># will not remain species: B_STRPT_GRPA</span>
|
||||
|
||||
<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Escherichia"</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Gram negative"</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -473,7 +473,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,45 +242,45 @@
|
||||
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S < I < R</code>. Values that cannot be interpreted will be returned as <code>NA</code> with a warning.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
|
||||
<pre class="usage"><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is.rsi</span>(<span class='kw'>x</span>)
|
||||
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>x</span>, threshold = <span class='fl'>0.05</span>)
|
||||
<span class='fu'>is.rsi.eligible</span><span class='op'>(</span><span class='va'>x</span>, threshold <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for mic</span>
|
||||
<span class='fu'>as.rsi</span>(
|
||||
<span class='kw'>x</span>,
|
||||
mo = <span class='kw'>NULL</span>,
|
||||
ab = <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>)),
|
||||
guideline = <span class='st'>"EUCAST"</span>,
|
||||
uti = <span class='fl'>FALSE</span>,
|
||||
conserve_capped_values = <span class='fl'>FALSE</span>,
|
||||
add_intrinsic_resistance = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
ab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
|
||||
uti <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for disk</span>
|
||||
<span class='fu'>as.rsi</span>(
|
||||
<span class='kw'>x</span>,
|
||||
mo = <span class='kw'>NULL</span>,
|
||||
ab = <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>)),
|
||||
guideline = <span class='st'>"EUCAST"</span>,
|
||||
uti = <span class='fl'>FALSE</span>,
|
||||
add_intrinsic_resistance = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
ab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
|
||||
uti <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for data.frame</span>
|
||||
<span class='fu'>as.rsi</span>(
|
||||
<span class='kw'>x</span>,
|
||||
<span class='kw'>...</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
guideline = <span class='st'>"EUCAST"</span>,
|
||||
uti = <span class='kw'>NULL</span>,
|
||||
conserve_capped_values = <span class='fl'>FALSE</span>,
|
||||
add_intrinsic_resistance = <span class='fl'>FALSE</span>
|
||||
)</pre>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
<span class='va'>...</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
|
||||
uti <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -334,43 +334,43 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
|
||||
<h3>How it works</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How it works</h3>
|
||||
|
||||
|
||||
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
|
||||
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"<0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
|
||||
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
|
||||
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
|
||||
<span class='kw'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
|
||||
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
|
||||
<span class='va'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
|
||||
</pre></li>
|
||||
<li><p>Operators like "<=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".</p></li>
|
||||
</ul></li>
|
||||
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
|
||||
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.disk</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
|
||||
<span class='kw'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
|
||||
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
|
||||
<span class='va'>your_data</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
|
||||
</pre></li>
|
||||
</ul></li>
|
||||
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
|
||||
</ol>
|
||||
|
||||
|
||||
<h3>Supported guidelines</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported guidelines</h3>
|
||||
|
||||
|
||||
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
|
||||
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
|
||||
|
||||
<h3>After interpretation</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After interpretation</h3>
|
||||
|
||||
|
||||
<p>After using <code>as.rsi()</code>, you can use the <code><a href='eucast_rules.html'>eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
|
||||
|
||||
<h3>Machine readable interpretation guidelines</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine readable interpretation guidelines</h3>
|
||||
|
||||
|
||||
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
|
||||
|
||||
<h3>Other</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
|
||||
|
||||
|
||||
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
|
||||
@@ -411,87 +411,87 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
|
||||
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
|
||||
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://docs.ropensci.org/skimr'>"skimr"</a></span>)) {
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='co'># support for skim() too:</span>
|
||||
<span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span>(<span class='kw'>example_isolates</span>)
|
||||
}
|
||||
<span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
|
||||
<span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
|
||||
|
||||
<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(microorganism = <span class='st'>"E. coli"</span>,
|
||||
AMP = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>8</span>),
|
||||
CIP = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>0.256</span>),
|
||||
GEN = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
|
||||
TOB = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>16</span>),
|
||||
NIT = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>32</span>))
|
||||
<span class='fu'>as.rsi</span>(<span class='kw'>df</span>)
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
|
||||
AMP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>8</span><span class='op'>)</span>,
|
||||
CIP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>0.256</span><span class='op'>)</span>,
|
||||
GEN <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
|
||||
TOB <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>16</span><span class='op'>)</span>,
|
||||
NIT <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>32</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># for single values</span>
|
||||
<span class='fu'>as.rsi</span>(x = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
|
||||
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
ab = <span class='st'>"AMP"</span>,
|
||||
guideline = <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span>,
|
||||
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,
|
||||
ab <span class='op'>=</span> <span class='st'>"AMP"</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>as.rsi</span>(x = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
|
||||
mo = <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
|
||||
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
|
||||
guideline = <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
|
||||
mo <span class='op'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
|
||||
ab <span class='op'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
|
||||
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'># the dplyr way</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>)
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='as.mic.html'>is.mic</a></span>(<span class='kw'>x</span>) <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span>(<span class='kw'>x</span>), <span class='kw'>as.rsi</span>)
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>))
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>, <span class='kw'>as.rsi</span>))
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
|
||||
<span class='va'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='as.mic.html'>is.mic</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
|
||||
<span class='va'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='va'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
|
||||
<span class='va'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>)
|
||||
<span class='va'>df</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># to include information about urinary tract infections (UTI)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
|
||||
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"<= 2"</span>, <span class='fl'>32</span>),
|
||||
from_the_bladder = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>TRUE</span>, <span class='fl'>FALSE</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'>as.rsi</span>(uti = <span class='st'>"from_the_bladder"</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='st'>"E. coli"</span>,
|
||||
NIT <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"<= 2"</span>, <span class='fl'>32</span><span class='op'>)</span>,
|
||||
from_the_bladder <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='cn'>TRUE</span>, <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span>uti <span class='op'>=</span> <span class='st'>"from_the_bladder"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
|
||||
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"<= 2"</span>, <span class='fl'>32</span>),
|
||||
specimen = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"urine"</span>, <span class='st'>"blood"</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='st'>"E. coli"</span>,
|
||||
NIT <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"<= 2"</span>, <span class='fl'>32</span><span class='op'>)</span>,
|
||||
specimen <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"urine"</span>, <span class='st'>"blood"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='co'># automatically determines urine isolates</span>
|
||||
|
||||
<span class='kw'>df</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>NIT</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>, uti = <span class='fl'>TRUE</span>)
|
||||
}
|
||||
<span class='va'>df</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>NIT</span><span class='op'>)</span>, <span class='va'>as.rsi</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span>, uti <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
|
||||
<span class='co'># For CLEANING existing R/SI values ------------------------------------</span>
|
||||
|
||||
<span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>, <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>))
|
||||
<span class='fu'>as.rsi</span>(<span class='st'>"<= 0.002; S"</span>) <span class='co'># will return "S"</span>
|
||||
<span class='kw'>rsi_data</span> <span class='op'><-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
|
||||
<span class='fu'>is.rsi</span>(<span class='kw'>rsi_data</span>)
|
||||
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for percentages</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for frequencies</span>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>, <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='st'>"<= 0.002; S"</span><span class='op'>)</span> <span class='co'># will return "S"</span>
|
||||
<span class='va'>rsi_data</span> <span class='op'><-</span> <span class='fu'>as.rsi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='st'>"S"</span>, <span class='fl'>474</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='st'>"I"</span>, <span class='fl'>36</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='st'>"R"</span>, <span class='fl'>370</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>rsi_data</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>rsi_data</span><span class='op'>)</span> <span class='co'># for percentages</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span><span class='va'>rsi_data</span><span class='op'>)</span> <span class='co'># for frequencies</span>
|
||||
|
||||
<span class='co'># the dplyr way</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>), <span class='kw'>as.rsi</span>)
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>PEN</span><span class='op'>:</span><span class='va'>RIF</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
|
||||
<span class='co'># same: </span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>as.rsi</span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>PEN</span><span class='op'>:</span><span class='va'>RIF</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># fastest way to transform all columns with already valid AMR results to class `rsi`:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.rsi.eligible</span>, <span class='kw'>as.rsi</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.rsi.eligible</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
|
||||
<span class='co'># example_isolates %>%</span>
|
||||
<span class='co'># mutate(across(where(is.rsi.eligible), as.rsi))</span>
|
||||
}
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -509,7 +509,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,17 +242,17 @@
|
||||
<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>atc_online_property</span>(
|
||||
<span class='kw'>atc_code</span>,
|
||||
<span class='kw'>property</span>,
|
||||
administration = <span class='st'>"O"</span>,
|
||||
url = <span class='st'>"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no"</span>,
|
||||
url_vet = <span class='st'>"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no"</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>atc_online_property</span><span class='op'>(</span>
|
||||
<span class='va'>atc_code</span>,
|
||||
<span class='va'>property</span>,
|
||||
administration <span class='op'>=</span> <span class='st'>"O"</span>,
|
||||
url <span class='op'>=</span> <span class='st'>"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no"</span>,
|
||||
url_vet <span class='op'>=</span> <span class='st'>"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no"</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>atc_online_groups</span>(<span class='kw'>atc_code</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>atc_online_groups</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>atc_online_ddd</span>(<span class='kw'>atc_code</span>, <span class='kw'>...</span>)</pre>
|
||||
<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -329,12 +329,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
|
||||
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span>)
|
||||
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
|
||||
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span>)
|
||||
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>atc_online_property</span>(<span class='st'>"J01CA04"</span>, property = <span class='st'>"groups"</span>) <span class='co'># search hierarchical groups of amoxicillin</span>
|
||||
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, property <span class='op'>=</span> <span class='st'>"groups"</span><span class='op'>)</span> <span class='co'># search hierarchical groups of amoxicillin</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -352,7 +352,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. <code><a href='proportion.html'>susceptibility()</a></code> and <code><a href='proportion.html'>resistance()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>availability</span>(<span class='kw'>tbl</span>, width = <span class='kw'>NULL</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>tbl</span>, width <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -277,14 +277,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'>availability</span>(<span class='kw'>example_isolates</span>)
|
||||
<pre class="examples"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='kw'>is.rsi</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>availability</span>()
|
||||
}
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span><span class='op'>(</span><span class='va'>is.rsi</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>availability</span><span class='op'>(</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,22 +242,22 @@
|
||||
<p>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><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publicable/printable format, see Examples.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='kw'>x</span>, col_mo = <span class='kw'>NULL</span>, FUN = <span class='kw'>mo_shortname</span>, <span class='kw'>...</span>)
|
||||
<pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for bug_drug_combinations</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(
|
||||
<span class='kw'>x</span>,
|
||||
translate_ab = <span class='st'>"name (ab, atc)"</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
minimum = <span class='fl'>30</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>,
|
||||
add_ab_group = <span class='fl'>TRUE</span>,
|
||||
remove_intrinsic_resistant = <span class='fl'>FALSE</span>,
|
||||
decimal.mark = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"OutDec"</span>),
|
||||
big.mark = <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>),
|
||||
<span class='kw'>...</span>
|
||||
)</pre>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name (ab, atc)"</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
add_ab_group <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
remove_intrinsic_resistant <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
decimal.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"OutDec"</span><span class='op'>)</span>,
|
||||
big.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span><span class='op'>)</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -343,18 +343,18 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='kw'>x</span> <span class='op'><-</span> <span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>)
|
||||
<span class='kw'>x</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='kw'>x</span>, translate_ab = <span class='st'>"name (atc)"</span>)
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
|
||||
<span class='va'>x</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='va'>x</span>, translate_ab <span class='op'>=</span> <span class='st'>"name (atc)"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># Use FUN to change to transformation of microorganism codes</span>
|
||||
<span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
|
||||
FUN = <span class='kw'>mo_gramstain</span>)
|
||||
<span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span>,
|
||||
FUN <span class='op'>=</span> <span class='va'>mo_gramstain</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>bug_drug_combinations</span>(<span class='kw'>example_isolates</span>,
|
||||
FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>),
|
||||
<span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span>,
|
||||
FUN <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>,
|
||||
<span class='st'>"E. coli"</span>,
|
||||
<span class='st'>"Others"</span>))
|
||||
<span class='st'>"Others"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -372,7 +372,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -278,32 +278,32 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># Get version info of included data set</span>
|
||||
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span>()
|
||||
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='co'># Get a note when a species was renamed</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='st'>"Chlamydophila psittaci"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span><span class='op'>(</span><span class='st'>"Chlamydophila psittaci"</span><span class='op'>)</span>
|
||||
<span class='co'># Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to</span>
|
||||
<span class='co'># 'Chlamydia psittaci' (Page, 1968)</span>
|
||||
<span class='co'># [1] "C. psittaci"</span>
|
||||
|
||||
<span class='co'># Get any property from the entire taxonomic tree for all included species</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_class</a></span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_class</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Gammaproteobacteria"</span>
|
||||
|
||||
<span class='fu'><a href='mo_property.html'>mo_family</a></span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_family</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Enterobacteriaceae"</span>
|
||||
|
||||
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># based on kingdom and phylum, see ?mo_gramstain</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># based on kingdom and phylum, see ?mo_gramstain</span>
|
||||
<span class='co'># [1] "Gram negative"</span>
|
||||
|
||||
<span class='fu'><a href='mo_property.html'>mo_ref</a></span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_ref</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Castellani et al., 1919"</span>
|
||||
|
||||
<span class='co'># Do not get mistaken - this package is about microorganisms</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Fungi" # Fungi?!</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Cladosporium elegans" # Because a microorganism was found</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -321,7 +321,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>This function returns information about the included data from the Catalogue of Life.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>catalogue_of_life_version</span>()</pre>
|
||||
<pre class="usage"><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
@@ -282,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</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">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -244,31 +244,31 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_susceptible</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_R</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_R</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_IR</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_IR</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_I</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_I</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_SI</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_SI</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_S</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_S</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_all</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>count_all</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>n_rsi</span>(<span class='kw'>...</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>count_df</span>(
|
||||
<span class='kw'>data</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>
|
||||
)</pre>
|
||||
<span class='fu'>count_df</span><span class='op'>(</span>
|
||||
<span class='va'>data</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -355,12 +355,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
--------------------------------------------------------------------
|
||||
</pre>
|
||||
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>=</span> <span class='fu'>count_all</span>()
|
||||
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='op'>=</span> <span class='fl'>1</span>
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
|
||||
</pre>
|
||||
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'>count_S</span>() <span class='op'>+</span> <span class='fu'>count_I</span>() <span class='op'>+</span> <span class='fu'>count_R</span>() <span class='op'>>=</span> <span class='fu'>count_all</span>()
|
||||
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='op'>>=</span> <span class='fl'>1</span>
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fl'>1</span>
|
||||
</pre>
|
||||
|
||||
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
|
||||
@@ -375,64 +375,64 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
|
||||
<span class='op'>?</span><span class='kw'>example_isolates</span>
|
||||
<span class='op'>?</span><span class='va'>example_isolates</span>
|
||||
|
||||
<span class='fu'>count_resistant</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "R"</span>
|
||||
<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S" and "I"</span>
|
||||
<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># counts "S", "I" and "R"</span>
|
||||
<span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "R"</span>
|
||||
<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "S" and "I"</span>
|
||||
<span class='fu'>count_all</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "S", "I" and "R"</span>
|
||||
|
||||
<span class='co'># be more specific</span>
|
||||
<span class='fu'>count_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_S</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>count_SI</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>count_I</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>count_IR</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>count_R</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># Count all available isolates</span>
|
||||
<span class='fu'>count_all</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_all</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># n_rsi() is an alias of count_all().</span>
|
||||
<span class='co'># Since it counts all available isolates, you can</span>
|
||||
<span class='co'># calculate back to count e.g. susceptible isolates.</span>
|
||||
<span class='co'># These results are the same:</span>
|
||||
<span class='fu'>count_susceptible</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'><a href='proportion.html'>susceptibility</a></span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='op'>*</span> <span class='fu'>n_rsi</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='proportion.html'>susceptibility</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>*</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>count_R</span>(<span class='kw'>CIP</span>),
|
||||
I = <span class='fu'>count_I</span>(<span class='kw'>CIP</span>),
|
||||
S = <span class='fu'>count_S</span>(<span class='kw'>CIP</span>),
|
||||
n1 = <span class='fu'>count_all</span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
n2 = <span class='fu'>n_rsi</span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>R <span class='op'>=</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
|
||||
I <span class='op'>=</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
|
||||
S <span class='op'>=</span> <span class='fu'>count_S</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
|
||||
n1 <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># the actual total; sum of all three</span>
|
||||
n2 <span class='op'>=</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># same - analogous to n_distinct</span>
|
||||
total <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
|
||||
<span class='co'># Please mind that `susceptibility()` calculates percentages right away instead.</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>) <span class='co'># 1433</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>) <span class='co'># 1879</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># 1433</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># 1879</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>GEN</span>) <span class='co'># 1399</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span>(<span class='kw'>GEN</span>) <span class='co'># 1855</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1399</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1855</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1764</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># 1936</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1764</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># 1936</span>
|
||||
|
||||
<span class='co'># Get number of S+I vs. R immediately of selected columns</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>count_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
}
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -449,7 +449,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -83,7 +83,7 @@ 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">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -244,16 +244,16 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>eucast_rules</span>(
|
||||
<span class='kw'>x</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
|
||||
rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_eucastrules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
|
||||
verbose = <span class='fl'>FALSE</span>,
|
||||
version_breakpoints = <span class='fl'>10</span>,
|
||||
version_expertrules = <span class='fl'>3.2</span>,
|
||||
<span class='kw'>...</span>
|
||||
)</pre>
|
||||
<pre class="usage"><span class='fu'>eucast_rules</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
rules <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_eucastrules"</span>, default <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
version_breakpoints <span class='op'>=</span> <span class='fl'>10</span>,
|
||||
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -311,7 +311,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
|
||||
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
|
||||
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
|
||||
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3>'Other' rules</h3>
|
||||
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' rules</h3>
|
||||
|
||||
|
||||
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
|
||||
@@ -349,21 +349,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='kw'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
|
||||
<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span>,
|
||||
<span class='st'>"Enterococcus faecalis"</span>,
|
||||
<span class='st'>"Escherichia coli"</span>,
|
||||
<span class='st'>"Klebsiella pneumoniae"</span>,
|
||||
<span class='st'>"Pseudomonas aeruginosa"</span>),
|
||||
VAN = <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
|
||||
AMX = <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
|
||||
COL = <span class='st'>"-"</span>, <span class='co'># Colistin</span>
|
||||
CAZ = <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
|
||||
CXM = <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
|
||||
PEN = <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
|
||||
FOX = <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
||||
stringsAsFactors = <span class='fl'>FALSE</span>)
|
||||
<span class='st'>"Pseudomonas aeruginosa"</span><span class='op'>)</span>,
|
||||
VAN <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
|
||||
AMX <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
|
||||
COL <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
|
||||
CAZ <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
|
||||
CXM <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
|
||||
PEN <span class='op'>=</span> <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
|
||||
FOX <span class='op'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
||||
stringsAsFactors <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>a</span>
|
||||
<span class='va'>a</span>
|
||||
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
|
||||
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
|
||||
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
|
||||
@@ -373,9 +373,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<span class='co'># apply EUCAST rules: some results wil be changed</span>
|
||||
<span class='kw'>b</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>)
|
||||
<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>b</span>
|
||||
<span class='va'>b</span>
|
||||
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
|
||||
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
|
||||
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
|
||||
@@ -386,7 +386,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
|
||||
<span class='co'># containing all details about the transformations:</span>
|
||||
<span class='kw'>c</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>)
|
||||
<span class='va'>c</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>a</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -404,7 +404,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read <a href='https://msberends.github.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>example_isolates</span></pre>
|
||||
<pre class="usage"><span class='va'>example_isolates</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -286,7 +286,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<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='kw'>example_isolates_unclean</span></pre>
|
||||
<pre class="usage"><span class='va'>example_isolates_unclean</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -281,7 +281,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,43 +242,43 @@
|
||||
<p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>first_isolate</span>(
|
||||
<span class='kw'>x</span>,
|
||||
col_date = <span class='kw'>NULL</span>,
|
||||
col_patient_id = <span class='kw'>NULL</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
col_testcode = <span class='kw'>NULL</span>,
|
||||
col_specimen = <span class='kw'>NULL</span>,
|
||||
col_icu = <span class='kw'>NULL</span>,
|
||||
col_keyantibiotics = <span class='kw'>NULL</span>,
|
||||
episode_days = <span class='fl'>365</span>,
|
||||
testcodes_exclude = <span class='kw'>NULL</span>,
|
||||
icu_exclude = <span class='fl'>FALSE</span>,
|
||||
specimen_group = <span class='kw'>NULL</span>,
|
||||
type = <span class='st'>"keyantibiotics"</span>,
|
||||
ignore_I = <span class='fl'>TRUE</span>,
|
||||
points_threshold = <span class='fl'>2</span>,
|
||||
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
|
||||
include_unknown = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>first_isolate</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_testcode <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_specimen <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_icu <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_keyantibiotics <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
episode_days <span class='op'>=</span> <span class='fl'>365</span>,
|
||||
testcodes_exclude <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
icu_exclude <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
specimen_group <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
type <span class='op'>=</span> <span class='st'>"keyantibiotics"</span>,
|
||||
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
|
||||
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
include_unknown <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>filter_first_isolate</span>(
|
||||
<span class='kw'>x</span>,
|
||||
col_date = <span class='kw'>NULL</span>,
|
||||
col_patient_id = <span class='kw'>NULL</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>filter_first_isolate</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>filter_first_weighted_isolate</span>(
|
||||
<span class='kw'>x</span>,
|
||||
col_date = <span class='kw'>NULL</span>,
|
||||
col_patient_id = <span class='kw'>NULL</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
col_keyantibiotics = <span class='kw'>NULL</span>,
|
||||
<span class='kw'>...</span>
|
||||
)</pre>
|
||||
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
col_keyantibiotics <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -369,16 +369,16 @@
|
||||
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
|
||||
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https:/pubmed.ncbi.nlm.nih.gov/17304462/'>(ref)</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
|
||||
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p>
|
||||
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to either:</p><pre> <span class='kw'>x</span>[<span class='fu'>first_isolate</span>(<span class='kw'>x</span>, <span class='kw'>...</span>), ]
|
||||
<span class='kw'>x</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'>first_isolate</span>(<span class='kw'>x</span>, <span class='kw'>...</span>))
|
||||
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to either:</p><pre> <span class='va'>x</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>, <span class='op'>]</span>
|
||||
<span class='va'>x</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span><span class='op'>)</span>
|
||||
</pre>
|
||||
|
||||
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='kw'>x</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(keyab = <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='kw'>.</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(only_weighted_firsts = <span class='fu'>first_isolate</span>(<span class='kw'>x</span>,
|
||||
col_keyantibiotics = <span class='st'>"keyab"</span>, <span class='kw'>...</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>only_weighted_firsts</span> <span class='op'>==</span> <span class='fl'>TRUE</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='op'>-</span><span class='kw'>only_weighted_firsts</span>, <span class='op'>-</span><span class='kw'>keyab</span>)
|
||||
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='va'>x</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>only_weighted_firsts <span class='op'>=</span> <span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>,
|
||||
col_keyantibiotics <span class='op'>=</span> <span class='st'>"keyab"</span>, <span class='va'>...</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>only_weighted_firsts</span> <span class='op'>==</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='op'>-</span><span class='va'>only_weighted_firsts</span>, <span class='op'>-</span><span class='va'>keyab</span><span class='op'>)</span>
|
||||
</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
|
||||
@@ -413,39 +413,39 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='co'># See ?example_isolates.</span>
|
||||
|
||||
<span class='co'># basic filtering on first isolates</span>
|
||||
<span class='kw'>example_isolates</span>[<span class='fu'>first_isolate</span>(<span class='kw'>example_isolates</span>), ]
|
||||
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>, <span class='op'>]</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='co'># Filter on first isolates:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(first_isolate = <span class='fu'>first_isolate</span>(<span class='kw'>.</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># Short-hand versions:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>filter_first_isolate</span>()
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>filter_first_isolate</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span>()
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># Now let's see if first isolates matter:</span>
|
||||
<span class='kw'>A</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(count = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>GEN</span>), <span class='co'># gentamicin availability</span>
|
||||
resistance = <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='kw'>GEN</span>)) <span class='co'># gentamicin resistance</span>
|
||||
<span class='va'>A</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>count <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span>, <span class='co'># gentamicin availability</span>
|
||||
resistance <span class='op'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># gentamicin resistance</span>
|
||||
|
||||
<span class='kw'>B</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span>() <span class='op'>%>%</span> <span class='co'># the 1st isolate filter</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(count = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>GEN</span>), <span class='co'># gentamicin availability</span>
|
||||
resistance = <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='kw'>GEN</span>)) <span class='co'># gentamicin resistance</span>
|
||||
<span class='va'>B</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span> <span class='co'># the 1st isolate filter</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>count <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span>, <span class='co'># gentamicin availability</span>
|
||||
resistance <span class='op'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># gentamicin resistance</span>
|
||||
|
||||
<span class='co'># Have a look at A and B.</span>
|
||||
<span class='co'># B is more reliable because every isolate is counted only once.</span>
|
||||
<span class='co'># Gentamicin resistance in hospital D appears to be 3.7% higher than</span>
|
||||
<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
|
||||
}
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -463,7 +463,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>g.test</span>(<span class='kw'>x</span>, y = <span class='kw'>NULL</span>, p = <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='kw'>x</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='kw'>x</span>)), rescale.p = <span class='fl'>FALSE</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, y <span class='op'>=</span> <span class='cn'>NULL</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, rescale.p <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -305,14 +305,14 @@
|
||||
<p>If <code>x</code> is a matrix with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of <code>x</code> must be non-negative integers. Otherwise, <code>x</code> and <code>y</code> must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.</p>
|
||||
<p>The p-value is computed from the asymptotic chi-squared distribution of the test statistic.</p>
|
||||
<p>In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (like the <em>G</em>-test) but rather that for Fisher's exact test.</p>
|
||||
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3><em>G</em>-test of goodness-of-fit (likelihood ratio test)</h3>
|
||||
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><em>G</em>-test of goodness-of-fit (likelihood ratio test)</h3>
|
||||
|
||||
|
||||
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
|
||||
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
|
||||
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p>
|
||||
|
||||
<h3><em>G</em>-test of independence</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><em>G</em>-test of independence</h3>
|
||||
|
||||
|
||||
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
|
||||
@@ -320,13 +320,13 @@
|
||||
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
|
||||
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p>
|
||||
|
||||
<h3>How the test works</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How the test works</h3>
|
||||
|
||||
|
||||
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
|
||||
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
|
||||
<p>\(G = 2 * sum(x * log(x / E))\)</p>
|
||||
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='kw'>p</span> <span class='op'><-</span> <span class='kw'>stats</span>::<span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span>(<span class='kw'>G</span>, <span class='kw'>df</span>, lower.tail = <span class='fl'>FALSE</span>)
|
||||
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='va'>p</span> <span class='op'><-</span> <span class='fu'>stats</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span><span class='op'>(</span><span class='va'>G</span>, <span class='va'>df</span>, lower.tail <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
</pre>
|
||||
|
||||
<p>where <code>df</code> are the degrees of freedom.</p>
|
||||
@@ -364,8 +364,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<span class='co'># by a single gene with two co-dominant alleles, you would expect a 1:2:1</span>
|
||||
<span class='co'># ratio.</span>
|
||||
|
||||
<span class='kw'>x</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>772</span>, <span class='fl'>1611</span>, <span class='fl'>737</span>)
|
||||
<span class='kw'>G</span> <span class='op'><-</span> <span class='fu'>g.test</span>(<span class='kw'>x</span>, p = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>1</span>) <span class='op'>/</span> <span class='fl'>4</span>)
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>772</span>, <span class='fl'>1611</span>, <span class='fl'>737</span><span class='op'>)</span>
|
||||
<span class='va'>G</span> <span class='op'><-</span> <span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>1</span><span class='op'>)</span> <span class='op'>/</span> <span class='fl'>4</span><span class='op'>)</span>
|
||||
<span class='co'># G$p.value = 0.12574.</span>
|
||||
|
||||
<span class='co'># There is no significant difference from a 1:2:1 ratio.</span>
|
||||
@@ -380,8 +380,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<span class='co'># keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992)</span>
|
||||
<span class='co'># observed 1752 right-billed and 1895 left-billed crossbills.</span>
|
||||
|
||||
<span class='kw'>x</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1752</span>, <span class='fl'>1895</span>)
|
||||
<span class='fu'>g.test</span>(<span class='kw'>x</span>)
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1752</span>, <span class='fl'>1895</span><span class='op'>)</span>
|
||||
<span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
<span class='co'># p = 0.01787343</span>
|
||||
|
||||
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
|
||||
@@ -403,7 +403,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,67 +242,67 @@
|
||||
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ggplot_rsi</span>(
|
||||
<span class='kw'>data</span>,
|
||||
position = <span class='kw'>NULL</span>,
|
||||
x = <span class='st'>"antibiotic"</span>,
|
||||
fill = <span class='st'>"interpretation"</span>,
|
||||
facet = <span class='kw'>NULL</span>,
|
||||
breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
|
||||
limits = <span class='kw'>NULL</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>,
|
||||
minimum = <span class='fl'>30</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
nrow = <span class='kw'>NULL</span>,
|
||||
colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(S = <span class='st'>"#61a8ff"</span>, SI = <span class='st'>"#61a8ff"</span>, I = <span class='st'>"#61f7ff"</span>, IR = <span class='st'>"#ff6961"</span>, R =
|
||||
<span class='st'>"#ff6961"</span>),
|
||||
datalabels = <span class='fl'>TRUE</span>,
|
||||
datalabels.size = <span class='fl'>2.5</span>,
|
||||
datalabels.colour = <span class='st'>"gray15"</span>,
|
||||
title = <span class='kw'>NULL</span>,
|
||||
subtitle = <span class='kw'>NULL</span>,
|
||||
caption = <span class='kw'>NULL</span>,
|
||||
x.title = <span class='st'>"Antimicrobial"</span>,
|
||||
y.title = <span class='st'>"Proportion"</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>ggplot_rsi</span><span class='op'>(</span>
|
||||
<span class='va'>data</span>,
|
||||
position <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
|
||||
fill <span class='op'>=</span> <span class='st'>"interpretation"</span>,
|
||||
facet <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span>,
|
||||
limits <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
nrow <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
|
||||
<span class='st'>"#ff6961"</span><span class='op'>)</span>,
|
||||
datalabels <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
datalabels.size <span class='op'>=</span> <span class='fl'>2.5</span>,
|
||||
datalabels.colour <span class='op'>=</span> <span class='st'>"gray15"</span>,
|
||||
title <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
subtitle <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
caption <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
x.title <span class='op'>=</span> <span class='st'>"Antimicrobial"</span>,
|
||||
y.title <span class='op'>=</span> <span class='st'>"Proportion"</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>geom_rsi</span>(
|
||||
position = <span class='kw'>NULL</span>,
|
||||
x = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
|
||||
fill = <span class='st'>"interpretation"</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
minimum = <span class='fl'>30</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>geom_rsi</span><span class='op'>(</span>
|
||||
position <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span><span class='op'>)</span>,
|
||||
fill <span class='op'>=</span> <span class='st'>"interpretation"</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>facet_rsi</span>(facet = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), nrow = <span class='kw'>NULL</span>)
|
||||
<span class='fu'>facet_rsi</span><span class='op'>(</span>facet <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span><span class='op'>)</span>, nrow <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>scale_y_percent</span>(breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), limits = <span class='kw'>NULL</span>)
|
||||
<span class='fu'>scale_y_percent</span><span class='op'>(</span>breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span>, limits <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>scale_rsi_colours</span>(
|
||||
colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(S = <span class='st'>"#61a8ff"</span>, SI = <span class='st'>"#61a8ff"</span>, I = <span class='st'>"#61f7ff"</span>, IR = <span class='st'>"#ff6961"</span>, R =
|
||||
<span class='st'>"#ff6961"</span>)
|
||||
)
|
||||
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span>
|
||||
colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>S <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, SI <span class='op'>=</span> <span class='st'>"#61a8ff"</span>, I <span class='op'>=</span> <span class='st'>"#61f7ff"</span>, IR <span class='op'>=</span> <span class='st'>"#ff6961"</span>, R <span class='op'>=</span>
|
||||
<span class='st'>"#ff6961"</span><span class='op'>)</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>theme_rsi</span>()
|
||||
<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>labels_rsi_count</span>(
|
||||
position = <span class='kw'>NULL</span>,
|
||||
x = <span class='st'>"antibiotic"</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
minimum = <span class='fl'>30</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>,
|
||||
datalabels.size = <span class='fl'>3</span>,
|
||||
datalabels.colour = <span class='st'>"gray15"</span>
|
||||
)</pre>
|
||||
<span class='fu'>labels_rsi_count</span><span class='op'>(</span>
|
||||
position <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
datalabels.size <span class='op'>=</span> <span class='fl'>3</span>,
|
||||
datalabels.colour <span class='op'>=</span> <span class='st'>"gray15"</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -403,7 +403,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df()</a></code>.</p><h3>The functions</h3>
|
||||
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The functions</h3>
|
||||
|
||||
|
||||
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
|
||||
@@ -427,80 +427,80 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>) <span class='op'>&</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<pre class="examples"><span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
|
||||
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>)) <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span>()
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># prettify the plot using some additional functions:</span>
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>)
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>df</span>) <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span>() <span class='op'>+</span>
|
||||
<span class='fu'>scale_y_percent</span>() <span class='op'>+</span>
|
||||
<span class='fu'>scale_rsi_colours</span>() <span class='op'>+</span>
|
||||
<span class='fu'>labels_rsi_count</span>() <span class='op'>+</span>
|
||||
<span class='fu'>theme_rsi</span>()
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>geom_rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>scale_y_percent</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>scale_rsi_colours</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>labels_rsi_count</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'>theme_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>()
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># get only proportions and no counts:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(datalabels = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># add other ggplot2 parameters as you like:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(width = <span class='fl'>0.5</span>,
|
||||
colour = <span class='st'>"black"</span>,
|
||||
size = <span class='fl'>1</span>,
|
||||
linetype = <span class='fl'>2</span>,
|
||||
alpha = <span class='fl'>0.25</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>width <span class='op'>=</span> <span class='fl'>0.5</span>,
|
||||
colour <span class='op'>=</span> <span class='st'>"black"</span>,
|
||||
size <span class='op'>=</span> <span class='fl'>1</span>,
|
||||
linetype <span class='op'>=</span> <span class='fl'>2</span>,
|
||||
alpha <span class='op'>=</span> <span class='fl'>0.25</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(colours = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(SI = <span class='st'>"yellow"</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>SI <span class='op'>=</span> <span class='st'>"yellow"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
}
|
||||
<span class='op'>}</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
|
||||
<span class='co'># resistance of ciprofloxacine per age group</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(first_isolate = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>first_isolate</span> <span class='op'>==</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%>%</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span>,
|
||||
<span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='co'># `age_groups` is also a function of this AMR package:</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(age_group = <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='kw'>age</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>age_group</span>,
|
||||
<span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(x = <span class='st'>"age_group"</span>)
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>,
|
||||
<span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>() <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
<span class='co'># a shorter version which also adjusts data label colours:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(colours = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>colours <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>NIT</span>, <span class='kw'>FOS</span>, <span class='kw'>TMP</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(x = <span class='st'>"hospital_id"</span>,
|
||||
facet = <span class='st'>"antibiotic"</span>,
|
||||
nrow = <span class='fl'>1</span>,
|
||||
title = <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
|
||||
x.title = <span class='st'>"Hospital"</span>,
|
||||
datalabels = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>NIT</span>, <span class='va'>FOS</span>, <span class='va'>TMP</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"hospital_id"</span>,
|
||||
facet <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
|
||||
nrow <span class='op'>=</span> <span class='fl'>1</span>,
|
||||
title <span class='op'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
|
||||
x.title <span class='op'>=</span> <span class='st'>"Hospital"</span>,
|
||||
datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -518,7 +518,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>This tries to find a column name in a data set based on information from the <a href='antibiotics.html'>antibiotics</a> data set. Also supports WHONET abbreviations.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>guess_ab_col</span>(x = <span class='kw'>NULL</span>, search_string = <span class='kw'>NULL</span>, verbose = <span class='fl'>FALSE</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>guess_ab_col</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, search_string <span class='op'>=</span> <span class='cn'>NULL</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -281,32 +281,32 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(amox = <span class='st'>"S"</span>,
|
||||
tetr = <span class='st'>"R"</span>)
|
||||
<pre class="examples"><span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>amox <span class='op'>=</span> <span class='st'>"S"</span>,
|
||||
tetr <span class='op'>=</span> <span class='st'>"R"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"amoxicillin"</span>)
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "amox"</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"J01AA07"</span><span class='op'>)</span> <span class='co'># ATC code of tetracycline</span>
|
||||
<span class='co'># [1] "tetr"</span>
|
||||
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>, verbose = <span class='fl'>TRUE</span>)
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"J01AA07"</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
<span class='co'># NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).</span>
|
||||
<span class='co'># [1] "tetr"</span>
|
||||
|
||||
<span class='co'># WHONET codes</span>
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ND10 = <span class='st'>"R"</span>,
|
||||
AMC_ED20 = <span class='st'>"S"</span>)
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>AMP_ND10 <span class='op'>=</span> <span class='st'>"R"</span>,
|
||||
AMC_ED20 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span>
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "AMP_ND10"</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01CR02"</span>)
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"J01CR02"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "AMC_ED20"</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"augmentin"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "AMC_ED20"</span>
|
||||
|
||||
<span class='co'># Longer names take precendence:</span>
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ED2 = <span class='st'>"S"</span>,
|
||||
AMP_ED20 = <span class='st'>"S"</span>)
|
||||
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>AMP_ED2 <span class='op'>=</span> <span class='st'>"S"</span>,
|
||||
AMP_ED20 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span>
|
||||
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "AMP_ED20"</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -324,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -652,7 +652,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>intrinsic_resistant</span></pre>
|
||||
<pre class="usage"><span class='va'>intrinsic_resistant</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -268,12 +268,12 @@
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>intrinsic_resistant</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='kw'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/pull.html'>pull</a></span>(<span class='kw'>microorganism</span>)
|
||||
<pre class="examples"><span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>intrinsic_resistant</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='va'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/pull.html'>pull</a></span><span class='op'>(</span><span class='va'>microorganism</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
|
||||
}
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -290,7 +290,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,17 +242,17 @@
|
||||
<p>Join the data set <a href='microorganisms.html'>microorganisms</a> easily to an existing table or character vector.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>inner_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
|
||||
<pre class="usage"><span class='fu'>inner_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>left_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
|
||||
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>right_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
|
||||
<span class='fu'>right_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>full_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, suffix = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"2"</span>, <span class='st'>""</span>), <span class='kw'>...</span>)
|
||||
<span class='fu'>full_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>semi_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>semi_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>anti_join_microorganisms</span>(<span class='kw'>x</span>, by = <span class='kw'>NULL</span>, <span class='kw'>...</span>)</pre>
|
||||
<span class='fu'>anti_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -293,25 +293,25 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
|
||||
<span class='fu'>left_join_microorganisms</span>(<span class='st'>"B_KLBSL_PNE"</span>)
|
||||
<pre class="examples"><span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='st'>"B_KLBSL_PNE"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>left_join_microorganisms</span>() <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>()
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(date = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(from = <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-01"</span>),
|
||||
to = <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span>(<span class='st'>"2018-01-07"</span>),
|
||||
by = <span class='fl'>1</span>),
|
||||
bacteria = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
|
||||
<span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>)),
|
||||
stringsAsFactors = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='kw'>df</span>)
|
||||
<span class='kw'>df_joined</span> <span class='op'><-</span> <span class='fu'>left_join_microorganisms</span>(<span class='kw'>df</span>, <span class='st'>"bacteria"</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='kw'>df_joined</span>)
|
||||
}
|
||||
<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span>from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span><span class='op'>(</span><span class='st'>"2018-01-01"</span><span class='op'>)</span>,
|
||||
to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.Date.html'>as.Date</a></span><span class='op'>(</span><span class='st'>"2018-01-07"</span><span class='op'>)</span>,
|
||||
by <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>,
|
||||
bacteria <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"S. aureus"</span>, <span class='st'>"MRSA"</span>, <span class='st'>"MSSA"</span>, <span class='st'>"STAAUR"</span>,
|
||||
<span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
stringsAsFactors <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
|
||||
<span class='va'>df_joined</span> <span class='op'><-</span> <span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"bacteria"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='va'>df_joined</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -329,7 +329,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,39 +242,39 @@
|
||||
<p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate()</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first <em>weighted</em> isolates.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>key_antibiotics</span>(
|
||||
<span class='kw'>x</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
universal_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"amoxicillin"</span>),
|
||||
universal_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>),
|
||||
universal_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"cefuroxime"</span>),
|
||||
universal_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"piperacillin/tazobactam"</span>),
|
||||
universal_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"ciprofloxacin"</span>),
|
||||
universal_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span>),
|
||||
GramPos_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"vancomycin"</span>),
|
||||
GramPos_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"teicoplanin"</span>),
|
||||
GramPos_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"tetracycline"</span>),
|
||||
GramPos_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"erythromycin"</span>),
|
||||
GramPos_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"oxacillin"</span>),
|
||||
GramPos_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"rifampin"</span>),
|
||||
GramNeg_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"gentamicin"</span>),
|
||||
GramNeg_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"tobramycin"</span>),
|
||||
GramNeg_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"colistin"</span>),
|
||||
GramNeg_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"cefotaxime"</span>),
|
||||
GramNeg_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"ceftazidime"</span>),
|
||||
GramNeg_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"meropenem"</span>),
|
||||
warnings = <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>key_antibiotics</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
universal_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>,
|
||||
universal_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span><span class='op'>)</span>,
|
||||
universal_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefuroxime"</span><span class='op'>)</span>,
|
||||
universal_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"piperacillin/tazobactam"</span><span class='op'>)</span>,
|
||||
universal_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ciprofloxacin"</span><span class='op'>)</span>,
|
||||
universal_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span><span class='op'>)</span>,
|
||||
GramPos_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"vancomycin"</span><span class='op'>)</span>,
|
||||
GramPos_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"teicoplanin"</span><span class='op'>)</span>,
|
||||
GramPos_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tetracycline"</span><span class='op'>)</span>,
|
||||
GramPos_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"erythromycin"</span><span class='op'>)</span>,
|
||||
GramPos_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"oxacillin"</span><span class='op'>)</span>,
|
||||
GramPos_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"rifampin"</span><span class='op'>)</span>,
|
||||
GramNeg_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"gentamicin"</span><span class='op'>)</span>,
|
||||
GramNeg_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tobramycin"</span><span class='op'>)</span>,
|
||||
GramNeg_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"colistin"</span><span class='op'>)</span>,
|
||||
GramNeg_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefotaxime"</span><span class='op'>)</span>,
|
||||
GramNeg_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ceftazidime"</span><span class='op'>)</span>,
|
||||
GramNeg_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"meropenem"</span><span class='op'>)</span>,
|
||||
warnings <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>key_antibiotics_equal</span>(
|
||||
<span class='kw'>y</span>,
|
||||
<span class='kw'>z</span>,
|
||||
type = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
|
||||
ignore_I = <span class='fl'>TRUE</span>,
|
||||
points_threshold = <span class='fl'>2</span>,
|
||||
info = <span class='fl'>FALSE</span>
|
||||
)</pre>
|
||||
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span>
|
||||
<span class='va'>y</span>,
|
||||
<span class='va'>z</span>,
|
||||
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span><span class='op'>)</span>,
|
||||
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
|
||||
info <span class='op'>=</span> <span class='cn'>FALSE</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -396,32 +396,32 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='co'># See ?example_isolates.</span>
|
||||
|
||||
<span class='co'># output of the `key_antibiotics` function could be like this:</span>
|
||||
<span class='kw'>strainA</span> <span class='op'><-</span> <span class='st'>"SSSRR.S.R..S"</span>
|
||||
<span class='kw'>strainB</span> <span class='op'><-</span> <span class='st'>"SSSIRSSSRSSS"</span>
|
||||
<span class='va'>strainA</span> <span class='op'><-</span> <span class='st'>"SSSRR.S.R..S"</span>
|
||||
<span class='va'>strainB</span> <span class='op'><-</span> <span class='st'>"SSSIRSSSRSSS"</span>
|
||||
|
||||
<span class='co'># can those strings can be compared with:</span>
|
||||
<span class='fu'>key_antibiotics_equal</span>(<span class='kw'>strainA</span>, <span class='kw'>strainB</span>)
|
||||
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span><span class='op'>)</span>
|
||||
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
|
||||
|
||||
<span class='fu'>key_antibiotics_equal</span>(<span class='kw'>strainA</span>, <span class='kw'>strainB</span>, ignore_I = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span>, ignore_I <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='co'># set key antibiotics to a new variable</span>
|
||||
<span class='kw'>my_patients</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(keyab = <span class='fu'>key_antibiotics</span>(<span class='kw'>.</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
|
||||
<span class='va'>my_patients</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'>key_antibiotics</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>
|
||||
<span class='co'># now calculate first isolates</span>
|
||||
first_regular = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>, col_keyantibiotics = <span class='fl'>FALSE</span>),
|
||||
first_regular <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, col_keyantibiotics <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
|
||||
<span class='co'># and first WEIGHTED isolates</span>
|
||||
first_weighted = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>, col_keyantibiotics = <span class='st'>"keyab"</span>)
|
||||
)
|
||||
first_weighted <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, col_keyantibiotics <span class='op'>=</span> <span class='st'>"keyab"</span><span class='op'>)</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='kw'>my_patients</span><span class='op'>$</span><span class='kw'>first_regular</span>, na.rm = <span class='fl'>TRUE</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='kw'>my_patients</span><span class='op'>$</span><span class='kw'>first_weighted</span>, na.rm = <span class='fl'>TRUE</span>)
|
||||
}
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_regular</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_weighted</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -439,7 +439,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,16 +242,16 @@
|
||||
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for default</span>
|
||||
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for matrix</span>
|
||||
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for data.frame</span>
|
||||
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)</pre>
|
||||
<span class='fu'>kurtosis</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, excess <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -301,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,11 +242,11 @@
|
||||
<p>Convenient wrapper around <code><a href='https://rdrr.io/r/base/grep.html'>grep()</a></code> to match a pattern: <code>x %like% pattern</code>. It always returns a <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector and is always case-insensitive (use <code>x %like_case% pattern</code> for case-sensitive matching). Also, <code>pattern</code> can be as long as <code>x</code> to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>like</span>(<span class='kw'>x</span>, <span class='kw'>pattern</span>, ignore.case = <span class='fl'>TRUE</span>)
|
||||
<pre class="usage"><span class='fu'>like</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>pattern</span>, ignore.case <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>x</span> <span class='op'>%like%</span> <span class='kw'>pattern</span>
|
||||
<span class='va'>x</span> <span class='op'>%like%</span> <span class='va'>pattern</span>
|
||||
|
||||
<span class='kw'>x</span> <span class='op'>%like_case%</span> <span class='kw'>pattern</span></pre>
|
||||
<span class='va'>x</span> <span class='op'>%like_case%</span> <span class='va'>pattern</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -299,25 +299,25 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># simple test</span>
|
||||
<span class='kw'>a</span> <span class='op'><-</span> <span class='st'>"This is a test"</span>
|
||||
<span class='kw'>b</span> <span class='op'><-</span> <span class='st'>"TEST"</span>
|
||||
<span class='kw'>a</span> <span class='op'>%like%</span> <span class='kw'>b</span>
|
||||
<span class='va'>a</span> <span class='op'><-</span> <span class='st'>"This is a test"</span>
|
||||
<span class='va'>b</span> <span class='op'><-</span> <span class='st'>"TEST"</span>
|
||||
<span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span>
|
||||
<span class='co'>#> TRUE</span>
|
||||
<span class='kw'>b</span> <span class='op'>%like%</span> <span class='kw'>a</span>
|
||||
<span class='va'>b</span> <span class='op'>%like%</span> <span class='va'>a</span>
|
||||
<span class='co'>#> FALSE</span>
|
||||
|
||||
<span class='co'># also supports multiple patterns, length must be equal to x</span>
|
||||
<span class='kw'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span>)
|
||||
<span class='kw'>b</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( <span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span>)
|
||||
<span class='kw'>a</span> <span class='op'>%like%</span> <span class='kw'>b</span>
|
||||
<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Test case"</span>, <span class='st'>"Something different"</span>, <span class='st'>"Yet another thing"</span><span class='op'>)</span>
|
||||
<span class='va'>b</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span> <span class='st'>"case"</span>, <span class='st'>"diff"</span>, <span class='st'>"yet"</span><span class='op'>)</span>
|
||||
<span class='va'>a</span> <span class='op'>%like%</span> <span class='va'>b</span>
|
||||
<span class='co'>#> TRUE TRUE TRUE</span>
|
||||
|
||||
<span class='co'># get isolates whose name start with 'Ent' or 'ent'</span>
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"^ent"</span>)
|
||||
}
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -335,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,26 +242,26 @@
|
||||
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>mdro</span>(
|
||||
<span class='kw'>x</span>,
|
||||
guideline = <span class='st'>"CMI2012"</span>,
|
||||
col_mo = <span class='kw'>NULL</span>,
|
||||
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
|
||||
pct_required_classes = <span class='fl'>0.5</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
verbose = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>mdro</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
guideline <span class='op'>=</span> <span class='st'>"CMI2012"</span>,
|
||||
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
pct_required_classes <span class='op'>=</span> <span class='fl'>0.5</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>brmo</span>(<span class='kw'>x</span>, guideline = <span class='st'>"BRMO"</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>brmo</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"BRMO"</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mrgn</span>(<span class='kw'>x</span>, guideline = <span class='st'>"MRGN"</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>mrgn</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"MRGN"</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mdr_tb</span>(<span class='kw'>x</span>, guideline = <span class='st'>"TB"</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>mdr_tb</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"TB"</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mdr_cmi2012</span>(<span class='kw'>x</span>, guideline = <span class='st'>"CMI2012"</span>, <span class='kw'>...</span>)
|
||||
<span class='fu'>mdr_cmi2012</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"CMI2012"</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='kw'>x</span>, guideline = <span class='st'>"EUCAST"</span>, <span class='kw'>...</span>)</pre>
|
||||
<span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>, <span class='va'>...</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -372,19 +372,19 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'>mdro</span>(<span class='kw'>example_isolates</span>, guideline = <span class='st'>"EUCAST"</span>)
|
||||
<pre class="examples"><span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>mdro</span>() <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span>()
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>mdro</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(EUCAST = <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='kw'>.</span>),
|
||||
BRMO = <span class='fu'>brmo</span>(<span class='kw'>.</span>),
|
||||
MRGN = <span class='fu'>mrgn</span>(<span class='kw'>.</span>))
|
||||
}
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>EUCAST <span class='op'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span>,
|
||||
BRMO <span class='op'>=</span> <span class='fu'>brmo</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span>,
|
||||
MRGN <span class='op'>=</span> <span class='fu'>mrgn</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -402,7 +402,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>microorganisms.codes</span></pre>
|
||||
<pre class="usage"><span class='va'>microorganisms.codes</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -288,7 +288,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>microorganisms</span></pre>
|
||||
<pre class="usage"><span class='va'>microorganisms</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -276,7 +276,7 @@
|
||||
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
|
||||
<li><p>7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
|
||||
</ul>
|
||||
<h3>Direct download</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
|
||||
|
||||
|
||||
<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
|
||||
@@ -331,7 +331,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href='as.mo.html'>as.mo()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>microorganisms.old</span></pre>
|
||||
<pre class="usage"><span class='va'>microorganisms.old</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -294,7 +294,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>This helper function is used by <code><a href='as.mo.html'>as.mo()</a></code> to determine the most probable match of taxonomic records, based on user input.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>mo_matching_score</span>(<span class='kw'>x</span>, <span class='kw'>n</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>mo_matching_score</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>n</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -276,11 +276,11 @@
|
||||
<p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., <code>"E. coli"</code> will return the microbial ID of <em>Escherichia coli</em> (\(m = 0.688\), a highly prevalent microorganism found in humans) and not <em>Entamoeba coli</em> (\(m = 0.079\), a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'><a href='as.mo.html'>mo_uncertainties</a></span>()
|
||||
<pre class="examples"><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='as.mo.html'>mo_uncertainties</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_matching_score</span>(x = <span class='st'>"E. coli"</span>,
|
||||
n = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Escherichia coli"</span>, <span class='st'>"Entamoeba coli"</span>))
|
||||
<span class='fu'>mo_matching_score</span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"E. coli"</span>,
|
||||
n <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Escherichia coli"</span>, <span class='st'>"Entamoeba coli"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -297,7 +297,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,53 +242,53 @@
|
||||
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. Please see <em>Examples</em>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>mo_name</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<pre class="usage"><span class='fu'>mo_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_fullname</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_shortname</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_subspecies</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_subspecies</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_species</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_species</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_genus</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_genus</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_family</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_family</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_order</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_order</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_class</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_class</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_phylum</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_phylum</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_kingdom</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_domain</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_domain</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_type</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_type</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_gramstain</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_snomed</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_snomed</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_ref</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_ref</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_authors</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_authors</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_year</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_year</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_rank</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_rank</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_taxonomy</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_synonyms</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_synonyms</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_info</span>(<span class='kw'>x</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_info</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_url</span>(<span class='kw'>x</span>, open = <span class='fl'>FALSE</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)
|
||||
<span class='fu'>mo_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>mo_property</span>(<span class='kw'>x</span>, property = <span class='st'>"fullname"</span>, language = <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>...</span>)</pre>
|
||||
<span class='fu'>mo_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"fullname"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -397,87 +397,87 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>
|
||||
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
|
||||
<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
|
||||
<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
|
||||
<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacterales"</span>
|
||||
<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span>
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
|
||||
<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># ""</span>
|
||||
<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria"</span>
|
||||
<span class='fu'>mo_phylum</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Proteobacteria"</span>
|
||||
<span class='fu'>mo_class</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Gammaproteobacteria"</span>
|
||||
<span class='fu'>mo_order</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Enterobacterales"</span>
|
||||
<span class='fu'>mo_family</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Enterobacteriaceae"</span>
|
||||
<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Escherichia"</span>
|
||||
<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "coli"</span>
|
||||
<span class='fu'>mo_subspecies</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># ""</span>
|
||||
|
||||
<span class='co'># colloquial properties ----------------------------------------------------</span>
|
||||
<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli" - same as mo_name()</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
|
||||
<span class='fu'>mo_name</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Escherichia coli"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Escherichia coli" - same as mo_name()</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "E. coli"</span>
|
||||
|
||||
<span class='co'># other properties ---------------------------------------------------------</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram-negative"</span>
|
||||
<span class='fu'>mo_snomed</span>(<span class='st'>"E. coli"</span>) <span class='co'># 112283007, 116395006, ... (SNOMED codes)</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
|
||||
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
|
||||
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
|
||||
<span class='fu'>mo_synonyms</span>(<span class='st'>"E. coli"</span>) <span class='co'># get previously accepted taxonomic names</span>
|
||||
<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Gram-negative"</span>
|
||||
<span class='fu'>mo_snomed</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># 112283007, 116395006, ... (SNOMED codes)</span>
|
||||
<span class='fu'>mo_type</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
|
||||
<span class='fu'>mo_rank</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "species"</span>
|
||||
<span class='fu'>mo_url</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># get the direct url to the online database entry</span>
|
||||
<span class='fu'>mo_synonyms</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># get previously accepted taxonomic names</span>
|
||||
|
||||
<span class='co'># scientific reference -----------------------------------------------------</span>
|
||||
<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al., 1919"</span>
|
||||
<span class='fu'>mo_authors</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al."</span>
|
||||
<span class='fu'>mo_year</span>(<span class='st'>"E. coli"</span>) <span class='co'># 1919</span>
|
||||
<span class='fu'>mo_ref</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Castellani et al., 1919"</span>
|
||||
<span class='fu'>mo_authors</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Castellani et al."</span>
|
||||
<span class='fu'>mo_year</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># 1919</span>
|
||||
|
||||
<span class='co'># abbreviations known in the field -----------------------------------------</span>
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"VISA"</span>) <span class='co'># "S. aureus"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"VISA"</span>) <span class='co'># "Gram-positive"</span>
|
||||
<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"MRSA"</span><span class='op'>)</span> <span class='co'># "Staphylococcus"</span>
|
||||
<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"MRSA"</span><span class='op'>)</span> <span class='co'># "aureus"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"VISA"</span><span class='op'>)</span> <span class='co'># "S. aureus"</span>
|
||||
<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"VISA"</span><span class='op'>)</span> <span class='co'># "Gram-positive"</span>
|
||||
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"EHEC"</span>) <span class='co'># "Escherichia"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"EHEC"</span>) <span class='co'># "coli"</span>
|
||||
<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"EHEC"</span><span class='op'>)</span> <span class='co'># "Escherichia"</span>
|
||||
<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"EHEC"</span><span class='op'>)</span> <span class='co'># "coli"</span>
|
||||
|
||||
<span class='co'># known subspecies ---------------------------------------------------------</span>
|
||||
<span class='fu'>mo_name</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter jejuni doylei"</span>
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"doylei"</span>) <span class='co'># "Campylobacter"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"doylei"</span>) <span class='co'># "jejuni"</span>
|
||||
<span class='fu'>mo_subspecies</span>(<span class='st'>"doylei"</span>) <span class='co'># "doylei"</span>
|
||||
<span class='fu'>mo_name</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "Campylobacter jejuni doylei"</span>
|
||||
<span class='fu'>mo_genus</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "Campylobacter"</span>
|
||||
<span class='fu'>mo_species</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "jejuni"</span>
|
||||
<span class='fu'>mo_subspecies</span><span class='op'>(</span><span class='st'>"doylei"</span><span class='op'>)</span> <span class='co'># "doylei"</span>
|
||||
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"K. pneu rh"</span>) <span class='co'># "K. pneumoniae"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"K. pneu rh"</span><span class='op'>)</span> <span class='co'># "Klebsiella pneumoniae rhinoscleromatis"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"K. pneu rh"</span><span class='op'>)</span> <span class='co'># "K. pneumoniae"</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='co'># Becker classification, see ?as.mo ----------------------------------------</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "Staphylococcus epidermidis"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. epi"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>) <span class='co'># "S. epidermidis"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. epi"</span>, Becker = <span class='fl'>TRUE</span>) <span class='co'># "CoNS"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. epi"</span><span class='op'>)</span> <span class='co'># "Staphylococcus epidermidis"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. epi"</span>, Becker <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. epi"</span><span class='op'>)</span> <span class='co'># "S. epidermidis"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. epi"</span>, Becker <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "CoNS"</span>
|
||||
|
||||
<span class='co'># Lancefield classification, see ?as.mo ------------------------------------</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "Streptococcus pyogenes"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyo"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># "Streptococcus group A"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>) <span class='co'># "S. pyogenes"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"S. pyo"</span>, Lancefield = <span class='fl'>TRUE</span>) <span class='co'># "GAS" (='Group A Streptococci')</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyo"</span><span class='op'>)</span> <span class='co'># "Streptococcus pyogenes"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyo"</span>, Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "Streptococcus group A"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. pyo"</span><span class='op'>)</span> <span class='co'># "S. pyogenes"</span>
|
||||
<span class='fu'>mo_shortname</span><span class='op'>(</span><span class='st'>"S. pyo"</span>, Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># "GAS" (='Group A Streptococci')</span>
|
||||
|
||||
|
||||
<span class='co'># language support for German, Dutch, Spanish, Portuguese, Italian and French</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"de"</span>) <span class='co'># "Gramnegativ"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"nl"</span>) <span class='co'># "Gram-negatief"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>, language = <span class='st'>"es"</span>) <span class='co'># "Gram negativo"</span>
|
||||
<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span>, language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span> <span class='co'># "Gramnegativ"</span>
|
||||
<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span>, language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span> <span class='co'># "Gram-negatief"</span>
|
||||
<span class='fu'>mo_gramstain</span><span class='op'>(</span><span class='st'>"E. coli"</span>, language <span class='op'>=</span> <span class='st'>"es"</span><span class='op'>)</span> <span class='co'># "Gram negativo"</span>
|
||||
|
||||
<span class='co'># mo_type is equal to mo_kingdom, but mo_kingdom will remain official</span>
|
||||
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on a German system</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bakterien" on a German system</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" on an English system</span>
|
||||
<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria" on a German system</span>
|
||||
<span class='fu'>mo_type</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bakterien" on a German system</span>
|
||||
<span class='fu'>mo_type</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria" on an English system</span>
|
||||
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield = <span class='fl'>TRUE</span>,
|
||||
language = <span class='st'>"de"</span>) <span class='co'># "Streptococcus Gruppe A"</span>
|
||||
<span class='fu'>mo_fullname</span>(<span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield = <span class='fl'>TRUE</span>,
|
||||
language = <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span> <span class='co'># "Streptococcus Gruppe A"</span>
|
||||
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='st'>"S. pyogenes"</span>,
|
||||
Lancefield <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span> <span class='co'># "Streptococcus groep A"</span>
|
||||
|
||||
|
||||
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'>mo_taxonomy</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># get a list with the taxonomy, the authors, Gram-stain and URL to the online database</span>
|
||||
<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='fu'>mo_info</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -495,7 +495,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -83,7 +83,7 @@ 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="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -244,9 +244,9 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='kw'>path</span>)
|
||||
<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='va'>path</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>get_mo_source</span>()</pre>
|
||||
<span class='fu'>get_mo_source</span><span class='op'>(</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -277,20 +277,20 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
4 | | |
|
||||
</pre>
|
||||
|
||||
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
|
||||
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='st'>"home/me/ourcodes.xlsx"</span><span class='op'>)</span>
|
||||
<span class='co'>#> NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
|
||||
<span class='co'>#> (columns "Organisation XYZ" and "mo")</span>
|
||||
</pre>
|
||||
|
||||
<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
|
||||
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
|
||||
<p>And now we can use it in our functions:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
|
||||
<span class='co'>#> [1] B_ESCHR_COLI</span>
|
||||
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_mo_kpneumoniae"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_mo_kpneumoniae"</span><span class='op'>)</span>
|
||||
<span class='co'>#> [1] "Klebsiella"</span>
|
||||
|
||||
<span class='co'># other input values still work too</span>
|
||||
<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</span>))
|
||||
<span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Escherichia coli"</span>, <span class='st'>"E. coli"</span>, <span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='co'>#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span>
|
||||
</pre>
|
||||
|
||||
@@ -303,16 +303,16 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
5 | | |
|
||||
</pre>
|
||||
|
||||
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
|
||||
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
|
||||
<span class='co'>#> NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'</span>
|
||||
<span class='co'>#> (columns "Organisation XYZ" and "mo")</span>
|
||||
<span class='co'>#> [1] B_ESCHR_COLI</span>
|
||||
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_Staph_aureus"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='st'>"lab_Staph_aureus"</span><span class='op'>)</span>
|
||||
<span class='co'>#> [1] "Staphylococcus"</span>
|
||||
</pre>
|
||||
|
||||
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
|
||||
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p><pre><span class='fu'>set_mo_source</span><span class='op'>(</span><span class='cn'>NULL</span><span class='op'>)</span>
|
||||
<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span>
|
||||
</pre>
|
||||
|
||||
@@ -345,7 +345,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>Return the symbol related to the p-value: 0 '<code>***</code>' 0.001 '<code>**</code>' 0.01 '<code><a href='https://rdrr.io/r/base/Arithmetic.html'>*</a></code>' 0.05 '<code>.</code>' 0.1 ' ' 1. Values above <code>p = 1</code> will return <code>NA</code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>p_symbol</span>(<span class='kw'>p</span>, emptychar = <span class='st'>" "</span>)</pre>
|
||||
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -290,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -243,48 +243,48 @@
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='co'># S3 method for mic</span>
|
||||
<span class='fu'>plot</span>(
|
||||
<span class='kw'>x</span>,
|
||||
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>))),
|
||||
ylab = <span class='st'>"Frequency"</span>,
|
||||
xlab = <span class='st'>"MIC value"</span>,
|
||||
axes = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>plot</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
|
||||
xlab <span class='op'>=</span> <span class='st'>"MIC value"</span>,
|
||||
axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for mic</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(
|
||||
<span class='kw'>height</span>,
|
||||
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>height</span>))),
|
||||
ylab = <span class='st'>"Frequency"</span>,
|
||||
xlab = <span class='st'>"MIC value"</span>,
|
||||
axes = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span>
|
||||
<span class='va'>height</span>,
|
||||
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>height</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
|
||||
xlab <span class='op'>=</span> <span class='st'>"MIC value"</span>,
|
||||
axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for rsi</span>
|
||||
<span class='fu'>plot</span>(
|
||||
<span class='kw'>x</span>,
|
||||
lwd = <span class='fl'>2</span>,
|
||||
ylim = <span class='kw'>NULL</span>,
|
||||
ylab = <span class='st'>"Percentage"</span>,
|
||||
xlab = <span class='st'>"Antimicrobial Interpretation"</span>,
|
||||
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>))),
|
||||
axes = <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>plot</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
lwd <span class='op'>=</span> <span class='fl'>2</span>,
|
||||
ylim <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
ylab <span class='op'>=</span> <span class='st'>"Percentage"</span>,
|
||||
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
|
||||
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
axes <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for rsi</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(
|
||||
<span class='kw'>height</span>,
|
||||
col = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"chartreuse4"</span>, <span class='st'>"chartreuse3"</span>, <span class='st'>"brown3"</span>),
|
||||
xlab = <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>beside</span>, <span class='st'>"Antimicrobial Interpretation"</span>, <span class='st'>""</span>),
|
||||
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>height</span>))),
|
||||
ylab = <span class='st'>"Frequency"</span>,
|
||||
beside = <span class='fl'>TRUE</span>,
|
||||
axes = <span class='kw'>beside</span>,
|
||||
<span class='kw'>...</span>
|
||||
)</pre>
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span>
|
||||
<span class='va'>height</span>,
|
||||
col <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"chartreuse4"</span>, <span class='st'>"chartreuse3"</span>, <span class='st'>"brown3"</span><span class='op'>)</span>,
|
||||
xlab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>beside</span>, <span class='st'>"Antimicrobial Interpretation"</span>, <span class='st'>""</span><span class='op'>)</span>,
|
||||
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>height</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
|
||||
beside <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
axes <span class='op'>=</span> <span class='va'>beside</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -375,7 +375,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</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">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -244,39 +244,39 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>resistance</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>resistance</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>susceptibility</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>proportion_R</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_R</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>proportion_IR</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_IR</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>proportion_I</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_I</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>proportion_SI</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_SI</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>proportion_S</span>(<span class='kw'>...</span>, minimum = <span class='fl'>30</span>, as_percent = <span class='fl'>FALSE</span>, only_all_tested = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='va'>...</span>, minimum <span class='op'>=</span> <span class='fl'>30</span>, as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>proportion_df</span>(
|
||||
<span class='kw'>data</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
minimum = <span class='fl'>30</span>,
|
||||
as_percent = <span class='fl'>FALSE</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>
|
||||
)
|
||||
<span class='fu'>proportion_df</span><span class='op'>(</span>
|
||||
<span class='va'>data</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>rsi_df</span>(
|
||||
<span class='kw'>data</span>,
|
||||
translate_ab = <span class='st'>"name"</span>,
|
||||
language = <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
minimum = <span class='fl'>30</span>,
|
||||
as_percent = <span class='fl'>FALSE</span>,
|
||||
combine_SI = <span class='fl'>TRUE</span>,
|
||||
combine_IR = <span class='fl'>FALSE</span>
|
||||
)</pre>
|
||||
<span class='fu'>rsi_df</span><span class='op'>(</span>
|
||||
<span class='va'>data</span>,
|
||||
translate_ab <span class='op'>=</span> <span class='st'>"name"</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
as_percent <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -353,12 +353,12 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
--------------------------------------------------------------------
|
||||
</pre>
|
||||
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
|
||||
<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>=</span> <span class='fl'>1</span>
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
|
||||
</pre>
|
||||
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span>() <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span>() <span class='op'>>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
|
||||
<span class='fu'>proportion_S</span>() <span class='op'>+</span> <span class='fu'>proportion_I</span>() <span class='op'>+</span> <span class='fu'>proportion_R</span>() <span class='op'>>=</span> <span class='fl'>1</span>
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='count.html'>count_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='op'>)</span>
|
||||
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>proportion_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>>=</span> <span class='fl'>1</span>
|
||||
</pre>
|
||||
|
||||
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
|
||||
@@ -394,76 +394,76 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
|
||||
<span class='op'>?</span><span class='kw'>example_isolates</span>
|
||||
<span class='op'>?</span><span class='va'>example_isolates</span>
|
||||
|
||||
<span class='fu'>resistance</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %R</span>
|
||||
<span class='fu'>susceptibility</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>) <span class='co'># determines %S+I</span>
|
||||
<span class='fu'>resistance</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># determines %R</span>
|
||||
<span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># determines %S+I</span>
|
||||
|
||||
<span class='co'># be more specific</span>
|
||||
<span class='fu'>proportion_S</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_SI</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_I</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_IR</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_R</span>(<span class='kw'>example_isolates</span><span class='op'>$</span><span class='kw'>AMX</span>)
|
||||
<span class='fu'>proportion_S</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>proportion_SI</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>proportion_I</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>proportion_IR</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
<span class='fu'>proportion_R</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(r = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>),
|
||||
n = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>r <span class='op'>=</span> <span class='fu'>resistance</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
|
||||
n <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># n_rsi works like n_distinct in dplyr, see ?n_rsi</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(R = <span class='fu'>resistance</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
SI = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
n1 = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
n2 = <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='kw'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
total = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>R <span class='op'>=</span> <span class='fu'>resistance</span><span class='op'>(</span><span class='va'>CIP</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
SI <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>CIP</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
n1 <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># the actual total; sum of all three</span>
|
||||
n2 <span class='op'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># same - analogous to n_distinct</span>
|
||||
total <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>) <span class='co'># %SI = 76.3%</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>) <span class='co'># n = 1879</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># %SI = 76.3%</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span><span class='op'>)</span> <span class='co'># n = 1879</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>) <span class='co'># %SI = 75.4%</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>) <span class='co'># n = 1855</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># %SI = 75.4%</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span> <span class='co'># n = 1855</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># %SI = 94.1%</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>) <span class='co'># n = 1939</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># %SI = 94.1%</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span> <span class='co'># n = 1939</span>
|
||||
|
||||
|
||||
<span class='co'># See Details on how `only_all_tested` works. Example:</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
|
||||
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>),
|
||||
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>numerator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span>,
|
||||
denominator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span>,
|
||||
proportion <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(numerator = <span class='fu'><a href='count.html'>count_susceptible</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
|
||||
denominator = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>),
|
||||
proportion = <span class='fu'>susceptibility</span>(<span class='kw'>AMC</span>, <span class='kw'>GEN</span>, only_all_tested = <span class='fl'>TRUE</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>numerator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_susceptible</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span>, only_all_tested <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
denominator <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span>, only_all_tested <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
proportion <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>GEN</span>, only_all_tested <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(cipro_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
cipro_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>),
|
||||
genta_p = <span class='fu'>susceptibility</span>(<span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
genta_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>GEN</span>),
|
||||
combination_p = <span class='fu'>susceptibility</span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>, as_percent = <span class='fl'>TRUE</span>),
|
||||
combination_n = <span class='fu'><a href='count.html'>count_all</a></span>(<span class='kw'>CIP</span>, <span class='kw'>GEN</span>))
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>cipro_p <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>CIP</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
cipro_n <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>,
|
||||
genta_p <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>GEN</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
genta_n <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>GEN</span><span class='op'>)</span>,
|
||||
combination_p <span class='op'>=</span> <span class='fu'>susceptibility</span><span class='op'>(</span><span class='va'>CIP</span>, <span class='va'>GEN</span>, as_percent <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>,
|
||||
combination_n <span class='op'>=</span> <span class='fu'><a href='count.html'>count_all</a></span><span class='op'>(</span><span class='va'>CIP</span>, <span class='va'>GEN</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># Get proportions S/I/R immediately of all rsi columns</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='kw'>hospital_id</span>, <span class='kw'>AMX</span>, <span class='kw'>CIP</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>hospital_id</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span>(translate = <span class='fl'>FALSE</span>)
|
||||
}
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>AMX</span>, <span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>proportion_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -480,7 +480,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,45 +242,45 @@
|
||||
<p>Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns <code>se_min</code> and <code>se_max</code>. See <em>Examples</em> for a real live example.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>resistance_predict</span>(
|
||||
<span class='kw'>x</span>,
|
||||
<span class='kw'>col_ab</span>,
|
||||
col_date = <span class='kw'>NULL</span>,
|
||||
year_min = <span class='kw'>NULL</span>,
|
||||
year_max = <span class='kw'>NULL</span>,
|
||||
year_every = <span class='fl'>1</span>,
|
||||
minimum = <span class='fl'>30</span>,
|
||||
model = <span class='kw'>NULL</span>,
|
||||
I_as_S = <span class='fl'>TRUE</span>,
|
||||
preserve_measurements = <span class='fl'>TRUE</span>,
|
||||
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<pre class="usage"><span class='fu'>resistance_predict</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
<span class='va'>col_ab</span>,
|
||||
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
year_min <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
year_max <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
year_every <span class='op'>=</span> <span class='fl'>1</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
model <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
I_as_S <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
preserve_measurements <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='fu'>rsi_predict</span>(
|
||||
<span class='kw'>x</span>,
|
||||
<span class='kw'>col_ab</span>,
|
||||
col_date = <span class='kw'>NULL</span>,
|
||||
year_min = <span class='kw'>NULL</span>,
|
||||
year_max = <span class='kw'>NULL</span>,
|
||||
year_every = <span class='fl'>1</span>,
|
||||
minimum = <span class='fl'>30</span>,
|
||||
model = <span class='kw'>NULL</span>,
|
||||
I_as_S = <span class='fl'>TRUE</span>,
|
||||
preserve_measurements = <span class='fl'>TRUE</span>,
|
||||
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
|
||||
<span class='kw'>...</span>
|
||||
)
|
||||
<span class='fu'>rsi_predict</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
<span class='va'>col_ab</span>,
|
||||
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
year_min <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
year_max <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
year_every <span class='op'>=</span> <span class='fl'>1</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>30</span>,
|
||||
model <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
I_as_S <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
preserve_measurements <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for resistance_predict</span>
|
||||
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>x</span>, main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='kw'>x_name</span>), <span class='kw'>...</span>)
|
||||
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>ggplot_rsi_predict</span>(
|
||||
<span class='kw'>x</span>,
|
||||
main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Resistance Prediction of"</span>, <span class='kw'>x_name</span>),
|
||||
ribbon = <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>...</span>
|
||||
)</pre>
|
||||
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
|
||||
<span class='va'>x</span>,
|
||||
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
|
||||
ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -395,55 +395,55 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<p>Models: <code><a href='https://rdrr.io/r/stats/lm.html'>lm()</a></code> <code><a href='https://rdrr.io/r/stats/glm.html'>glm()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='kw'>x</span> <span class='op'><-</span> <span class='fu'>resistance_predict</span>(<span class='kw'>example_isolates</span>,
|
||||
col_ab = <span class='st'>"AMX"</span>,
|
||||
year_min = <span class='fl'>2010</span>,
|
||||
model = <span class='st'>"binomial"</span>)
|
||||
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>x</span>)
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>)) {
|
||||
<span class='fu'>ggplot_rsi_predict</span>(<span class='kw'>x</span>)
|
||||
}
|
||||
<pre class="examples"><span class='va'>x</span> <span class='op'><-</span> <span class='fu'>resistance_predict</span><span class='op'>(</span><span class='va'>example_isolates</span>,
|
||||
col_ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
|
||||
year_min <span class='op'>=</span> <span class='fl'>2010</span>,
|
||||
model <span class='op'>=</span> <span class='st'>"binomial"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
|
||||
<span class='co'># using dplyr:</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
|
||||
<span class='kw'>x</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>) <span class='op'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='op'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, model = <span class='st'>"binomial"</span>)
|
||||
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>x</span>)
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>"Staphylococcus"</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span><span class='op'>(</span><span class='st'>"PEN"</span>, model <span class='op'>=</span> <span class='st'>"binomial"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># get the model from the object</span>
|
||||
<span class='kw'>mymodel</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span>(<span class='kw'>x</span>)<span class='op'>$</span><span class='kw'>model</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>mymodel</span>)
|
||||
}
|
||||
<span class='va'>mymodel</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/attributes.html'>attributes</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>$</span><span class='va'>model</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>mymodel</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
|
||||
<span class='co'># create nice plots with ggplot2 yourself</span>
|
||||
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>) <span class='op'>&</span> <span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span>)) {
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span> <span class='op'>&</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
|
||||
<span class='kw'>data</span> <span class='op'><-</span> <span class='kw'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='kw'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='op'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span>(col_ab = <span class='st'>"AMX"</span>,
|
||||
col_date = <span class='st'>"date"</span>,
|
||||
model = <span class='st'>"binomial"</span>,
|
||||
info = <span class='fl'>FALSE</span>,
|
||||
minimum = <span class='fl'>15</span>)
|
||||
<span class='va'>data</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span><span class='op'>(</span>col_ab <span class='op'>=</span> <span class='st'>"AMX"</span>,
|
||||
col_date <span class='op'>=</span> <span class='st'>"date"</span>,
|
||||
model <span class='op'>=</span> <span class='st'>"binomial"</span>,
|
||||
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
minimum <span class='op'>=</span> <span class='fl'>15</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='kw'>data</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(x = <span class='kw'>year</span>)) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(y = <span class='kw'>value</span>),
|
||||
fill = <span class='st'>"grey75"</span>) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(ymin = <span class='kw'>se_min</span>,
|
||||
ymax = <span class='kw'>se_max</span>),
|
||||
colour = <span class='st'>"grey50"</span>) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(limits = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
|
||||
breaks = <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
|
||||
labels = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(title = <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Forecast of Amoxicillin Resistance in "</span>,
|
||||
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span>(<span class='st'>"E. coli"</span>))),
|
||||
y = <span class='st'>"%R"</span>,
|
||||
x = <span class='st'>"Year"</span>) <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(base_size = <span class='fl'>13</span>)
|
||||
}
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>data</span>,
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>year</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span><span class='op'>(</span><span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>y <span class='op'>=</span> <span class='va'>value</span><span class='op'>)</span>,
|
||||
fill <span class='op'>=</span> <span class='st'>"grey75"</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span><span class='op'>(</span><span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span><span class='op'>(</span>ymin <span class='op'>=</span> <span class='va'>se_min</span>,
|
||||
ymax <span class='op'>=</span> <span class='va'>se_max</span><span class='op'>)</span>,
|
||||
colour <span class='op'>=</span> <span class='st'>"grey50"</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span><span class='op'>(</span>limits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span><span class='op'>)</span>,
|
||||
breaks <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span>,
|
||||
labels <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span><span class='op'>)</span>, <span class='st'>"%"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span><span class='op'>(</span>title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Forecast of Amoxicillin Resistance in "</span>,
|
||||
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
y <span class='op'>=</span> <span class='st'>"%R"</span>,
|
||||
x <span class='op'>=</span> <span class='st'>"Year"</span><span class='op'>)</span> <span class='op'>+</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span><span class='op'>(</span>base_size <span class='op'>=</span> <span class='fl'>13</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
@@ -460,7 +460,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,7 +242,7 @@
|
||||
<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='kw'>rsi_translation</span></pre>
|
||||
<pre class="usage"><span class='va'>rsi_translation</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
@@ -292,7 +292,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
</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">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -244,16 +244,16 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<p>When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for default</span>
|
||||
<span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for matrix</span>
|
||||
<span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
|
||||
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># S3 method for data.frame</span>
|
||||
<span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
|
||||
<span class='fu'>skewness</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -299,7 +299,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -242,14 +242,14 @@
|
||||
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code> and <code><a href='ab_property.html'>ab_name()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>get_locale</span>()</pre>
|
||||
<pre class="usage"><span class='fu'>get_locale</span><span class='op'>(</span><span class='op'>)</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property()</a></code> functions (<code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.) and <code><a href='ab_property.html'>ab_property()</a></code> functions (<code><a href='ab_property.html'>ab_name()</a></code>, <code><a href='ab_property.html'>ab_group()</a></code> etc.).</p>
|
||||
<p>Currently supported languages are: Dutch, English, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
|
||||
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3>Changing the default language</h3>
|
||||
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Changing the default language</h3>
|
||||
|
||||
|
||||
<p>The system language will be used at default (as returned by <code><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href='https://rdrr.io/r/base/locales.html'>Sys.getlocale()</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol>
|
||||
@@ -278,27 +278,27 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='co'># with get_locale()</span>
|
||||
|
||||
<span class='co'># English</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"en"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"en"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
|
||||
<span class='co'># German</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"de"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"de"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Koagulase-negative Staphylococcus (KNS)"</span>
|
||||
|
||||
<span class='co'># Dutch</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"nl"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Coagulase-negatieve Staphylococcus (CNS)"</span>
|
||||
|
||||
<span class='co'># Spanish</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"es"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"es"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Staphylococcus coagulasa negativo (SCN)"</span>
|
||||
|
||||
<span class='co'># Italian</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"it"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"it"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Staphylococcus negativo coagulasi (CoNS)"</span>
|
||||
|
||||
<span class='co'># Portuguese</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"pt"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"pt"</span><span class='op'>)</span>
|
||||
<span class='co'>#> "Staphylococcus coagulase negativo (CoNS)"</span>
|
||||
</pre>
|
||||
</div>
|
||||
@@ -316,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -255,7 +255,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -61,7 +61,7 @@ The actual result is the same every time: it returns its microorganism code ``r
|
||||
|
||||
But the calculation time differs a lot:
|
||||
|
||||
```{r, warning=FALSE}
|
||||
```{r, warning=FALSE, message=FALSE}
|
||||
S.aureus <- microbenchmark(
|
||||
as.mo("sau"), # WHONET code
|
||||
as.mo("stau"),
|
||||
@@ -117,7 +117,7 @@ So getting official taxonomic names of `r format(length(x), big.mark = ",")` (!!
|
||||
|
||||
What about precalculated results? If the input is an already precalculated result of a helper function like `mo_name()`, it almost doesn't take any time at all (see 'C' below):
|
||||
|
||||
```{r}
|
||||
```{r, warning=FALSE, message=FALSE}
|
||||
run_it <- microbenchmark(A = mo_name("STAAUR"),
|
||||
B = mo_name("S. aureus"),
|
||||
C = mo_name("Staphylococcus aureus"),
|
||||
|
||||
Reference in New Issue
Block a user