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(v1.4.0.9008) like variations

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dr. M.S. (Matthijs) Berends
2020-10-26 12:23:03 +01:00
parent f720c9ba0b
commit 760d69a3e0
64 changed files with 919 additions and 582 deletions
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2
docs/reference/AMR-deprecated.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

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docs/reference/age.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/antibiotic_class_selectors.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -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">1.4.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/as.rsi.html
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@ -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">1.4.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

68
docs/reference/filter_ab_class.html
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@ -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">1.4.0.9008</span>
</span>
</div>
@ -242,33 +242,33 @@
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.</p>
</div>
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='kw'>x</span>, <span class='kw'>ab_class</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<pre class="usage"><span class='fu'>filter_ab_class</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>ab_class</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_carbapenems</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_carbapenems</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_1st_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_1st_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_2nd_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_2nd_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_3rd_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_3rd_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_4th_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_4th_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_5th_cephalosporins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_5th_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_glycopeptides</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_glycopeptides</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_macrolides</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_macrolides</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_penicillins</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)
<span class='fu'>filter_penicillins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_tetracyclines</span>(<span class='kw'>x</span>, result = <span class='kw'>NULL</span>, scope = <span class='st'>"any"</span>, <span class='kw'>...</span>)</pre>
<span class='fu'>filter_tetracyclines</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</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">
@ -310,43 +310,43 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='antibiotic_class_selectors.html'>antibiotic_class_selectors()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code> equivalent.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>filter_aminoglycosides</span>(<span class='kw'>example_isolates</span>)
<pre class="examples"><span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='va'>example_isolates</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 isolates that have any result for any aminoglycoside</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_ab_class</span><span class='op'>(</span><span class='st'>"aminoglycoside"</span><span class='op'>)</span>
<span class='co'># this is essentially the same as (but without determination of column names):</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span>(.vars = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"GEN"</span>, <span class='st'>"TOB"</span>, <span class='st'>"AMK"</span>, <span class='st'>"KAN"</span>)),
.vars_predicate = <span class='fu'><a href='https://dplyr.tidyverse.org/reference/all_vars.html'>any_vars</a></span>(<span class='kw'>.</span> <span class='op'>%in%</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='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span><span class='op'>(</span>.vars <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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"GEN"</span>, <span class='st'>"TOB"</span>, <span class='st'>"AMK"</span>, <span class='st'>"KAN"</span><span class='op'>)</span><span class='op'>)</span>,
.vars_predicate <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/all_vars.html'>any_vars</a></span><span class='op'>(</span><span class='va'>.</span> <span class='op'>%in%</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><span class='op'>)</span><span class='op'>)</span>
<span class='co'># filter on isolates that show resistance to ANY aminoglycoside</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"any"</span><span class='op'>)</span>
<span class='co'># filter on isolates that show resistance to ALL aminoglycosides</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
<span class='co'># filter on isolates that show resistance to</span>
<span class='co'># any aminoglycoside and any fluoroquinolone</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>) <span class='op'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>)
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='st'>"R"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span><span class='st'>"R"</span><span class='op'>)</span>
<span class='co'># filter on isolates that show resistance to</span>
<span class='co'># all aminoglycosides and all fluoroquinolones</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='op'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_aminoglycosides</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_carbapenems</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span>(), <span class='op'>~</span><span class='kw'>.</span> <span class='op'>==</span> <span class='st'>"R"</span>))
}
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'>filter_carbapenems</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</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://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</div>
@ -364,7 +364,7 @@ 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>

2
docs/reference/ggplot_pca.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@ -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">1.4.0.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

6
docs/reference/index.html
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@ -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">1.4.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>
@ -581,9 +581,9 @@
</tr><tr>
<td>
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%not_like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> <code><a href="like.html">`%not_like_case%`</a></code> </p>
</td>
<td><p>Pattern Matching</p></td>
<td><p>Pattern matching with keyboard shortcut</p></td>
</tr><tr>
<td>

2
docs/reference/key_antibiotics.html
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@ -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">1.4.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>

4
docs/reference/lifecycle.html
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@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.4.0.9008</span>
</span>
</div>
@ -295,7 +295,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
</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>
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17
docs/reference/like.html
View File

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Pattern Matching — like • AMR (for R)</title>
<title>Pattern matching with keyboard shortcut — like • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Pattern Matching — like" />
<meta property="og:title" content="Pattern matching with keyboard shortcut — like" />
<meta property="og:description" content="Convenient wrapper around grep() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -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">1.4.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>
@ -233,7 +233,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Pattern Matching</h1>
<h1>Pattern matching with keyboard shortcut</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
<div class="hidden name"><code>like.Rd</code></div>
</div>
@ -246,7 +246,11 @@
<span class='va'>x</span> <span class='op'>%like%</span> <span class='va'>pattern</span>
<span class='va'>x</span> <span class='op'>%like_case%</span> <span class='va'>pattern</span></pre>
<span class='va'>x</span> <span class='op'>%not_like%</span> <span class='va'>pattern</span>
<span class='va'>x</span> <span class='op'>%like_case%</span> <span class='va'>pattern</span>
<span class='va'>x</span> <span class='op'>%not_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">
@ -280,7 +284,8 @@
<li><p>Tries again with <code>perl = TRUE</code> if regex fails</p></li>
</ul>
<p>Using RStudio? This function can also be inserted from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>).</p>
<p>Using RStudio? This function can also be inserted in your code from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> &gt; <code>Modify Keyboard Shortcuts...</code>). This addin iterates over all 'like' variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code>%like%</code> and by pressing it again it will be replaced with <code>%not_like%</code>, then <code>%like_case%</code>, then <code>%not_like_case%</code> and then back to <code>%like%</code>.</p>
<p>The <code>"%not_like%"</code> and <code>"%not_like_case%"</code> functions are wrappers around <code>"%like%"</code> and <code>"%like_case%"</code>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

8
docs/reference/mo_property.html
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@ -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">1.4.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>
@ -270,9 +270,9 @@
<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'>is_gram_negative</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is_gram_negative</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'>is_gram_positive</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is_gram_positive</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='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>
@ -303,7 +303,7 @@
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale = "de")</a></code>, see <a href='translate.html'>translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale = "de")</a></code>, see <a href='translate.html'>translate</a>. Also used to translate text like "no growth". Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
</tr>
<tr>
<th>...</th>

46
docs/reference/pca.html
View File

@ -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">1.4.0.9008</span>
</span>
</div>
@ -242,15 +242,15 @@
<p>Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.</p>
</div>
<pre class="usage"><span class='fu'>pca</span>(
<span class='kw'>x</span>,
<span class='kw'>...</span>,
retx = <span class='fl'>TRUE</span>,
center = <span class='fl'>TRUE</span>,
scale. = <span class='fl'>TRUE</span>,
tol = <span class='kw'>NULL</span>,
rank. = <span class='kw'>NULL</span>
)</pre>
<pre class="usage"><span class='fu'>pca</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>...</span>,
retx <span class='op'>=</span> <span class='cn'>TRUE</span>,
center <span class='op'>=</span> <span class='cn'>TRUE</span>,
scale. <span class='op'>=</span> <span class='cn'>TRUE</span>,
tol <span class='op'>=</span> <span class='cn'>NULL</span>,
rank. <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">
@ -324,22 +324,22 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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'># calculate the resistance per group first </span>
<span class='kw'>resistance_data</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(order = <span class='fu'><a href='mo_property.html'>mo_order</a></span>(<span class='kw'>mo</span>), <span class='co'># group on anything, like order</span>
genus = <span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>)) <span class='op'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span>(<span class='kw'>is.rsi</span>, <span class='kw'>resistance</span>) <span class='co'># then get resistance of all drugs</span>
<span class='va'>resistance_data</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>order <span class='op'>=</span> <span class='fu'><a href='mo_property.html'>mo_order</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span>, <span class='co'># group on anything, like order</span>
genus <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='op'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span><span class='op'>(</span><span class='va'>is.rsi</span>, <span class='va'>resistance</span><span class='op'>)</span> <span class='co'># then get resistance of all drugs</span>
<span class='co'># now conduct PCA for certain antimicrobial agents</span>
<span class='kw'>pca_result</span> <span class='op'>&lt;-</span> <span class='kw'>resistance_data</span> <span class='op'>%&gt;%</span>
<span class='fu'>pca</span>(<span class='kw'>AMC</span>, <span class='kw'>CXM</span>, <span class='kw'>CTX</span>, <span class='kw'>CAZ</span>, <span class='kw'>GEN</span>, <span class='kw'>TOB</span>, <span class='kw'>TMP</span>, <span class='kw'>SXT</span>)
<span class='va'>pca_result</span> <span class='op'>&lt;-</span> <span class='va'>resistance_data</span> <span class='op'>%&gt;%</span>
<span class='fu'>pca</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>CXM</span>, <span class='va'>CTX</span>, <span class='va'>CAZ</span>, <span class='va'>GEN</span>, <span class='va'>TOB</span>, <span class='va'>TMP</span>, <span class='va'>SXT</span><span class='op'>)</span>
<span class='kw'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>pca_result</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='kw'>pca_result</span>)
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='kw'>pca_result</span>) <span class='co'># a new and convenient plot function</span>
}
<span class='va'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span>
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span> <span class='co'># a new and convenient plot function</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</div>
@ -357,7 +357,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
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<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>
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