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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9002</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -198,10 +198,13 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="st">"This is a test"</span></span></span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># data.table has a more limited version of %like%, so:</span></span></span>
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<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/detach.html" class="external-link">detach</a></span><span class="op">(</span><span class="st">"package:data.table"</span>, unload <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="st">"This is a test"</span></span></span>
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<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="st">"TEST"</span></span></span>
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<span class="r-in"><span><span class="va">a</span> <span class="op">%like%</span> <span class="va">b</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
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<span class="r-in"><span><span class="va">b</span> <span class="op">%like%</span> <span class="va">a</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] FALSE</span>
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<span class="r-in"><span></span></span>
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@ -209,14 +212,12 @@
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<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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></span>
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<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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></span>
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<span class="r-in"><span><span class="va">a</span> <span class="op">%like%</span> <span class="va">b</span></span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>argument 'pattern' has length > 1 and only the first element will be used</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE</span>
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<span class="r-in"><span><span class="va">a</span> <span class="op">%unlike%</span> <span class="va">b</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] FALSE FALSE FALSE</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">a</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">%like%</span> <span class="va">b</span></span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>argument 'pattern' has length > 1 and only the first element will be used</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE</span>
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<span class="r-in"><span><span class="va">a</span> <span class="op">%like%</span> <span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE</span>
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<span class="r-in"><span></span></span>
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@ -224,28 +225,52 @@
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<span class="r-in"><span><span class="co"># get isolates whose name start with 'Entero' (case-insensitive)</span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^entero"</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_name()</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 0 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 46 variables: date <date>, patient <chr>, age <dbl>, gender <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ward <chr>, mo <mo>, PEN <sir>, OXA <sir>, FLC <sir>, AMX <sir>, AMC <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, …</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinic… B_ENTRC_FACM NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU B_ENTRC NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_name()</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 0 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 46 variables: date <date>, patient <chr>, age <dbl>, gender <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ward <chr>, mo <mo>, PEN <sir>, OXA <sir>, FLC <sir>, AMX <sir>, AMC <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, …</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinic… B_ENTRC_FACM NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU B_ENTRC NA NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></span></span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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