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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="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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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@ -283,7 +283,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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@ -421,12 +421,14 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span></span>
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<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
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<span class="r-in"><span> language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
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<span class="r-in"><span> language <span class="op">=</span> <span class="st">"de"</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-out co"><span class="r-pr">#></span> [1] "Streptococcus Gruppe A"</span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span></span>
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<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
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<span class="r-in"><span> language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
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<span class="r-in"><span> language <span class="op">=</span> <span class="st">"nl"</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-out co"><span class="r-pr">#></span> [1] "Streptococcus groep A"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span></span></span>
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@ -439,32 +441,32 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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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">mo_is_gram_positive</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></span>
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<span class="r-in"><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">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</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_is_gram_positive()`</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 709 × 49</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </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;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-19 D FALSE TRUE FALSE 71 M 738003 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-19 D FALSE TRUE FALSE 71 M 738003 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-21 D FALSE TRUE FALSE 75 F 462081 B_CTRBC_FRND</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-22 B TRUE FALSE FALSE 50 M F35553 B_PROTS_MRBL</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-22 B TRUE FALSE FALSE 50 M F35553 B_PROTS_MRBL</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 699 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 709 × 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;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-21 462081 75 F Clinical B_CTRBC_FRND R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 699 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
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<span class="r-in"><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="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
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