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<![endif]--></head><body>
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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="">2.1.1</small>
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||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9001</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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@ -216,28 +216,33 @@
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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>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-in"><span><span class="va">sir</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sir' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S R R S I I R S S R</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sir' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 1.1618950 1.1618950 -0.7745967 -0.7745967 -0.7745967</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 -0.7745967 -0.7745967 1.1618950</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-in"><span><span class="va">mic</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'mic' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.002 >=64 0.125 >=64 2 16 0.005 <=0.001 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 </span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'mic' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.2773949 1.1399840 -0.3137594 1.1399840 0.3323488 0.8169299</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.0638678 -1.4389220 0.8169299 -0.1522324</span>
|
||||
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
|
||||
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'mic' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -1.2773949 1.1399840 -0.3137594 1.1399840 0.3323488 0.8169299</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -1.0638678 -1.4389220 0.8169299 -0.1522324</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-in"><span><span class="va">disk</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'disk' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 34 26 14 50 7 45 18 40 19 24</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'disk' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.4467074 -0.1205401 -0.9714114 1.5812024 -1.4677529 1.2266727</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.6877876 0.8721430 -0.6168817 -0.2623520</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
|
||||
@ -246,15 +251,27 @@
|
||||
<span class="r-in"><span> gent <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"gent"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-in"><span><span class="va">y</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A R 30 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 24 <=0.5 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 C S 19 2 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 D I 21 <=0.5 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 >=16 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 F I 28 8 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 G I 19 4 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 H I 29 <=0.5 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I I 26 >=16 <=0.5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 J R 21 8 1</span>
|
||||
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.23945841 0.03375462 -0.73801392 -0.62254823 0.04563698 0.52522389</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] -0.61650763 -0.37448920 0.05108107 0.45640401</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
|
||||
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in order(y$amr_distance):</span> argument 1 is not a vector</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@ -264,7 +281,19 @@
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and "tobr"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C S 19 2 <=0.5 -0.73801392 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D I 21 <=0.5 1 -0.62254823 0.1154657</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 G I 19 4 <=0.5 -0.61650763 0.1215063</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H I 29 <=0.5 <=0.5 -0.37448920 0.3635247</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B I 24 <=0.5 4 0.03375462 0.7717685</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E I 22 >=16 1 0.04563698 0.7836509</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 I I 26 >=16 <=0.5 0.05108107 0.7890950</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 J R 21 8 1 0.45640401 1.1944179</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 F I 28 8 2 0.52522389 1.2632378</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 A R 30 8 2 1.23945841 1.9774723</span>
|
||||
<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>
|
||||
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
|
||||
<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>
|
||||
@ -274,10 +303,25 @@
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in filter(., mo_genus() == "Enterococcus" & mo_species() != ""):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mo_genus() == "Enterococcus" & mo_species() != ""`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in mo_genus(): argument x is missing and no column with info about</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> microorganisms could be found.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_species()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo TCY IPM MEM dist</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA 0 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA 0 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 53 more rows</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user