prerelease 1.8.1

Merge branch 'development' of https://github.com/msberends/AMR into development # Conflicts: # docs/articles/AMR.html # docs/articles/AMR_files/figure-html/disk_plots-1.png # docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots-1.png # docs/articles/AMR_files/figure-html/mic_plots-2.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png # docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png # docs/articles/AMR_files/figure-html/plot 1-1.png # docs/articles/AMR_files/figure-html/plot 3-1.png # docs/articles/AMR_files/figure-html/plot 4-1.png # docs/articles/AMR_files/figure-html/plot 5-1.png # docs/articles/EUCAST.html # docs/articles/MDR.html # docs/articles/PCA.html # docs/articles/PCA_files/figure-html/unnamed-chunk-6-1.png # docs/articles/PCA_files/figure-html/unnamed-chunk-7-1.png # docs/articles/SPSS.html # docs/articles/WHONET.html # docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png # docs/articles/benchmarks.html # docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png # docs/articles/datasets.html # docs/articles/resistance_predict.html # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png # docs/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png # docs/articles/welcome_to_AMR.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/AMR-deprecated.html # docs/reference/AMR.html # docs/reference/WHOCC.html # docs/reference/WHONET.html # docs/reference/antibiotics.html # docs/reference/catalogue_of_life.html # docs/reference/catalogue_of_life_version.html # docs/reference/dosage.html # docs/reference/example_isolates.html # docs/reference/example_isolates_unclean.html # docs/reference/g.test.html # docs/reference/intrinsic_resistant.html # docs/reference/microorganisms.codes.html # docs/reference/microorganisms.html # docs/reference/microorganisms.old.html # docs/reference/rsi_translation.html
2025-07-17 23:13:14 +02:00 · 2022-03-14 16:37:37 +01:00
parent 1b0983e382 8c9feea087
commit 45e9546538
73 changed files with 1231 additions and 1020 deletions
--- a/docs/articles/benchmarks.html
+++ b/docs/articles/benchmarks.html
@ -44,7 +44,11 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
+<<<<<<< HEAD
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
+=======
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
      </span>
    </div>

@ -185,7 +189,7 @@

      

-      </header><div class="row">
+      </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Benchmarks</h1>
@ -238,8 +242,9 @@ microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
  <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
  times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
+<<<<<<< HEAD
 <span class="co">#                                   expr   min  lq  mean median    uq max neval</span>
 <span class="co">#                           as.mo("sau")  12.0  13  18.0   14.0  15.0  48    25</span>
 <span class="co">#                          as.mo("stau")  54.0  59  80.0   91.0  96.0  99    25</span>
@ -263,6 +268,24 @@ determine.</p>
 <p>To improve performance, we implemented two important algorithms to
 save unnecessary calculations: <strong>repetitive results</strong> and
 <strong>already precalculated results</strong>.</p>
+=======
+<span class="co">#                                   expr   min    lq  mean median  uq max neval</span>
+<span class="co">#                           as.mo("sau")  20.0  20.0  25.0   20.0  21  57    25</span>
+<span class="co">#                          as.mo("stau")  94.0  94.0 110.0   95.0 130 130    25</span>
+<span class="co">#                          as.mo("STAU")  94.0  95.0 110.0  130.0 130 130    25</span>
+<span class="co">#                        as.mo("staaur")  20.0  20.0  28.0   20.0  21  58    25</span>
+<span class="co">#                        as.mo("STAAUR")  20.0  20.0  25.0   20.0  21  57    25</span>
+<span class="co">#                     as.mo("S. aureus")  56.0  56.0  72.0   57.0  92  97    25</span>
+<span class="co">#                      as.mo("S aureus")  55.0  56.0  66.0   56.0  75  93    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   5.7   5.8   7.3    5.9   6  41    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 370.0 370.0 390.0  380.0 410 410    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 260.0 290.0 300.0  290.0 300 330    25</span>
+<span class="co">#                          as.mo("MRSA")  20.0  20.0  23.0   20.0  20  56    25</span>
+<span class="co">#                          as.mo("VISA")  34.0  35.0  48.0   35.0  35 220    25</span></code></pre></div>
+<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
+<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 65 times slower to determine.</p>
+<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
 <div class="section level3">
 <h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
 </h3>
@ -287,8 +310,13 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
+<<<<<<< HEAD
 <span class="co"># [1] B_ESCHR_COLI B_STRPT_MITS B_STRPT_ANGN B_STPHY_CONS B_ESCHR_COLI</span>
 <span class="co"># [6] B_ESCHR_COLI</span>
+=======
+<span class="co"># [1] B_PROTS_MRBL B_STPHY_CONS B_ESCHR_COLI B_PSDMN_AERG B_ENTRC_FCLS</span>
+<span class="co"># [6] B_STPHY_AURS</span>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
  
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
 <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -301,14 +329,19 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
 <span class="co"># now let's see:</span>
 <span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#        expr min  lq mean median  uq max neval</span>
+<<<<<<< HEAD
 <span class="co">#  mo_name(x) 207 225  288    233 370 414    10</span></code></pre></div>
 <p>So getting official taxonomic names of 2,000,000 (!!) items
 consisting of 90 unique values only takes 0.233 seconds. That is 117
 nanoseconds on average. You only lose time on your unique input
 values.</p>
+=======
+<span class="co">#  mo_name(x) 265 269  357    298 471 516    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.298 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
 </div>
 <div class="section level3">
 <h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
@ -323,8 +356,9 @@ will return the results immediately (see ‘C’ below):</p>
                         B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
                         C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
+<<<<<<< HEAD
 <span class="co">#  expr  min    lq  mean median    uq   max neval</span>
 <span class="co">#     A 10.3 10.90 11.20  11.10 11.20 12.40    10</span>
 <span class="co">#     B 31.3 32.70 38.20  33.90 35.20 79.80    10</span>
@ -333,6 +367,13 @@ will return the results immediately (see ‘C’ below):</p>
 <code>"Staphylococcus aureus"</code> takes 0.0028 seconds - it doesn’t
 even start calculating <em>if the result would be the same as the
 expected resulting value</em>. That goes for all helper functions:</p>
+=======
+<span class="co">#  expr   min    lq  mean median    uq  max neval</span>
+<span class="co">#     A 12.30 12.30 12.60  12.50 12.60 14.2    10</span>
+<span class="co">#     B 61.70 61.90 62.70  62.40 62.50 66.2    10</span>
+<span class="co">#     C  3.04  3.05  6.92   3.12  3.21 40.9    10</span></code></pre></div>
+<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0031 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                         B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -343,9 +384,10 @@ expected resulting value</em>. That goes for all helper functions:</p>
                         G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
                         H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr  min   lq mean median   uq  max neval</span>
+<<<<<<< HEAD
 <span class="co">#     A 2.30 2.55 2.68   2.66 2.85 2.94    10</span>
 <span class="co">#     B 2.27 2.38 2.59   2.56 2.83 2.88    10</span>
 <span class="co">#     C 2.22 2.25 2.51   2.47 2.74 2.87    10</span>
@ -360,6 +402,17 @@ function has zero knowledge about the actual microorganism, namely
 <code>"Firmicutes"</code> anyway, there is no point in calculating the
 result. And because this package contains all phyla of all known
 bacteria, it can just return the initial value immediately.</p>
+=======
+<span class="co">#     A 3.02 3.09 3.22   3.10 3.46 3.55    10</span>
+<span class="co">#     B 3.03 3.04 3.21   3.12 3.42 3.48    10</span>
+<span class="co">#     C 3.03 3.05 3.08   3.06 3.12 3.16    10</span>
+<span class="co">#     D 2.98 3.01 3.17   3.09 3.40 3.47    10</span>
+<span class="co">#     E 3.01 3.06 3.19   3.12 3.43 3.43    10</span>
+<span class="co">#     F 2.95 2.99 3.11   3.05 3.16 3.46    10</span>
+<span class="co">#     G 2.94 3.06 3.19   3.13 3.41 3.54    10</span>
+<span class="co">#     H 2.93 3.01 3.12   3.08 3.19 3.42    10</span></code></pre></div>
+<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
 </div>
 <div class="section level3">
 <h3 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
@ -394,8 +447,9 @@ with the other languages):</p>
                         ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
                         sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
                         times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
+<<<<<<< HEAD
 <span class="co">#  expr    min    lq  mean median    uq    max neval</span>
 <span class="co">#    da 2.1730 2.476 3.956  2.609 2.873 45.180   100</span>
 <span class="co">#    de 2.2170 2.497 3.161  2.646 2.855 48.260   100</span>
@ -409,6 +463,20 @@ with the other languages):</p>
 <span class="co">#    sv 2.2030 2.443 3.077  2.545 2.703 43.350   100</span></code></pre></div>
 <p>Currently supported languages are Danish, Dutch, English, French,
 German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
+=======
+<span class="co">#  expr   min    lq  mean median    uq    max neval</span>
+<span class="co">#    da 3.579 3.689 3.811  3.737 3.894  4.626   100</span>
+<span class="co">#    de 3.600 3.694 4.205  3.750 3.869 43.820   100</span>
+<span class="co">#    en 1.686 1.720 1.828  1.766 1.822  2.244   100</span>
+<span class="co">#    es 3.618 3.688 4.633  3.772 4.083 43.890   100</span>
+<span class="co">#    fr 3.493 3.602 4.104  3.658 3.785 41.860   100</span>
+<span class="co">#    it 3.543 3.628 4.152  3.702 3.810 44.040   100</span>
+<span class="co">#    nl 3.625 3.716 5.024  3.763 3.924 44.220   100</span>
+<span class="co">#    pt 3.510 3.610 3.742  3.684 3.861  4.096   100</span>
+<span class="co">#    ru 3.568 3.680 4.534  3.742 3.871 41.170   100</span>
+<span class="co">#    sv 3.585 3.664 3.833  3.748 4.046  4.987   100</span></code></pre></div>
+<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
 </div>
  </div>

@ -428,8 +496,12 @@ Erwin E. A. Hassing.</p>

 <div class="pkgdown">
  <p></p>
+<<<<<<< HEAD
 <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
 2.0.2.</p>
+=======
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
 </div>

      </footer>