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(v0.7.1.9069) documentation update

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dr. M.S. (Matthijs) Berends 2019-09-01 13:16:57 +02:00
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4
DESCRIPTION
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Package: AMR Package: AMR
Version: 0.7.1.9068 Version: 0.7.1.9069
Date: 2019-08-30 Date: 2019-09-01
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

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NEWS.md
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# AMR 0.7.1.9068 # AMR 0.7.1.9069
<small>Last updated: 01-Sep-2019</small>
### Breaking ### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`: * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@ -26,7 +27,7 @@
### New ### New
* Function `bug_drug_combinations()` to quickly get a `data.frame` with the antimicrobial resistance of any bug-drug combination in a data set: * Function `bug_drug_combinations()` to quickly get a `data.frame` with the antimicrobial resistance of any bug-drug combination in a data set:
```r ```r
x <- bug_drug_combinations(septic_patients) x <- bug_drug_combinations(example_isolates)
x x
#> ab mo S I R total #> ab mo S I R total
#> 1 AMC B_ESCHR_COL 332 74 61 467 #> 1 AMC B_ESCHR_COL 332 74 61 467
@ -65,7 +66,7 @@
```r ```r
# (run this on your own console, as this page does not support colour printing) # (run this on your own console, as this page does not support colour printing)
library(dplyr) library(dplyr)
septic_patients %>% example_isolates %>%
select(mo:AMC) %>% select(mo:AMC) %>%
as_tibble() as_tibble()
``` ```

3
R/mo.R
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@ -692,7 +692,8 @@ exec_as.mo <- function(x,
# - STEC (Shiga-toxin producing E. coli) # - STEC (Shiga-toxin producing E. coli)
# - UPEC (Uropathogenic E. coli) # - UPEC (Uropathogenic E. coli)
if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC") if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC")
| x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") { # also support O-antigens of E. coli: O26, O103, O104, O111, O121, O145, O157
| x_backup_without_spp[i] %like% "O?(26|103|104|111|121|145|157)") {
x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L] x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
if (initial_search == TRUE) { if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history) set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)

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docs/LICENSE-text.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">0.7.1.9068</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>

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docs/articles/benchmarks.html
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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9067</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>
@ -185,7 +185,7 @@
<h1>Benchmarks</h1> <h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">28 August 2019</h4> <h4 class="date">01 September 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div> <div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -194,30 +194,62 @@
<p><small>Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" class="uri">https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd</a></small></p>
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p> <p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p> <p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(microbenchmark)</a> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(microbenchmark)</a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a></code></pre></div> <a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a></code></pre></div>
<p>In the next test, we try to ‘coerce’ different input values for <em>Staphylococcus aureus</em>. The actual result is the same every time: it returns its MO code <code>B_STPHY_AUR</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p> <p>In the next test, we try to ‘coerce’ different input values for <em>Staphylococcus aureus</em>. The actual result is the same every time: it returns its MO code <code>B_STPHY_AUR</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
<p>But the calculation time differs a lot:</p> <p>But the calculation time differs a lot:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>),</a> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a> <a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span></a>
<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a> <a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a> <a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),</a>
<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a> <a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a>
<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a> <a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a> <a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),</a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a> <a class="sourceLine" id="cb2-9" data-line-number="9"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb2-10" data-line-number="10"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># expr min lq mean median uq max neval</span></a> <a class="sourceLine" id="cb2-11" data-line-number="11"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># as.mo("sau") 8.4 8.5 16.0 9.7 25.0 27 10</span></a> <a class="sourceLine" id="cb2-12" data-line-number="12"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># as.mo("stau") 31.0 31.0 33.0 31.0 33.0 49 10</span></a> <a class="sourceLine" id="cb2-13" data-line-number="13"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># as.mo("staaur") 8.1 8.3 13.0 8.5 23.0 24 10</span></a> <a class="sourceLine" id="cb2-14" data-line-number="14"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># as.mo("STAAUR") 8.2 8.5 9.1 8.9 9.4 11 10</span></a> <a class="sourceLine" id="cb2-15" data-line-number="15"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="dv">22242419</span>), <span class="co"># Catalogue of Life ID</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co"># as.mo("S. aureus") 22.0 22.0 23.0 23.0 23.0 24 10</span></a> <a class="sourceLine" id="cb2-16" data-line-number="16"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co"># as.mo("S. aureus") 22.0 23.0 34.0 23.0 24.0 110 10</span></a> <a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># as.mo("Staphylococcus aureus") 3.8 3.9 5.0 4.0 4.3 12 10</span></a></code></pre></div> <a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.6 8.9 12.0 9.6 10.0</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 33.0 33.0 39.0 34.0 50.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 33.0 33.0 40.0 35.0 49.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 9.0 9.2 11.0 9.6 9.8</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.8 9.2 11.0 9.6 9.9</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 23.0 25.0 29.0 26.0 27.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 24.0 24.0 26.0 25.0 25.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.0 4.2 4.4 4.2 4.6</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 1500.0 1500.0 1600.0 1600.0 1700.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 530.0 540.0 550.0 550.0 560.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.2 8.7 12.0 9.1 9.5</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 19.0 20.0 35.0 21.0 37.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 19.0 19.0 23.0 20.0 21.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 18.0 19.0 20.0 19.0 20.0</span></a>
<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co"># max neval</span></a>
<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co"># 25.0 10</span></a>
<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co"># 52.0 10</span></a>
<a class="sourceLine" id="cb2-37" data-line-number="37"><span class="co"># 53.0 10</span></a>
<a class="sourceLine" id="cb2-38" data-line-number="38"><span class="co"># 29.0 10</span></a>
<a class="sourceLine" id="cb2-39" data-line-number="39"><span class="co"># 28.0 10</span></a>
<a class="sourceLine" id="cb2-40" data-line-number="40"><span class="co"># 50.0 10</span></a>
<a class="sourceLine" id="cb2-41" data-line-number="41"><span class="co"># 40.0 10</span></a>
<a class="sourceLine" id="cb2-42" data-line-number="42"><span class="co"># 5.2 10</span></a>
<a class="sourceLine" id="cb2-43" data-line-number="43"><span class="co"># 1700.0 10</span></a>
<a class="sourceLine" id="cb2-44" data-line-number="44"><span class="co"># 580.0 10</span></a>
<a class="sourceLine" id="cb2-45" data-line-number="45"><span class="co"># 36.0 10</span></a>
<a class="sourceLine" id="cb2-46" data-line-number="46"><span class="co"># 110.0 10</span></a>
<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="co"># 35.0 10</span></a>
<a class="sourceLine" id="cb2-48" data-line-number="48"><span class="co"># 34.0 10</span></a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="1125"></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 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</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 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p> <p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -229,128 +261,116 @@
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a> <a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max neval</span></a> <a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("theisl") 260 280 280 280 290 290 10</span></a> <a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("theisl") 300 300 310 320 320 330 10</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("THEISL") 250 260 280 280 290 300 10</span></a> <a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("THEISL") 290 300 300 300 320 320 10</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("T. islandicus") 120 130 130 130 150 150 10</span></a> <a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("T. islandicus") 130 140 150 140 150 160 10</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("T. islandicus") 120 130 140 140 140 150 10</span></a> <a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("T. islandicus") 140 160 160 160 170 170 10</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Thermus islandicus") 47 47 53 48 62 67 10</span></a></code></pre></div> <a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Thermus islandicus") 49 52 57 55 56 72 10</span></a></code></pre></div>
<p>That takes 9.3 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p> <p>That takes 1.1 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p> <p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a> <p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="1125"><img src="benchmarks_files/figure-html/unnamed-chunk-6-2.png" width="1125"><img src="benchmarks_files/figure-html/unnamed-chunk-6-3.png" width="1125"></p>
<a class="sourceLine" id="cb4-2" data-line-number="2"></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb4-4" data-line-number="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Prevotella brevis"</span>),</a>
<a class="sourceLine" id="cb4-5" data-line-number="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Escherichia coli"</span>),</a>
<a class="sourceLine" id="cb4-6" data-line-number="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb4-7" data-line-number="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<a class="sourceLine" id="cb4-8" data-line-number="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
<a class="sourceLine" id="cb4-9" data-line-number="9"> <span class="dt">times =</span> <span class="dv">10</span>),</a>
<a class="sourceLine" id="cb4-10" data-line-number="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
<a class="sourceLine" id="cb4-11" data-line-number="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
<a class="sourceLine" id="cb4-12" data-line-number="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p> <p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3"> <div id="repetitive-results" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3> <a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p> <p>Repetitive results are unique values that are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a> <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># take all MO codes from the example_isolates data set</span></a> <a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># take all MO codes from the example_isolates data set</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3">x &lt;-<span class="st"> </span>example_isolates<span class="op">$</span>mo <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb4-3" data-line-number="3">x &lt;-<span class="st"> </span>example_isolates<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a> <a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb4-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a> <a class="sourceLine" id="cb4-6" data-line-number="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb4-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a> <a class="sourceLine" id="cb4-8" data-line-number="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb4-9" data-line-number="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="st"> </span><span class="co"># scramble it</span></a> <a class="sourceLine" id="cb4-10" data-line-number="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a> <a class="sourceLine" id="cb4-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb5-12" data-line-number="12"> </a> <a class="sourceLine" id="cb4-12" data-line-number="12"> </a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a> <a class="sourceLine" id="cb4-13" data-line-number="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a> <a class="sourceLine" id="cb4-14" data-line-number="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># [1] 500000</span></a> <a class="sourceLine" id="cb4-15" data-line-number="15"><span class="co"># [1] 500000</span></a>
<a class="sourceLine" id="cb5-16" data-line-number="16"></a> <a class="sourceLine" id="cb4-16" data-line-number="16"></a>
<a class="sourceLine" id="cb5-17" data-line-number="17"><span class="co"># and how many unique values do we have?</span></a> <a class="sourceLine" id="cb4-17" data-line-number="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb5-18" data-line-number="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a> <a class="sourceLine" id="cb4-18" data-line-number="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb5-19" data-line-number="19"><span class="co"># [1] 50</span></a> <a class="sourceLine" id="cb4-19" data-line-number="19"><span class="co"># [1] 50</span></a>
<a class="sourceLine" id="cb5-20" data-line-number="20"></a> <a class="sourceLine" id="cb4-20" data-line-number="20"></a>
<a class="sourceLine" id="cb5-21" data-line-number="21"><span class="co"># now let's see:</span></a> <a class="sourceLine" id="cb4-21" data-line-number="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb5-22" data-line-number="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(x),</a> <a class="sourceLine" id="cb4-22" data-line-number="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(x),</a>
<a class="sourceLine" id="cb5-23" data-line-number="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb4-23" data-line-number="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-24" data-line-number="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a> <a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a> <a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" data-line-number="27"><span class="co"># mo_name(x) 587 591 604 594 612 653 10</span></a></code></pre></div> <a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 582 614 622 620 624 677 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.59 seconds (594 ms). You only lose time on your unique input values.</p> <p>So transforming 500,000 values (!!) of 50 unique values only takes 0.62 seconds (619 ms). You only lose time on your unique input values.</p>
</div> </div>
<div id="precalculated-results" class="section level3"> <div id="precalculated-results" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3> <a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p> <p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a> <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),</a> <a class="sourceLine" id="cb5-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb5-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.520 6.600 6.790 6.800 6.930 7.080 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 22.100 22.300 25.600 23.200 23.500 42.800 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.705 0.772 0.816 0.806 0.854 0.977 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 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>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a> <a class="sourceLine" id="cb6-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb6-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb6-4" data-line-number="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a> <a class="sourceLine" id="cb6-5" data-line-number="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb6-6" data-line-number="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a> <a class="sourceLine" id="cb6-7" data-line-number="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># A 6.270 6.300 6.69 6.540 6.990 7.93 10</span></a> <a class="sourceLine" id="cb6-8" data-line-number="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="co"># B 21.600 22.700 25.80 23.300 24.400 43.70 10</span></a> <a class="sourceLine" id="cb6-9" data-line-number="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co"># C 0.795 0.812 0.89 0.879 0.962 1.03 10</span></a></code></pre></div> <a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 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> <a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a> <a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a> <a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.470 0.477 0.506 0.492 0.498 0.674 10</span></a>
<a class="sourceLine" id="cb7-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a> <a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.623 0.634 0.674 0.669 0.708 0.744 10</span></a>
<a class="sourceLine" id="cb7-4" data-line-number="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a> <a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.778 0.819 0.845 0.844 0.866 0.915 10</span></a>
<a class="sourceLine" id="cb7-5" data-line-number="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a> <a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.462 0.471 0.483 0.482 0.492 0.515 10</span></a>
<a class="sourceLine" id="cb7-6" data-line-number="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a> <a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.462 0.464 0.476 0.472 0.479 0.518 10</span></a>
<a class="sourceLine" id="cb7-7" data-line-number="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a> <a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.460 0.466 0.475 0.470 0.482 0.510 10</span></a>
<a class="sourceLine" id="cb7-8" data-line-number="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a> <a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.456 0.465 0.478 0.477 0.486 0.513 10</span></a>
<a class="sourceLine" id="cb7-9" data-line-number="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.459 0.464 0.472 0.470 0.475 0.509 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># A 0.452 0.459 0.473 0.464 0.475 0.518 10</span></a>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># B 0.607 0.610 0.654 0.616 0.639 0.860 10</span></a>
<a class="sourceLine" id="cb7-15" data-line-number="15"><span class="co"># C 0.661 0.686 0.724 0.729 0.763 0.796 10</span></a>
<a class="sourceLine" id="cb7-16" data-line-number="16"><span class="co"># D 0.441 0.448 0.473 0.458 0.471 0.596 10</span></a>
<a class="sourceLine" id="cb7-17" data-line-number="17"><span class="co"># E 0.412 0.439 0.464 0.449 0.458 0.593 10</span></a>
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="co"># F 0.437 0.447 0.471 0.454 0.483 0.586 10</span></a>
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># G 0.437 0.446 0.478 0.454 0.477 0.580 10</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># H 0.435 0.445 0.467 0.454 0.459 0.581 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p> <p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div> </div>
<div id="results-in-other-languages" class="section level3"> <div id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3> <a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p> <p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span></a> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a> <a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"></a> <a class="sourceLine" id="cb7-3" data-line-number="3"></a>
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span></a> <a class="sourceLine" id="cb7-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span></a> <a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span></a>
<a class="sourceLine" id="cb8-6" data-line-number="6"></a> <a class="sourceLine" id="cb7-6" data-line-number="6"></a>
<a class="sourceLine" id="cb8-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span></a> <a class="sourceLine" id="cb7-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb8-8" data-line-number="8"><span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a> <a class="sourceLine" id="cb7-8" data-line-number="8"><span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb8-9" data-line-number="9"></a> <a class="sourceLine" id="cb7-9" data-line-number="9"></a>
<a class="sourceLine" id="cb8-10" data-line-number="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a> <a class="sourceLine" id="cb7-10" data-line-number="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a> <a class="sourceLine" id="cb7-11" data-line-number="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb8-12" data-line-number="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a> <a class="sourceLine" id="cb7-12" data-line-number="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb8-13" data-line-number="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a> <a class="sourceLine" id="cb7-13" data-line-number="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb8-14" data-line-number="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a> <a class="sourceLine" id="cb7-14" data-line-number="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a> <a class="sourceLine" id="cb7-15" data-line-number="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb8-16" data-line-number="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a> <a class="sourceLine" id="cb7-16" data-line-number="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb8-17" data-line-number="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a> <a class="sourceLine" id="cb7-17" data-line-number="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-18" data-line-number="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a> <a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a> <a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" data-line-number="21"><span class="co"># en 17.56 18.00 22.17 18.14 26.18 35.39 10</span></a> <a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 17.64 17.88 20.31 18.36 19.05 37.62 10</span></a>
<a class="sourceLine" id="cb8-22" data-line-number="22"><span class="co"># de 18.94 19.20 19.99 19.86 20.44 21.82 10</span></a> <a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 19.15 19.25 21.73 19.75 20.40 37.72 10</span></a>
<a class="sourceLine" id="cb8-23" data-line-number="23"><span class="co"># nl 23.95 25.02 29.17 25.22 28.39 45.95 10</span></a> <a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 24.34 24.48 36.33 24.88 26.21 121.60 10</span></a>
<a class="sourceLine" id="cb8-24" data-line-number="24"><span class="co"># es 19.05 19.34 22.98 19.75 20.59 36.66 10</span></a> <a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 18.95 19.09 19.29 19.28 19.53 19.61 10</span></a>
<a class="sourceLine" id="cb8-25" data-line-number="25"><span class="co"># it 18.70 19.27 19.36 19.35 19.57 19.79 10</span></a> <a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 19.02 19.10 22.80 19.24 20.42 36.65 10</span></a>
<a class="sourceLine" id="cb8-26" data-line-number="26"><span class="co"># fr 18.54 19.07 21.03 19.24 19.37 37.92 10</span></a> <a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 19.01 19.04 19.21 19.15 19.20 19.94 10</span></a>
<a class="sourceLine" id="cb8-27" data-line-number="27"><span class="co"># pt 18.57 18.92 19.58 19.31 20.32 21.21 10</span></a></code></pre></div> <a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 18.94 19.08 22.28 19.55 20.36 38.81 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p> <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div> </div>
</div> </div>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9068</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>

2
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">0.7.1.9068</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>

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@ -109,6 +109,9 @@ kbd {
li, p { li, p {
line-height: 1.5; line-height: 1.5;
} }
li p {
margin-top: 10.5px;
}
/* slightly smaller blockquote */ /* slightly smaller blockquote */
blockquote { blockquote {

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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">0.7.1.9068</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>
@ -201,11 +201,11 @@
<a href="#partners" class="anchor"></a>Partners</h4> <a href="#partners" class="anchor"></a>Partners</h4>
<p>The development of this package is part of, related to, or made possible by:</p> <p>The development of this package is part of, related to, or made possible by:</p>
<div align="center"> <div align="center">
<a href="https://www.rug.nl"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a>
<a href="https://www.umcg.nl"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
</div> </div>
</div> </div>
</div> </div>

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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9068</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>
@ -225,10 +225,11 @@
</div> </div>
<div id="amr-0-7-1-9068" class="section level1"> <div id="amr-0-7-1-9069" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9068" class="anchor"></a>AMR 0.7.1.9068<small> Unreleased </small> <a href="#amr-0-7-1-9069" class="anchor"></a>AMR 0.7.1.9069<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 01-Sep-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3> <a href="#breaking" class="anchor"></a>Breaking</h3>
@ -260,7 +261,7 @@ This is important, because a value like <code>"testvalue"</code> could never be
<ul> <ul>
<li> <li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set:</p> <p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(septic_patients)</a> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2">x</a> <a class="sourceLine" id="cb3-2" data-line-number="2">x</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co">#&gt; ab mo S I R total</span></a> <a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co">#&gt; ab mo S I R total</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#&gt; 1 AMC B_ESCHR_COL 332 74 61 467</span></a> <a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#&gt; 1 AMC B_ESCHR_COL 332 74 61 467</span></a>
@ -294,7 +295,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p> <p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a> <a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb6-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb6-3" data-line-number="3">example_isolates <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb6-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
</li> </li>
@ -1258,7 +1259,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9068">0.7.1.9068</a></li> <li><a href="#amr-0-7-1-9069">0.7.1.9069</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.1.9068</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9069</span>
</span> </span>
</div> </div>

6
git_premaster.sh
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@ -36,12 +36,14 @@ fi
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
# update 1st line of NEWS.md # update 1st line of NEWS.md
sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
# add date to 2nd line of NEWS.md
sed -i -- "2s/.*/\<small\>Last updated: $(date '+%d-%b-%Y')\<\/small\>/" NEWS.md
rm *-- || true rm *-- || true
echo "• First 3 lines of DESCRIPTION:" echo "• First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION head -3 DESCRIPTION
echo echo
echo "• First line of NEWS.md:" echo "• First 2 lines of NEWS.md:"
head -1 NEWS.md head -2 NEWS.md
echo echo
echo "•••••••••••••••••••••••••••••••••" echo "•••••••••••••••••••••••••••••••••"
echo "• Reloading/documenting package •" echo "• Reloading/documenting package •"

10
index.md
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@ -19,11 +19,11 @@ We created this package for both routine analysis and academic research (as part
The development of this package is part of, related to, or made possible by: The development of this package is part of, related to, or made possible by:
<div align="center"> <div align="center">
<a href="https://www.rug.nl"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a>
<a href="https://www.umcg.nl"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
</div> </div>
### What can you do with this package? ### What can you do with this package?

3
pkgdown/extra.css
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@ -109,6 +109,9 @@ kbd {
li, p { li, p {
line-height: 1.5; line-height: 1.5;
} }
li p {
margin-top: 10.5px;
}
/* slightly smaller blockquote */ /* slightly smaller blockquote */
blockquote { blockquote {

4
tests/testthat/test-freq.R
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@ -26,8 +26,8 @@ test_that("frequency table works", {
# mo # mo
expect_true(is.freq(freq(example_isolates$mo))) expect_true(is.freq(freq(example_isolates$mo)))
# for this to work, the output of mo_gramstain() is to be expected as follows: # for this to work, the output of mo_gramstain() is to be expected as follows:
expect_equal(mo_gramstain("B_ESCHR_COL"), "Gram-negative") expect_equal(mo_gramstain("B_ESCHR_COL", language = NULL), "Gram-negative")
expect_equal(mo_gramstain("B_STPHY_AUR"), "Gram-positive") expect_equal(mo_gramstain("B_STPHY_AUR", language = NULL), "Gram-positive")
# rsi # rsi
expect_true(is.freq(freq(example_isolates$AMX))) expect_true(is.freq(freq(example_isolates$AMX)))

88
vignettes/benchmarks.Rmd
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@ -19,16 +19,44 @@ knitr::opts_chunk$set(
collapse = TRUE, collapse = TRUE,
comment = "#", comment = "#",
fig.width = 7.5, fig.width = 7.5,
fig.height = 4.5 fig.height = 4.5,
dpi = 150
) )
``` ```
<small>Source: https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd</small>
One of the most important features of this package is the complete microbial taxonomic database, supplied by the [Catalogue of Life](http://catalogueoflife.org). We created a function `as.mo()` that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life. One of the most important features of this package is the complete microbial taxonomic database, supplied by the [Catalogue of Life](http://catalogueoflife.org). We created a function `as.mo()` that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.
Using the `microbenchmark` package, we can review the calculation performance of this function. Its function `microbenchmark()` runs different input expressions independently of each other and measures their time-to-result. Using the `microbenchmark` package, we can review the calculation performance of this function. Its function `microbenchmark()` runs different input expressions independently of each other and measures their time-to-result.
```{r, message = FALSE, echo = FALSE} ```{r, message = FALSE, echo = FALSE}
library(dplyr) library(dplyr)
library(ggplot2)
ggplot.bm <- function(df, title = NULL) {
p <- df %>%
group_by(expr) %>%
summarise(t = median(time) / 1e+06) %>%
arrange(t) %>%
mutate(expr = factor(as.character(expr), levels = rev(as.character(expr))),
t_round = round(t, 1))
suppressWarnings(
print(
p %>%
ggplot(aes(x = expr, y = t)) +
geom_linerange(aes(ymin = 0, ymax = t), colour = "#555555") +
geom_text(aes(label = t_round, hjust = -0.5), size = 3) +
geom_point(size = 3, colour = "#555555") +
coord_flip() +
scale_y_log10(breaks = c(1, 2, 5,
10, 20, 50,
100, 200, 500,
1000, 2000, 5000),
limits = c(1, max(p$t) * 2)) +
labs(x = "Expression", y = "Median time in milliseconds (log scale)", title = title)
)
)
}
``` ```
```{r, message = FALSE} ```{r, message = FALSE}
@ -40,17 +68,28 @@ In the next test, we try to 'coerce' different input values for *Staphylococcus
But the calculation time differs a lot: But the calculation time differs a lot:
```{r} ```{r, warning=FALSE}
S.aureus <- microbenchmark(as.mo("sau"), S.aureus <- microbenchmark(
as.mo("stau"), as.mo("sau"), # WHONET code
as.mo("staaur"), as.mo("stau"),
as.mo("STAAUR"), as.mo("STAU"),
as.mo("S. aureus"), as.mo("staaur"),
as.mo("S. aureus"), as.mo("STAAUR"),
as.mo("Staphylococcus aureus"), as.mo("S. aureus"),
times = 10) as.mo("S aureus"),
as.mo("Staphylococcus aureus"), # official taxonomic name
as.mo("Staphylococcus aureus (MRSA)"), # additional text
as.mo("Sthafilokkockus aaureuz"), # incorrect spelling
as.mo("MRSA"), # Methicillin Resistant S. aureus
as.mo("VISA"), # Vancomycin Intermediate S. aureus
as.mo("VRSA"), # Vancomycin Resistant S. aureus
as.mo(22242419), # Catalogue of Life ID
times = 10)
print(S.aureus, unit = "ms", signif = 2) print(S.aureus, unit = "ms", signif = 2)
``` ```
```{r, echo = FALSE}
ggplot.bm(S.aureus)
```
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 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred. 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 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.
@ -68,24 +107,25 @@ print(T.islandicus, unit = "ms", signif = 2)
That takes `r round(mean(T.islandicus$time, na.rm = TRUE) / mean(S.aureus$time, na.rm = TRUE), 1)` times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like *Thermus islandicus*) are almost fast - these are the most probable input from most data sets. That takes `r round(mean(T.islandicus$time, na.rm = TRUE) / mean(S.aureus$time, na.rm = TRUE), 1)` times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like *Thermus islandicus*) are almost fast - these are the most probable input from most data sets.
In the figure below, we compare *Escherichia coli* (which is very common) with *Prevotella brevis* (which is moderately common) and with *Thermus islandicus* (which is very uncommon): In the figure below, we compare *Escherichia coli* (which is very common) with *Prevotella brevis* (which is moderately common) and with *Thermus islandicus* (which is uncommon):
```{r} ```{r, echo = FALSE}
par(mar = c(5, 16, 4, 2)) # set more space for left margin text (16) ggplot.bm(
microbenchmark(as.mo("Escherichia coli"),
as.mo("E. coli"),
times = 10), title = "Very common")
boxplot(microbenchmark(as.mo("Thermus islandicus"), ggplot.bm(
as.mo("Prevotella brevis"), microbenchmark(as.mo("Prevotella brevis"),
as.mo("Escherichia coli"), as.mo("P. brevis"),
as.mo("T. islandicus"), times = 10), title = "Moderately common")
as.mo("P. brevis"),
as.mo("E. coli"), ggplot.bm(
times = 10), microbenchmark(as.mo("Thermus islandicus"),
horizontal = TRUE, las = 1, unit = "s", log = FALSE, as.mo("T. islandicus"),
xlab = "", ylab = "Time in seconds", times = 10), title = "Uncommon")
main = "Benchmarks per prevalence")
``` ```
```{r, echo = FALSE, eval = FALSE} ```{r, echo = FALSE, eval = FALSE}
# In reality, the `as.mo()` functions **learns from its own output to speed up determinations for next times**. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use `as.mo()` yourself: # In reality, the `as.mo()` functions **learns from its own output to speed up determinations for next times**. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use `as.mo()` yourself: