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(v0.9.0.9021) inheritance fix

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dr. M.S. (Matthijs) Berends 2020-02-10 12:25:02 +01:00
parent c7a76ba713
commit b4356a299c
19 changed files with 73 additions and 89 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.9.0.9020
Date: 2020-02-09
Version: 0.9.0.9021
Date: 2020-02-10
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.9.0.9020
## <small>Last updated: 09-Feb-2020</small>
# AMR 0.9.0.9021
## <small>Last updated: 10-Feb-2020</small>
### New
* Support for LOINC and SNOMED codes

2
R/disk.R
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@ -81,7 +81,7 @@ as.disk <- function(x, na.rm = FALSE) {
#' @export
#' @importFrom dplyr %>%
is.disk <- function(x) {
class(x) %>% identical(c("disk", "integer"))
inherits(x, c("disk", "integer"))
}
#' @exportMethod print.disk

2
R/mic.R
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@ -130,7 +130,7 @@ as.mic <- function(x, na.rm = FALSE) {
#' @export
#' @importFrom dplyr %>%
is.mic <- function(x) {
class(x) %>% identical(c("mic", "ordered", "factor"))
inherits(x, c("mic", "factor"))
}
#' @exportMethod as.double.mic

3
R/rsi.R
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@ -346,8 +346,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
#' @rdname as.rsi
#' @export
is.rsi <- function(x) {
identical(class(x),
c("rsi", "ordered", "factor"))
inherits(x, c("rsi", "factor"))
}
#' @rdname as.rsi

2
docs/404.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

111
docs/articles/benchmarks.html
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@ -41,7 +41,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 February 2020</h4>
<h4 class="date">10 February 2020</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -221,36 +221,21 @@
<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="kw"><a href="https://rdrr.io/r/base/print.html">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"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.0 8.3 14 8.5 9.2 38.0</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 36.0 37.0 42 38.0 43.0 64.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 37.0 38.0 50 45.0 64.0 74.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 7.9 8.3 12 8.9 9.3 37.0</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.0 8.2 14 8.3 9.5 36.0</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 14.0 14.0 22 15.0 37.0 40.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 13.0 14.0 16 14.0 15.0 36.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.6 4.8 5 4.9 5.3 5.4</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 630.0 650.0 730 690.0 710.0 1100.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 370.0 400 380.0 420.0 500.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.0 8.2 11 8.3 9.3 33.0</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 24.0 25.0 46 36.0 49.0 140.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 23.0 25.0 37 37.0 48.0 49.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 120.0 130.0 140 140.0 150.0 150.0</span></a>
<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co"># neval</span></a>
<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-37" data-line-number="37"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-38" data-line-number="38"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-39" data-line-number="39"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-40" data-line-number="40"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-41" data-line-number="41"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-42" data-line-number="42"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-43" data-line-number="43"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-44" data-line-number="44"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-45" data-line-number="45"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-46" data-line-number="46"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-48" data-line-number="48"><span class="co"># 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.0 8.2 11.0 8.4 8.6 34 10</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 37.0 37.0 41.0 38.0 40.0 65 10</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 37.0 38.0 47.0 41.0 62.0 69 10</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 8.1 8.2 16.0 8.4 8.8 57 10</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.1 8.3 11.0 8.5 8.9 34 10</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 14.0 14.0 21.0 14.0 36.0 37 10</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 13.0 14.0 20.0 15.0 16.0 47 10</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.7 4.8 8.6 4.9 6.2 39 10</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 640.0 650.0 680.0 660.0 680.0 790 10</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 330.0 350.0 390.0 390.0 430.0 500 10</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.0 8.5 17.0 9.0 33.0 43 10</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 24.0 24.0 36.0 30.0 47.0 56 10</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 24.0 25.0 60.0 36.0 50.0 270 10</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 120.0 120.0 130.0 130.0 140.0 150 10</span></a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></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.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
@ -263,17 +248,17 @@
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <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="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</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1412.000 1475.000 1514.00 1503.00 1553.000</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1348.000 1448.000 1470.00 1471.00 1512.000</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 14.410 14.600 20.03 14.84 16.170</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 14.640 15.070 26.61 18.52 41.270</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 5.289 5.508 11.34 5.63 5.837</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1422.000 1474.000 1511.000 1515.000 1544.00</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1381.000 1446.000 1457.000 1458.000 1477.00</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 14.390 14.520 18.050 15.000 17.64</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 14.330 14.570 17.690 14.740 15.14</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 5.261 5.342 7.848 5.459 5.63</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># max neval</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1634.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1554.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 41.27 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 45.83 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 35.94 10</span></a></code></pre></div>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1617.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1520.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 39.73 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 39.72 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 29.36 10</span></a></code></pre></div>
<p>That takes 5.6 times as much time on average. 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>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they 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>Methanosarcina semesiae</em> (which is uncommon):</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
@ -308,8 +293,8 @@
<a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</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="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 574 626 649 644 660 787 100</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.64 seconds (643 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 566 598 628 621 645 782 100</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.62 seconds (620 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -322,10 +307,10 @@
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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 6.370 6.460 9.890 6.53 6.900 39.400 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 13.400 13.500 13.800 13.60 14.100 14.500 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.795 0.825 0.851 0.84 0.849 0.973 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>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.120 6.540 7.44 6.900 8.830 9.12 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 13.600 13.800 14.50 14.200 15.000 16.30 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.841 0.859 3.82 0.876 0.917 30.30 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 0.0009 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>
<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://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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>
@ -338,14 +323,14 @@
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</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="cb6-13" data-line-number="13"><span class="co"># A 0.451 0.485 0.488 0.489 0.495 0.518 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.507 0.510 0.526 0.522 0.538 0.554 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.732 0.742 0.769 0.781 0.786 0.807 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.507 0.514 0.534 0.531 0.549 0.585 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.469 0.486 0.492 0.489 0.499 0.532 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.473 0.479 0.483 0.481 0.482 0.513 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.466 0.469 0.481 0.480 0.486 0.517 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.468 0.476 0.502 0.483 0.494 0.665 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.517 0.522 0.570 0.540 0.575 0.756 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.536 0.550 0.584 0.559 0.579 0.801 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.696 0.776 0.804 0.828 0.841 0.908 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.531 0.552 0.597 0.576 0.616 0.784 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.520 0.529 0.549 0.534 0.569 0.626 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.483 0.491 0.519 0.517 0.521 0.580 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.509 0.514 0.545 0.520 0.537 0.763 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.464 0.514 0.555 0.542 0.593 0.698 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> anyway, 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 id="results-in-other-languages" class="section level3">
@ -372,13 +357,13 @@
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</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="cb7-21" data-line-number="21"><span class="co"># en 24.62 25.46 32.22 25.95 27.72 146.70 100</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 25.97 26.93 33.24 27.52 29.66 64.41 100</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 31.00 32.90 37.58 33.48 35.16 69.10 100</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 25.86 26.98 32.09 27.47 28.42 67.33 100</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 25.71 26.95 33.87 27.67 31.49 62.06 100</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 25.80 27.00 31.05 27.41 28.07 72.99 100</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 25.80 27.02 33.26 27.51 31.44 63.41 100</span></a></code></pre></div>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 23.52 25.12 30.94 26.03 26.90 68.07 100</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 24.94 26.64 33.82 27.81 30.86 152.10 100</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 30.28 32.60 37.42 33.81 35.15 72.52 100</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 24.86 26.55 31.91 27.42 28.91 80.24 100</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 24.54 26.61 32.10 27.45 28.35 69.43 100</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 24.75 26.30 30.43 27.50 28.37 64.56 100</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 24.95 26.38 31.37 27.32 28.38 66.08 100</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/index.html
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@ -45,7 +45,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

12
docs/news/index.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>
@ -231,13 +231,13 @@
</div>
<div id="amr-0-9-0-9020" class="section level1">
<div id="amr-0-9-0-9021" class="section level1">
<h1 class="page-header">
<a href="#amr-0-9-0-9020" class="anchor"></a>AMR 0.9.0.9020<small> Unreleased </small>
<a href="#amr-0-9-0-9021" class="anchor"></a>AMR 0.9.0.9021<small> Unreleased </small>
</h1>
<div id="last-updated-09-feb-2020" class="section level2">
<div id="last-updated-10-feb-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-09-feb-2020" class="anchor"></a><small>Last updated: 09-Feb-2020</small>
<a href="#last-updated-10-feb-2020" class="anchor"></a><small>Last updated: 10-Feb-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -1467,7 +1467,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-9-0-9020">0.9.0.9020</a></li>
<li><a href="#amr-0-9-0-9021">0.9.0.9021</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>

2
docs/reference/antibiotics.html
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@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html
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@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>

2
docs/reference/microorganisms.html
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@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<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">0.9.0.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
</span>
</div>