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dr. M.S. (Matthijs) Berends 2019-08-28 17:12:48 +02:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.1.9066 Version: 0.7.1.9067
Date: 2019-08-27 Date: 2019-08-28
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9066 # AMR 0.7.1.9067
### 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`:

4
R/first_isolate.R
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@ -496,7 +496,7 @@ first_isolate <- function(x,
big.mark <- ifelse(decimal.mark != ",", ",", ".") big.mark <- ifelse(decimal.mark != ",", ",", ".")
# handle empty microorganisms # handle empty microorganisms
if (any(all_first$newvar_mo == "UNKNOWN", na.rm = TRUE)) { if (any(all_first$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
if (include_unknown == TRUE) { if (include_unknown == TRUE) {
message(blue(paste0("NOTE: Included ", format(sum(all_first$newvar_mo == "UNKNOWN"), message(blue(paste0("NOTE: Included ", format(sum(all_first$newvar_mo == "UNKNOWN"),
decimal.mark = decimal.mark, big.mark = big.mark), decimal.mark = decimal.mark, big.mark = big.mark),
@ -511,7 +511,7 @@ first_isolate <- function(x,
all_first[which(all_first$newvar_mo == "UNKNOWN"), 'real_first_isolate'] <- include_unknown all_first[which(all_first$newvar_mo == "UNKNOWN"), 'real_first_isolate'] <- include_unknown
# exclude all NAs # exclude all NAs
if (any(is.na(all_first$newvar_mo))) { if (any(is.na(all_first$newvar_mo)) & info == TRUE) {
message(blue(paste0("NOTE: Excluded ", format(sum(is.na(all_first$newvar_mo)), message(blue(paste0("NOTE: Excluded ", format(sum(is.na(all_first$newvar_mo)),
decimal.mark = decimal.mark, big.mark = big.mark), decimal.mark = decimal.mark, big.mark = big.mark),
' isolates with a microbial ID "NA" (column `', bold(col_mo), '`).'))) ' isolates with a microbial ID "NA" (column `', bold(col_mo), '`).')))

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docs/LICENSE-text.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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

486
docs/articles/AMR.html
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@ -40,7 +40,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>
@ -185,7 +185,7 @@
<h1>How to conduct AMR analysis</h1> <h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 August 2019</h4> <h4 class="date">28 August 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div> <div class="hidden name"><code>AMR.Rmd</code></div>
@ -194,7 +194,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 27 August 2019.</p> <p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 28 August 2019.</p>
<div id="introduction" class="section level1"> <div id="introduction" class="section level1">
<h1 class="hasAnchor"> <h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1> <a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2019-08-27</td> <td align="center">2019-08-28</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2019-08-27</td> <td align="center">2019-08-28</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2019-08-27</td> <td align="center">2019-08-28</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>
@ -320,71 +320,71 @@
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2014-06-23</td> <td align="center">2017-06-03</td>
<td align="center">O4</td> <td align="center">E4</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">M</td>
<td align="center">F</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2016-10-05</td> <td align="center">2015-02-25</td>
<td align="center">W5</td> <td align="center">J4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-12-26</td>
<td align="center">S8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-11-26</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td> <td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2014-04-03</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-06-06</td>
<td align="center">F9</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
</tr> </tr>
<tr class="odd">
<td align="center">2014-08-28</td>
<td align="center">F7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-12-16</td>
<td align="center">U7</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-02-09</td>
<td align="center">C8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-11-26</td>
<td align="center">Y5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody> </tbody>
</table> </table>
<p>Now, let’s start the cleaning and the analysis!</p> <p>Now, let’s start the cleaning and the analysis!</p>
@ -406,8 +406,8 @@
# #
# Item Count Percent Cum. Count Cum. Percent # Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- ------------- # --- ----- ------- -------- ----------- -------------
# 1 M 10,514 52.6% 10,514 52.6% # 1 M 10,360 51.8% 10,360 51.8%
# 2 F 9,486 47.4% 20,000 100.0%</code></pre> # 2 F 9,640 48.2% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p> <p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p> <p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a> <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -437,14 +437,14 @@
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no changes)</span></a> <a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no changes)</span></a> <a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a> <a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,504 values changed)</span></a> <a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,477 values changed)</span></a>
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no changes)</span></a> <a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a> <a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a> <a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,298 values changed)</span></a> <a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,306 values changed)</span></a>
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a> <a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a> <a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,705 values changed)</span></a> <a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,760 values changed)</span></a>
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a> <a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a> <a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a> <a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
@ -452,24 +452,24 @@
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a> <a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a> <a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a> <a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,323 values changed)</span></a> <a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,250 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (118 values changed)</span></a> <a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (100 values changed)</span></a>
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a> <a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a> <a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a> <a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a> <a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a> <a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a> <a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,559 out of 20,000 rows, making a total of 7,948 edits</span></a> <a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,548 out of 20,000 rows, making a total of 7,893 edits</span></a>
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</span></a> <a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a> <a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,948 test results</span></a> <a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,893 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 115 test results changed from S to I</span></a> <a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 102 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,723 test results changed from S to R</span></a> <a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,732 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,098 test results changed from I to S</span></a> <a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,108 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 338 test results changed from I to R</span></a> <a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 328 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,648 test results changed from R to S</span></a> <a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,603 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 26 test results changed from R to I</span></a> <a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 20 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a> <a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a> <a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div> <a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -497,7 +497,7 @@
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a> <a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a> <a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a> <a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,672 first isolates (28.4% of total)</span></a></code></pre></div> <a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,693 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p> <p>So only is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div> <a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
@ -508,7 +508,7 @@
<div id="first-weighted-isolates" class="section level2"> <div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2> <a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient K7, sorted on date:</p> <p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Q3, sorted on date:</p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="center">isolate</th> <th align="center">isolate</th>
@ -524,43 +524,43 @@
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">1</td> <td align="center">1</td>
<td align="center">2010-02-15</td> <td align="center">2010-01-10</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2</td> <td align="center">2</td>
<td align="center">2010-03-24</td> <td align="center">2010-03-10</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">3</td> <td align="center">3</td>
<td align="center">2010-06-05</td> <td align="center">2010-04-30</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">4</td> <td align="center">4</td>
<td align="center">2010-07-16</td> <td align="center">2010-07-02</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">I</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -568,8 +568,19 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">5</td> <td align="center">5</td>
<td align="center">2010-09-22</td> <td align="center">2010-10-10</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-26</td>
<td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
@ -577,21 +588,10 @@
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-01-18</td>
<td align="center">K7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd"> <tr class="odd">
<td align="center">7</td> <td align="center">7</td>
<td align="center">2011-01-26</td> <td align="center">2011-01-09</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -601,30 +601,30 @@
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">8</td> <td align="center">8</td>
<td align="center">2011-02-11</td> <td align="center">2011-02-01</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-20</td>
<td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-02-17</td>
<td align="center">K7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even"> <tr class="even">
<td align="center">10</td> <td align="center">10</td>
<td align="center">2011-04-01</td> <td align="center">2011-08-04</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -645,7 +645,7 @@
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a> <a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a> <a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a> <a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,107 first weighted isolates (75.5% of total)</span></a></code></pre></div> <a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,134 first weighted isolates (75.7% of total)</span></a></code></pre></div>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="center">isolate</th> <th align="center">isolate</th>
@ -662,23 +662,23 @@
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">1</td> <td align="center">1</td>
<td align="center">2010-02-15</td> <td align="center">2010-01-10</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2</td> <td align="center">2</td>
<td align="center">2010-03-24</td> <td align="center">2010-03-10</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
@ -686,32 +686,20 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">3</td> <td align="center">3</td>
<td align="center">2010-06-05</td> <td align="center">2010-04-30</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">4</td> <td align="center">4</td>
<td align="center">2010-07-16</td> <td align="center">2010-07-02</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-22</td>
<td align="center">K7</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
@ -720,13 +708,25 @@
<td align="center">FALSE</td> <td align="center">FALSE</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
</tr> </tr>
<tr class="even"> <tr class="odd">
<td align="center">6</td> <td align="center">5</td>
<td align="center">2011-01-18</td> <td align="center">2010-10-10</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-26</td>
<td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
@ -734,44 +734,44 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">7</td> <td align="center">7</td>
<td align="center">2011-01-26</td> <td align="center">2011-01-09</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">FALSE</td> <td align="center">FALSE</td>
<td align="center">FALSE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">8</td> <td align="center">8</td>
<td align="center">2011-02-11</td> <td align="center">2011-02-01</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">9</td> <td align="center">9</td>
<td align="center">2011-02-17</td> <td align="center">2011-03-20</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">TRUE</td> <td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">10</td> <td align="center">10</td>
<td align="center">2011-04-01</td> <td align="center">2011-08-04</td>
<td align="center">K7</td> <td align="center">Q3</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -782,11 +782,11 @@
</tr> </tr>
</tbody> </tbody>
</table> </table>
<p>Instead of 2, now 7 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p> <p>Instead of 2, now 8 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p> <p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,107 isolates for analysis.</p> <p>So we end up with 15,134 isolates for analysis.</p>
<p>We can remove unneeded columns:</p> <p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div> <a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -812,15 +812,15 @@
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td>1</td> <td>1</td>
<td align="center">2014-06-23</td> <td align="center">2017-06-03</td>
<td align="center">O4</td> <td align="center">E4</td>
<td align="center">Hospital A</td> <td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td> <td align="center">Gram-negative</td>
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">coli</td> <td align="center">coli</td>
@ -828,41 +828,41 @@
</tr> </tr>
<tr class="even"> <tr class="even">
<td>2</td> <td>2</td>
<td align="center">2016-10-05</td> <td align="center">2015-02-25</td>
<td align="center">W5</td> <td align="center">J4</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td> <td align="center">M</td>
<td align="center">F</td> <td align="center">Gram-positive</td>
<td align="center">Gram-negative</td> <td align="center">Streptococcus</td>
<td align="center">Escherichia</td> <td align="center">pneumoniae</td>
<td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td>3</td> <td>4</td>
<td align="center">2017-12-26</td> <td align="center">2011-12-16</td>
<td align="center">S8</td> <td align="center">U7</td>
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_STPHY_AUR</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">R</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
<td align="center">Gram-negative</td> <td align="center">Gram-positive</td>
<td align="center">Escherichia</td> <td align="center">Staphylococcus</td>
<td align="center">coli</td> <td align="center">aureus</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td>5</td> <td>6</td>
<td align="center">2014-04-03</td> <td align="center">2014-11-26</td>
<td align="center">Y7</td> <td align="center">Y5</td>
<td align="center">Hospital B</td> <td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
@ -876,29 +876,29 @@
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td>7</td> <td>7</td>
<td align="center">2011-05-16</td> <td align="center">2010-08-09</td>
<td align="center">I8</td> <td align="center">C5</td>
<td align="center">Hospital D</td> <td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNE</td> <td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td> <td align="center">M</td>
<td align="center">Gram-negative</td> <td align="center">Gram-negative</td>
<td align="center">Klebsiella</td> <td align="center">Escherichia</td>
<td align="center">pneumoniae</td> <td align="center">coli</td>
<td align="center">TRUE</td> <td align="center">TRUE</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td>8</td> <td>8</td>
<td align="center">2014-12-28</td> <td align="center">2011-07-24</td>
<td align="center">Z2</td> <td align="center">W6</td>
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td> <td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">F</td> <td align="center">F</td>
<td align="center">Gram-positive</td> <td align="center">Gram-positive</td>
@ -925,7 +925,7 @@
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div> <div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p> <p><strong>Frequency table</strong></p>
<p>Class: character<br> <p>Class: character<br>
Length: 15,107 (of which NA: 0 = 0.00%)<br> Length: 15,134 (of which NA: 0 = 0.00%)<br>
Unique: 4</p> Unique: 4</p>
<p>Shortest: 16<br> <p>Shortest: 16<br>
Longest: 24</p> Longest: 24</p>
@ -942,33 +942,33 @@ Longest: 24</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Escherichia coli</td> <td align="left">Escherichia coli</td>
<td align="right">7,471</td> <td align="right">7,330</td>
<td align="right">49.5%</td> <td align="right">48.4%</td>
<td align="right">7,471</td> <td align="right">7,330</td>
<td align="right">49.5%</td> <td align="right">48.4%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Staphylococcus aureus</td> <td align="left">Staphylococcus aureus</td>
<td align="right">3,789</td> <td align="right">3,816</td>
<td align="right">25.1%</td> <td align="right">25.2%</td>
<td align="right">11,260</td> <td align="right">11,146</td>
<td align="right">74.5%</td> <td align="right">73.6%</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td> <td align="left">Streptococcus pneumoniae</td>
<td align="right">2,296</td> <td align="right">2,386</td>
<td align="right">15.2%</td> <td align="right">15.8%</td>
<td align="right">13,556</td> <td align="right">13,532</td>
<td align="right">89.7%</td> <td align="right">89.4%</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td> <td align="left">Klebsiella pneumoniae</td>
<td align="right">1,551</td> <td align="right">1,602</td>
<td align="right">10.3%</td> <td align="right">10.6%</td>
<td align="right">15,107</td> <td align="right">15,134</td>
<td align="right">100.0%</td> <td align="right">100.0%</td>
</tr> </tr>
</tbody> </tbody>
@ -979,7 +979,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2> <a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p> <p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a> <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4685245</span></a></code></pre></div> <a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4649795</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p> <p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb27-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -992,19 +992,19 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.4686054</td> <td align="center">0.4684865</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.4644004</td> <td align="center">0.4595616</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.4821269</td> <td align="center">0.4685616</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.4655684</td> <td align="center">0.4664897</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital A</td> <td align="center">Hospital A</td>
<td align="center">0.4686054</td> <td align="center">0.4684865</td>
<td align="center">4539</td> <td align="center">4506</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital B</td> <td align="center">Hospital B</td>
<td align="center">0.4644004</td> <td align="center">0.4595616</td>
<td align="center">5295</td> <td align="center">5292</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Hospital C</td> <td align="center">Hospital C</td>
<td align="center">0.4821269</td> <td align="center">0.4685616</td>
<td align="center">2238</td> <td align="center">2322</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Hospital D</td> <td align="center">Hospital D</td>
<td align="center">0.4655684</td> <td align="center">0.4664897</td>
<td align="center">3035</td> <td align="center">3014</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -1058,27 +1058,27 @@ Longest: 24</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">Escherichia</td> <td align="center">Escherichia</td>
<td align="center">0.9243742</td> <td align="center">0.9289222</td>
<td align="center">0.8933208</td> <td align="center">0.8896317</td>
<td align="center">0.9950475</td> <td align="center">0.9924966</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Klebsiella</td> <td align="center">Klebsiella</td>
<td align="center">0.8149581</td> <td align="center">0.8021223</td>
<td align="center">0.8884591</td> <td align="center">0.9082397</td>
<td align="center">0.9787234</td> <td align="center">0.9812734</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">Staphylococcus</td> <td align="center">Staphylococcus</td>
<td align="center">0.9192399</td> <td align="center">0.9263627</td>
<td align="center">0.9160728</td> <td align="center">0.9129979</td>
<td align="center">0.9912906</td> <td align="center">0.9900419</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">Streptococcus</td> <td align="center">Streptococcus</td>
<td align="center">0.5997387</td> <td align="center">0.6240570</td>
<td align="center">0.0000000</td> <td align="center">0.0000000</td>
<td align="center">0.5997387</td> <td align="center">0.6240570</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>

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@ -40,7 +40,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</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">27 August 2019</h4> <h4 class="date">28 August 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div> <div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -210,14 +210,14 @@
<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="dt">times =</span> <span class="dv">10</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="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="cb2-10" data-line-number="10"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Unit: milliseconds</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="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># as.mo("sau") 8.1 8.1 8.3 8.3 8.4 8.6 10</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="cb2-13" data-line-number="13"><span class="co"># as.mo("stau") 31.0 31.0 48.0 40.0 48.0 130.0 10</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="cb2-14" data-line-number="14"><span class="co"># as.mo("staaur") 8.1 8.3 10.0 8.4 8.6 24.0 10</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="cb2-15" data-line-number="15"><span class="co"># as.mo("STAAUR") 8.1 8.1 12.0 8.4 9.2 28.0 10</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="cb2-16" data-line-number="16"><span class="co"># as.mo("S. aureus") 22.0 23.0 26.0 23.0 24.0 40.0 10</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="cb2-17" data-line-number="17"><span class="co"># as.mo("S. aureus") 22.0 23.0 23.0 23.0 23.0 24.0 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="cb2-18" data-line-number="18"><span class="co"># as.mo("Staphylococcus aureus") 3.6 3.8 4.0 3.9 4.0 5.2 10</span></a></code></pre></div> <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>
<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>
@ -229,12 +229,12 @@
<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") 260 270 280 280 290 300 10</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="cb3-11" data-line-number="11"><span class="co"># as.mo("THEISL") 260 280 300 290 300 370 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="cb3-12" data-line-number="12"><span class="co"># as.mo("T. islandicus") 130 140 140 140 150 150 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="cb3-13" data-line-number="13"><span class="co"># as.mo("T. islandicus") 130 130 130 130 140 150 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="cb3-14" data-line-number="14"><span class="co"># as.mo("Thermus islandicus") 47 48 53 50 52 71 10</span></a></code></pre></div> <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>
<p>That takes 9.6 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 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>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 very 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> <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>
<a class="sourceLine" id="cb4-2" data-line-number="2"></a> <a class="sourceLine" id="cb4-2" data-line-number="2"></a>
@ -280,8 +280,8 @@
<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="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="cb5-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb5-25" 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="cb5-26" 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) 611 618 646 642 656 720 10</span></a></code></pre></div> <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>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.64 seconds (641 ms). You only lose time on your unique input values.</p> <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>
</div> </div>
<div id="precalculated-results" class="section level3"> <div id="precalculated-results" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -293,11 +293,11 @@
<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">times =</span> <span class="dv">10</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="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="cb6-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># Unit: milliseconds</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="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># A 6.440 6.690 9.070 7.040 7.500 27.800 10</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="cb6-9" data-line-number="9"><span class="co"># B 21.800 22.200 23.600 23.400 23.800 30.200 10</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="cb6-10" data-line-number="10"><span class="co"># C 0.661 0.826 0.844 0.836 0.928 0.936 10</span></a></code></pre></div> <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>
<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> <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="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> <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="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="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="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="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>
@ -310,14 +310,14 @@
<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="cb7-10" 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="cb7-11" 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="cb7-12" 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 0.468 0.472 0.483 0.483 0.487 0.520 10</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 0.619 0.621 0.649 0.648 0.656 0.698 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 0.702 0.732 0.770 0.788 0.799 0.809 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 0.456 0.457 0.487 0.466 0.475 0.684 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 0.451 0.463 0.466 0.466 0.471 0.479 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 0.457 0.464 0.463 0.469 0.497 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 0.450 0.454 0.468 0.466 0.477 0.495 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 0.454 0.458 0.471 0.464 0.471 0.510 10</span></a></code></pre></div> <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">
@ -344,13 +344,13 @@
<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="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="cb8-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a> <a class="sourceLine" id="cb8-19" 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="cb8-20" 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 17.37 18.13 21.04 18.34 20.65 35.24 10</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="cb8-22" data-line-number="22"><span class="co"># de 18.69 19.32 19.49 19.44 19.77 20.06 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="cb8-23" data-line-number="23"><span class="co"># nl 24.85 25.07 27.07 25.37 25.58 42.68 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="cb8-24" data-line-number="24"><span class="co"># es 18.96 19.55 23.91 19.88 21.02 41.15 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="cb8-25" data-line-number="25"><span class="co"># it 18.85 19.34 21.08 19.52 20.22 35.18 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="cb8-26" data-line-number="26"><span class="co"># fr 18.80 19.32 21.40 19.56 20.29 37.00 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="cb8-27" data-line-number="27"><span class="co"># pt 18.81 19.45 19.57 19.59 19.64 20.20 10</span></a></code></pre></div> <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>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p> <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
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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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
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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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>
@ -185,7 +185,7 @@
<h1>How to predict antimicrobial resistance</h1> <h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">27 August 2019</h4> <h4 class="date">28 August 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div> <div class="hidden name"><code>resistance_predict.Rmd</code></div>

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<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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
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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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

8
docs/news/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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9066" class="section level1"> <div id="amr-0-7-1-9067" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9066" class="anchor"></a>AMR 0.7.1.9066<small> Unreleased </small> <a href="#amr-0-7-1-9067" class="anchor"></a>AMR 0.7.1.9067<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -1258,7 +1258,7 @@ 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-0-7-1-9066">0.7.1.9066</a></li> <li><a href="#amr-0-7-1-9067">0.7.1.9067</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/WHONET.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/age_groups.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</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">0.7.1.9065</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/availability.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/bug_drug_combinations.html
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@ -80,7 +80,7 @@
</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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/count.html
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</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">0.7.1.9065</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/example_isolates.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/filter_ab_class.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/first_isolate.html
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@ -80,7 +80,7 @@
</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">0.7.1.9065</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

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">0.7.1.9066</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/join.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.1.9065</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/like.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/mdro.html
View File

@ -80,7 +80,7 @@
</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">0.7.1.9065</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>

2
docs/reference/resistance_predict.html
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@ -80,7 +80,7 @@
</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">0.7.1.9063</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
</span> </span>
</div> </div>