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(v1.3.0.9015) as.mo() speedup for valid taxonomic names

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dr. M.S. (Matthijs) Berends
2020-09-03 20:59:21 +02:00
parent c4b87fe241
commit 68e9cb78e9
104 changed files with 542 additions and 529 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.3.0.9014
Version: 1.3.0.9015
Date: 2020-09-03
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.3.0.9014
# AMR 1.3.0.9015
## <small>Last updated: 3 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!

1
R/globals.R
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@ -40,6 +40,7 @@ globalVariables(c(".rowid",
"intrinsic_resistant",
"isolates",
"lang",
"language",
"lookup",
"microorganism",
"microorganisms",

7
R/mo.R
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@ -179,6 +179,13 @@ as.mo <- function(x,
check_dataset_integrity()
if (tryCatch(all(tolower(x) %in% MO_lookup$fullname_lower, na.rm = TRUE)
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# to improve speed, special case for taxonomically correct full names (case-insensitive)
return(MO_lookup[match(tolower(x), MO_lookup$fullname_lower), "mo", drop = TRUE])
}
# start off with replaced language-specific non-ASCII characters with ASCII characters
x <- parse_and_convert(x)
# replace mo codes used in older package versions

6
R/zzz.R
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@ -29,7 +29,7 @@
envir = asNamespace("AMR"))
assign(x = "LANGUAGES_SUPPORTED",
value = sort(c("en", unique(AMR:::translations_file$lang))),
value = sort(c("en", unique(translations_file$lang))),
envir = asNamespace("AMR"))
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
@ -50,13 +50,13 @@
}
.onAttach <- function(...) {
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(getOption("AMR_silentstart", FALSE)))) {
return()
}
packageStartupMessage("Thank you for using the AMR package! ",
"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities:",
"\nhttps://msberends.github.io/AMR/survey.html",
"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use Sys.setenv(AMR_silentstart = TRUE) ]")
"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use options(AMR_silentstart = TRUE) ]")
}
create_MO_lookup <- function() {

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docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

538
docs/articles/AMR.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">21 August 2020</h4>
<h4 class="date">03 September 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@
<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 21 August 2020.</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 03 September 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-08-21</td>
<td align="center">2020-09-03</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2020-08-21</td>
<td align="center">2020-09-03</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2020-08-21</td>
<td align="center">2020-09-03</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -361,68 +361,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-03-20</td>
<td align="center">W2</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2014-05-29</td>
<td align="center">B4</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">R</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-12-03</td>
<td align="center">X9</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-11-11</td>
<td align="center">A5</td>
<td align="center">Hospital D</td>
<td align="center">2017-04-19</td>
<td align="center">S1</td>
<td align="center">Hospital C</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">2012-09-03</td>
<td align="center">Y3</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-11-19</td>
<td align="center">I3</td>
<td align="center">Hospital C</td>
<td align="center">2017-04-21</td>
<td align="center">L3</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-06-05</td>
<td align="center">Q7</td>
<td align="center">2011-01-19</td>
<td align="center">A7</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">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-01-24</td>
<td align="center">H10</td>
<td align="center">Hospital B</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">M</td>
</tr>
<tr class="even">
<td align="center">2011-01-31</td>
<td align="center">T9</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</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>
@ -459,16 +459,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,358</td>
<td align="right">51.79%</td>
<td align="right">10,358</td>
<td align="right">51.79%</td>
<td align="right">10,409</td>
<td align="right">52.05%</td>
<td align="right">10,409</td>
<td align="right">52.05%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,642</td>
<td align="right">48.21%</td>
<td align="right">9,591</td>
<td align="right">47.96%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -518,7 +518,7 @@ Longest: 1</p>
<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span>
</pre></div>
<p>So only 28.3% 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 28.6% 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="cb16"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">first</span> <span class="op">==</span> <span class="fl">TRUE</span>)
@ -532,7 +532,7 @@ Longest: 1</p>
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<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 C8, 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 M8, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -548,21 +548,21 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-13</td>
<td align="center">C8</td>
<td align="center">2010-01-28</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-19</td>
<td align="center">C8</td>
<td align="center">2010-05-23</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_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">S</td>
@ -570,10 +570,10 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-03-12</td>
<td align="center">C8</td>
<td align="center">2010-07-11</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_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">S</td>
@ -581,30 +581,30 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-25</td>
<td align="center">C8</td>
<td align="center">2010-10-01</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-04-28</td>
<td align="center">C8</td>
<td align="center">2010-12-02</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-07-22</td>
<td align="center">C8</td>
<td align="center">2010-12-23</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -614,8 +614,8 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-12-05</td>
<td align="center">C8</td>
<td align="center">2011-01-16</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -625,33 +625,33 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-01-18</td>
<td align="center">C8</td>
<td align="center">2011-03-14</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-24</td>
<td align="center">C8</td>
<td align="center">2011-04-02</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-06-24</td>
<td align="center">C8</td>
<td align="center">2011-04-05</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
@ -686,34 +686,34 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-13</td>
<td align="center">C8</td>
<td align="center">2010-01-28</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-02-19</td>
<td align="center">C8</td>
<td align="center">2010-05-23</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_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">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-03-12</td>
<td align="center">C8</td>
<td align="center">2010-07-11</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_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">S</td>
@ -722,32 +722,32 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-25</td>
<td align="center">C8</td>
<td align="center">2010-10-01</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-04-28</td>
<td align="center">C8</td>
<td align="center">2010-12-02</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</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">2010-07-22</td>
<td align="center">C8</td>
<td align="center">2010-12-23</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -758,8 +758,8 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-12-05</td>
<td align="center">C8</td>
<td align="center">2011-01-16</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -770,11 +770,11 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-01-18</td>
<td align="center">C8</td>
<td align="center">2011-03-14</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">TRUE</td>
@ -782,23 +782,23 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-24</td>
<td align="center">C8</td>
<td align="center">2011-04-02</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-06-24</td>
<td align="center">C8</td>
<td align="center">2011-04-05</td>
<td align="center">M8</td>
<td align="center">B_ESCHR_COLI</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">FALSE</td>
@ -806,13 +806,13 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.1% 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, 79.1% of all isolates are marked ‘first weighted’ - 50.5% 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>
<div class="sourceCode" id="cb19"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()
</pre></div>
<p>So we end up with 15,686 isolates for analysis.</p>
<p>So we end up with 15,813 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data_1st</span> <span class="op">%&gt;%</span>
@ -857,13 +857,77 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2011-03-20</td>
<td align="center">W2</td>
<td align="left">2</td>
<td align="center">2017-04-19</td>
<td align="center">S1</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2017-04-21</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2011-01-19</td>
<td align="center">A7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</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">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2011-01-24</td>
<td align="center">H10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-01-31</td>
<td align="center">T9</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</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">R</td>
<td align="center">F</td>
@ -873,85 +937,21 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2012-11-11</td>
<td align="center">A5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2012-09-03</td>
<td align="center">Y3</td>
<td align="center">Hospital C</td>
<td align="left">7</td>
<td align="center">2012-12-27</td>
<td align="center">Q9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2012-11-19</td>
<td align="center">I3</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2013-11-06</td>
<td align="center">B1</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2017-01-21</td>
<td align="center">U3</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</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">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -975,8 +975,8 @@ Longest: 1</p>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,686<br>
Available: 15,686 (100%, NA: 0 = 0%)<br>
Length: 15,813<br>
Available: 15,813 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -993,33 +993,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,774</td>
<td align="right">49.56%</td>
<td align="right">7,774</td>
<td align="right">49.56%</td>
<td align="right">7,901</td>
<td align="right">49.97%</td>
<td align="right">7,901</td>
<td align="right">49.97%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,952</td>
<td align="right">25.19%</td>
<td align="right">11,726</td>
<td align="right">74.75%</td>
<td align="right">3,946</td>
<td align="right">24.95%</td>
<td align="right">11,847</td>
<td align="right">74.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,367</td>
<td align="right">15.09%</td>
<td align="right">14,093</td>
<td align="right">89.84%</td>
<td align="right">2,394</td>
<td align="right">15.14%</td>
<td align="right">14,241</td>
<td align="right">90.06%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,593</td>
<td align="right">10.16%</td>
<td align="right">15,686</td>
<td align="right">1,572</td>
<td align="right">9.94%</td>
<td align="right">15,813</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1048,50 +1048,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3685</td>
<td align="center">3774</td>
<td align="center">257</td>
<td align="center">3832</td>
<td align="center">7774</td>
<td align="center">3870</td>
<td align="center">7901</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6104</td>
<td align="center">275</td>
<td align="center">1395</td>
<td align="center">7774</td>
<td align="center">6189</td>
<td align="center">306</td>
<td align="center">1406</td>
<td align="center">7901</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5979</td>
<td align="center">6042</td>
<td align="center">0</td>
<td align="center">1795</td>
<td align="center">7774</td>
<td align="center">1859</td>
<td align="center">7901</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">6986</td>
<td align="center">7094</td>
<td align="center">0</td>
<td align="center">788</td>
<td align="center">7774</td>
<td align="center">807</td>
<td align="center">7901</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1593</td>
<td align="center">1593</td>
<td align="center">1572</td>
<td align="center">1572</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1269</td>
<td align="center">57</td>
<td align="center">267</td>
<td align="center">1593</td>
<td align="center">1245</td>
<td align="center">56</td>
<td align="center">271</td>
<td align="center">1572</td>
</tr>
</tbody>
</table>
@ -1116,34 +1116,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">5979</td>
<td align="center">6042</td>
<td align="center">0</td>
<td align="center">1795</td>
<td align="center">7774</td>
<td align="center">1859</td>
<td align="center">7901</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1213</td>
<td align="center">1182</td>
<td align="center">0</td>
<td align="center">380</td>
<td align="center">1593</td>
<td align="center">390</td>
<td align="center">1572</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">3003</td>
<td align="center">2966</td>
<td align="center">0</td>
<td align="center">949</td>
<td align="center">3952</td>
<td align="center">980</td>
<td align="center">3946</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1820</td>
<td align="center">1834</td>
<td align="center">0</td>
<td align="center">547</td>
<td align="center">2367</td>
<td align="center">560</td>
<td align="center">2394</td>
</tr>
</tbody>
</table>
@ -1156,7 +1156,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb28"><pre class="downlit">
<span class="kw">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>)
<span class="co"># [1] 0.5350631</span>
<span class="co"># [1] 0.5330424</span>
</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>
<div class="sourceCode" id="cb29"><pre class="downlit">
@ -1173,19 +1173,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5338783</td>
<td align="center">0.5262478</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5368875</td>
<td align="center">0.5401022</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5367068</td>
<td align="center">0.5257556</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5322422</td>
<td align="center">0.5357938</td>
</tr>
</tbody>
</table>
@ -1206,23 +1206,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5338783</td>
<td align="center">4649</td>
<td align="center">0.5262478</td>
<td align="center">4648</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5368875</td>
<td align="center">5571</td>
<td align="center">0.5401022</td>
<td align="center">5673</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5367068</td>
<td align="center">2411</td>
<td align="center">0.5257556</td>
<td align="center">2349</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5322422</td>
<td align="center">3055</td>
<td align="center">0.5357938</td>
<td align="center">3143</td>
</tr>
</tbody>
</table>
@ -1245,27 +1245,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8205557</td>
<td align="center">0.8986365</td>
<td align="center">0.9855930</td>
<td align="center">0.8220478</td>
<td align="center">0.8978610</td>
<td align="center">0.9860777</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8323917</td>
<td align="center">0.8901444</td>
<td align="center">0.9855618</td>
<td align="center">0.8276081</td>
<td align="center">0.9001272</td>
<td align="center">0.9860051</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8276822</td>
<td align="center">0.9210526</td>
<td align="center">0.9868421</td>
<td align="center">0.8335023</td>
<td align="center">0.9206792</td>
<td align="center">0.9878358</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5504858</td>
<td align="center">0.5396825</td>
<td align="center">0.0000000</td>
<td align="center">0.5504858</td>
<td align="center">0.5396825</td>
</tr>
</tbody>
</table>

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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>

68
docs/articles/MDR.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@ -320,19 +320,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I S S S S R</span>
<span class="co"># 2 S S S R R I</span>
<span class="co"># 3 R S S R S I</span>
<span class="co"># 4 R S S R S S</span>
<span class="co"># 5 S R I R I R</span>
<span class="co"># 6 R R S R R R</span>
<span class="co"># 1 S R S S R S</span>
<span class="co"># 2 S R R S R S</span>
<span class="co"># 3 S R R S S R</span>
<span class="co"># 4 R R S S S R</span>
<span class="co"># 5 I S I S S S</span>
<span class="co"># 6 S S R R S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 I</span>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span>
<span class="co"># 1 R</span>
<span class="co"># 2 I</span>
<span class="co"># 3 S</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 S</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
@ -368,40 +368,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3233</td>
<td align="right">64.66%</td>
<td align="right">3233</td>
<td align="right">64.66%</td>
<td align="right">3297</td>
<td align="right">65.94%</td>
<td align="right">3297</td>
<td align="right">65.94%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">698</td>
<td align="right">13.96%</td>
<td align="right">3931</td>
<td align="right">78.62%</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">614</td>
<td align="right">12.28%</td>
<td align="right">3911</td>
<td align="right">78.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">556</td>
<td align="right">11.12%</td>
<td align="right">4487</td>
<td align="right">89.74%</td>
<td align="left">Negative</td>
<td align="right">603</td>
<td align="right">12.06%</td>
<td align="right">4514</td>
<td align="right">90.28%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">300</td>
<td align="right">6.00%</td>
<td align="right">4787</td>
<td align="right">95.74%</td>
<td align="right">278</td>
<td align="right">5.56%</td>
<td align="right">4792</td>
<td align="right">95.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">213</td>
<td align="right">4.26%</td>
<td align="right">208</td>
<td align="right">4.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

84
docs/articles/PCA.html
View File

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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</a>
</li>
<li>
@ -224,46 +224,46 @@
<span class="co"># $ gender &lt;chr&gt; "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span>
<span class="co"># $ patient_id &lt;chr&gt; "A77334", "A77334", "067927", "067927", "067927", "06…</span>
<span class="co"># $ mo &lt;mo&gt; "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STP…</span>
<span class="co"># $ PEN &lt;ord&gt; R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
<span class="co"># $ OXA &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ FLC &lt;ord&gt; NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
<span class="co"># $ AMX &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ AMC &lt;ord&gt; I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
<span class="co"># $ AMP &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ TZP &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CZO &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ FEP &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CXM &lt;ord&gt; I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
<span class="co"># $ FOX &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CTX &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
<span class="co"># $ CAZ &lt;ord&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
<span class="co"># $ CRO &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
<span class="co"># $ GEN &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ TOB &lt;ord&gt; NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
<span class="co"># $ AMK &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ KAN &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ TMP &lt;ord&gt; R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
<span class="co"># $ SXT &lt;ord&gt; R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
<span class="co"># $ NIT &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ FOS &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ LNZ &lt;ord&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
<span class="co"># $ CIP &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
<span class="co"># $ MFX &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ VAN &lt;ord&gt; R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
<span class="co"># $ TEC &lt;ord&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
<span class="co"># $ TCY &lt;ord&gt; R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
<span class="co"># $ TGC &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ DOX &lt;ord&gt; NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
<span class="co"># $ ERY &lt;ord&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
<span class="co"># $ CLI &lt;ord&gt; NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
<span class="co"># $ AZM &lt;ord&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
<span class="co"># $ IPM &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
<span class="co"># $ MEM &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ MTR &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CHL &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ COL &lt;ord&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
<span class="co"># $ MUP &lt;ord&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ RIF &lt;ord&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
<span class="co"># $ PEN &lt;rsi&gt; R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
<span class="co"># $ OXA &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ FLC &lt;rsi&gt; NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
<span class="co"># $ AMX &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ AMC &lt;rsi&gt; I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
<span class="co"># $ AMP &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ TZP &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CZO &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ FEP &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CXM &lt;rsi&gt; I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
<span class="co"># $ FOX &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CTX &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
<span class="co"># $ CAZ &lt;rsi&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
<span class="co"># $ CRO &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
<span class="co"># $ GEN &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ TOB &lt;rsi&gt; NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
<span class="co"># $ AMK &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ KAN &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ TMP &lt;rsi&gt; R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
<span class="co"># $ SXT &lt;rsi&gt; R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
<span class="co"># $ NIT &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ FOS &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ LNZ &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
<span class="co"># $ CIP &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
<span class="co"># $ MFX &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ VAN &lt;rsi&gt; R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
<span class="co"># $ TEC &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
<span class="co"># $ TCY &lt;rsi&gt; R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
<span class="co"># $ TGC &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ DOX &lt;rsi&gt; NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
<span class="co"># $ ERY &lt;rsi&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
<span class="co"># $ CLI &lt;rsi&gt; NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
<span class="co"># $ AZM &lt;rsi&gt; R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
<span class="co"># $ IPM &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
<span class="co"># $ MEM &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ MTR &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ CHL &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ COL &lt;rsi&gt; NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
<span class="co"># $ MUP &lt;rsi&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
<span class="co"># $ RIF &lt;rsi&gt; R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
</pre></div>
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
<div class="sourceCode" id="cb2"><pre class="downlit">

6
docs/articles/SPSS.html
View File

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">21 August 2020</h4>
<h4 class="date">03 September 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>

5
docs/articles/WHONET.html
View File

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
</a>
</li>
<li>
@ -352,6 +352,7 @@ Length: 500<br>
Levels: 3: S &lt; I &lt; R<br>
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
Unique: 3</p>
<p>%SI: 78.59%</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>

110
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -79,7 +79,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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</a>
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<li>
@ -225,28 +225,40 @@
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fl">22242419</span>), <span class="co"># Catalogue of Life ID</span>
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 8.7 9.3 13 9.8 12 40 10</span>
<span class="co"># as.mo("stau") 160.0 180.0 200 200.0 210 220 10</span>
<span class="co"># as.mo("STAU") 160.0 180.0 190 190.0 200 210 10</span>
<span class="co"># as.mo("staaur") 9.8 12.0 15 12.0 12 42 10</span>
<span class="co"># as.mo("STAAUR") 8.4 8.7 13 10.0 12 37 10</span>
<span class="co"># as.mo("S. aureus") 13.0 16.0 38 18.0 45 150 10</span>
<span class="co"># as.mo("S aureus") 12.0 17.0 21 17.0 18 48 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 7.1 8.7 12 9.7 11 38 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 880.0 920.0 930 930.0 960 980 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 400.0 430.0 450 440.0 460 500 10</span>
<span class="co"># as.mo("MRSA") 8.6 12.0 20 12.0 37 42 10</span>
<span class="co"># as.mo("VISA") 15.0 17.0 20 18.0 19 40 10</span>
<span class="co"># as.mo("VRSA") 13.0 14.0 19 17.0 19 46 10</span>
<span class="co"># as.mo(22242419) 140.0 140.0 160 150.0 170 210 10</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 12.0 12.0 24.0 15.0 40.0 43.0</span>
<span class="co"># as.mo("stau") 170.0 170.0 190.0 180.0 210.0 250.0</span>
<span class="co"># as.mo("STAU") 160.0 180.0 200.0 190.0 220.0 230.0</span>
<span class="co"># as.mo("staaur") 9.4 11.0 21.0 13.0 40.0 48.0</span>
<span class="co"># as.mo("STAAUR") 9.0 13.0 34.0 14.0 43.0 140.0</span>
<span class="co"># as.mo("S. aureus") 16.0 18.0 20.0 19.0 21.0 25.0</span>
<span class="co"># as.mo("S aureus") 15.0 16.0 20.0 18.0 21.0 39.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.1 1.1 1.4 1.6 1.6 1.7</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 920.0 950.0 940.0 980.0 1000.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 390.0 410.0 440.0 440.0 460.0 490.0</span>
<span class="co"># as.mo("MRSA") 11.0 12.0 30.0 13.0 40.0 130.0</span>
<span class="co"># as.mo("VISA") 16.0 18.0 30.0 20.0 46.0 69.0</span>
<span class="co"># as.mo("VRSA") 14.0 19.0 33.0 33.0 47.0 51.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
</pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
<p>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. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
<p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
@ -255,22 +267,18 @@
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="co"># take all MO codes from the example_isolates data set</span>
<span class="kw">x</span> <span class="op">&lt;-</span> <span class="kw">example_isolates</span><span class="op">$</span><span class="kw">mo</span> <span class="op">%&gt;%</span>
<span class="co"># keep only the unique ones</span>
<span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="op">%&gt;%</span>
<span class="co"># pick 50 of them at random</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="op">%&gt;%</span>
<span class="co"># paste that 10,000 times</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">10000</span>) <span class="op">%&gt;%</span>
<span class="co"># scramble it</span>
<span class="co"># and copy them a thousand times</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">1000</span>) <span class="op">%&gt;%</span>
<span class="co"># then scramble them</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>()
<span class="co"># got indeed 50 times 10,000 = half a million?</span>
<span class="co"># as the example_isolates has 2,000 rows, we should have 2 million items</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="kw">x</span>)
<span class="co"># [1] 500000</span>
<span class="co"># [1] 2000000</span>
<span class="co"># and how many unique values do we have?</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="kw">x</span>)
<span class="co"># [1] 50</span>
<span class="co"># [1] 90</span>
<span class="co"># now let's see:</span>
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">x</span>),
@ -278,27 +286,27 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 1750 1790 1830 1810 1850 1950 10</span>
<span class="co"># mo_name(x) 90.3 101 120 102 141 202 10</span>
</pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.81 seconds. You only lose time on your unique input values.</p>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.102 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
<div class="sourceCode" id="cb4"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"STAAUR"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
C = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 6.08 6.23 10.40 6.56 7.03 44.90 10</span>
<span class="co"># B 11.70 12.00 12.70 12.70 13.60 13.90 10</span>
<span class="co"># C 1.05 1.11 1.19 1.13 1.25 1.55 10</span>
<span class="co"># A 7.08 7.29 8.00 8.25 8.49 9.22 10</span>
<span class="co"># B 12.30 13.50 14.20 14.50 14.70 14.80 10</span>
<span class="co"># C 2.14 2.26 7.35 2.38 2.51 52.30 10</span>
</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 0.0011 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 0.0024 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="cb5"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -312,14 +320,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.886 1.010 1.040 1.020 1.06 1.25 10</span>
<span class="co"># B 1.010 1.030 1.150 1.040 1.27 1.64 10</span>
<span class="co"># C 0.885 1.030 1.110 1.060 1.26 1.29 10</span>
<span class="co"># D 0.812 0.822 1.000 1.000 1.05 1.43 10</span>
<span class="co"># E 0.827 0.989 1.070 1.030 1.23 1.35 10</span>
<span class="co"># F 0.887 0.994 1.070 1.040 1.08 1.35 10</span>
<span class="co"># G 0.812 0.839 0.969 0.916 1.04 1.32 10</span>
<span class="co"># H 0.815 1.020 1.090 1.050 1.30 1.37 10</span>
<span class="co"># A 1.29 1.38 1.64 1.47 1.84 2.28 10</span>
<span class="co"># B 1.27 1.62 1.76 1.69 1.82 2.71 10</span>
<span class="co"># C 1.28 1.32 1.56 1.48 1.77 2.09 10</span>
<span class="co"># D 1.29 1.46 1.68 1.66 1.77 2.24 10</span>
<span class="co"># E 1.26 1.39 5.34 1.64 1.77 39.00 10</span>
<span class="co"># F 1.26 1.33 1.58 1.44 1.80 2.14 10</span>
<span class="co"># G 1.32 1.51 1.65 1.68 1.75 2.05 10</span>
<span class="co"># H 1.31 1.43 1.71 1.68 1.86 2.49 10</span>
</pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
@ -348,13 +356,13 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 12.88 13.52 16.72 14.63 16.00 55.03 100</span>
<span class="co"># de 13.79 14.51 18.36 15.11 16.67 136.90 100</span>
<span class="co"># nl 17.72 18.59 22.30 20.15 21.87 54.69 100</span>
<span class="co"># es 13.78 14.38 19.16 15.35 16.86 49.96 100</span>
<span class="co"># it 13.83 14.40 18.57 15.24 16.32 58.12 100</span>
<span class="co"># fr 13.72 14.47 19.67 15.21 17.46 52.22 100</span>
<span class="co"># pt 13.73 14.43 17.76 15.10 16.85 51.69 100</span>
<span class="co"># en 13.29 13.54 17.53 13.70 14.93 58.25 100</span>
<span class="co"># de 14.25 14.46 19.09 14.69 16.23 58.96 100</span>
<span class="co"># nl 17.89 18.46 24.37 19.05 21.14 70.25 100</span>
<span class="co"># es 14.05 14.41 18.08 14.72 16.11 57.07 100</span>
<span class="co"># it 14.07 14.38 19.18 14.63 16.40 58.14 100</span>
<span class="co"># fr 13.98 14.42 17.30 14.57 15.31 56.81 100</span>
<span class="co"># pt 13.95 14.38 17.78 14.60 16.32 57.53 100</span>
</pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>

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@ -79,7 +79,7 @@
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<span class="navbar-brand">
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@ -79,7 +79,7 @@
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docs/index.html
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@ -43,7 +43,7 @@
</button>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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docs/news/index.html
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<span class="navbar-brand">
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@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309014" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9014">
<a href="#amr-1309014" class="anchor"></a>AMR 1.3.0.9014<small> Unreleased </small>
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<a href="#amr-1309015" class="anchor"></a>AMR 1.3.0.9015<small> Unreleased </small>
</h1>
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-09-03T10:29Z
last_built: 2020-09-03T18:57Z
urls:
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@ -122,7 +122,7 @@
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2
docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

2
docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

2
docs/reference/atc_online.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

4
docs/reference/availability.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
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Download our reference data sets for own use
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2
docs/reference/bug_drug_combinations.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

4
docs/reference/catalogue_of_life.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/catalogue_of_life_version.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
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4
docs/reference/count.html
View File

@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -123,7 +123,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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docs/reference/eucast_rules.html
View File

@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -123,7 +123,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
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4
docs/reference/example_isolates.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
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docs/reference/example_isolates_unclean.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/filter_ab_class.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/first_isolate.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/g.test.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/ggplot_pca.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/ggplot_rsi.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/guess_ab_col.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

4
docs/reference/intrinsic_resistant.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
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4
docs/reference/join.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/key_antibiotics.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/kurtosis.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/lifecycle.html
View File

@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -124,7 +124,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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2
docs/reference/like.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

4
docs/reference/mdro.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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2
docs/reference/microorganisms.codes.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

4
docs/reference/microorganisms.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/microorganisms.old.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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2
docs/reference/mo_property.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>

4
docs/reference/mo_source.html
View File

@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -123,7 +123,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/p_symbol.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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</li>
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4
docs/reference/pca.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/proportion.html
View File

@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -123,7 +123,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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docs/reference/resistance_predict.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
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4
docs/reference/rsi_translation.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -122,7 +122,7 @@
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
Data sets for download / own use
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4
docs/reference/skewness.html
View File

@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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<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">1.3.0.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
</span>
</div>
@ -123,7 +123,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
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