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

DESCRIPTION

@@ -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(

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.3.0.9014
-## <small>Last updated:  3 September 2020</small>
+# 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!
 

R/globals.R

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

R/mo.R

@@ -178,6 +178,13 @@ 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)

R/zzz.R

@@ -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() {

docs/404.html

@@ -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>
 

docs/LICENSE-text.html

@@ -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>
 

docs/articles/AMR.html

@@ -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>
@@ -361,66 +361,66 @@
 </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">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">S</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">Staphylococcus aureus</td>
-<td align="center">S</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">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">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">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">R</td>
-<td align="center">R</td>
-<td align="center">F</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">2012-11-19</td>
-<td align="center">I3</td>
-<td align="center">Hospital C</td>
+<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">R</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">Hospital B</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
+<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>
@@ -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> 
@@ -857,63 +857,63 @@ 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="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</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">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</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">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">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-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</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">2012-09-03</td>
-<td align="center">Y3</td>
-<td align="center">Hospital C</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">R</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">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">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">2012-11-19</td>
-<td align="center">I3</td>
-<td align="center">Hospital C</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">R</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
@@ -921,35 +921,35 @@ Longest: 1</p>
 <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="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">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">Gram-negative</td>
-<td align="center">Klebsiella</td>
+<td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</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="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">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">Escherichia</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@@ -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>

docs/articles/EUCAST.html

@@ -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>

docs/articles/MDR.html

@@ -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>