(v1.7.1.9014) rep() for S3 classes

1 year ago · ad10693a1a
parent 16b4c74d44
commit ad10693a1a
38 changed files with 363 additions and 300 deletions
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9013
-Date: 2021-07-04
+Version: 1.7.1.9014
+Date: 2021-07-06
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
    person(role = c("aut", "cre"), 
--- a/6
+++ b/6
@ -93,6 +93,7 @@ S3method(exp,mic)
 S3method(expm1,mic)
 S3method(floor,mic)
 S3method(format,bug_drug_combinations)
+S3method(format,taxonomic_name)
 S3method(gamma,mic)
 S3method(hist,mic)
 S3method(kurtosis,data.frame)
@ -127,7 +128,12 @@ S3method(print,taxonomic_name)
 S3method(prod,mic)
 S3method(quantile,mic)
 S3method(range,mic)
+S3method(rep,ab)
+S3method(rep,disk)
+S3method(rep,mic)
 S3method(rep,mo)
+S3method(rep,rsi)
+S3method(rep,taxonomic_name)
 S3method(round,mic)
 S3method(sign,mic)
 S3method(signif,mic)
--- a/NEWS.md
+++ b/NEWS.md
@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9013
-## <small>Last updated:  4 July 2021</small>
+# `AMR` 1.7.1.9014
+## <small>Last updated:  6 July 2021</small>

 ### Changed
 * Antibiotic class selectors (see `ab_class()`)
--- a/R/ab.R
+++ b/R/ab.R
@ -580,6 +580,15 @@ unique.ab <- function(x, incomparables = FALSE, ...) {
  y
 }

+#' @method rep ab
+#' @export
+#' @noRd
+rep.ab <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 generalise_antibiotic_name <- function(x) {
  x <- toupper(x)
  # remove suffices
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@ -113,7 +113,7 @@ bug_drug_combinations <- function(x,
        data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
      })
      merged <- do.call(rbind, pivot)
-      out_group <- data.frame(mo = unique_mo[i],
+      out_group <- data.frame(mo = rep(unique_mo[i], NROW(merged)),
                              ab = rownames(merged),
                              S = merged$S,
                              I = merged$I,
--- a/R/disk.R
+++ b/R/disk.R
@ -195,6 +195,15 @@ unique.disk <- function(x, incomparables = FALSE, ...) {
  y
 }

+#' @method rep disk
+#' @export
+#' @noRd
+rep.disk <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 # will be exported using s3_register() in R/zzz.R
 get_skimmers.disk <- function(column) {
  skimr::sfl(
--- a/R/mic.R
+++ b/R/mic.R
@ -320,6 +320,15 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
  y
 }

+#' @method rep mic
+#' @export
+#' @noRd
+rep.mic <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 #' @method sort mic
 #' @export
 #' @noRd
@ -337,7 +346,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("Use `plot()` or `ggplot()` for optimal plotting of MIC values", call = FALSE)
+  warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
  hist(log2(x))
 }

--- a/R/mo_property.R
+++ b/R/mo_property.R
@ -48,7 +48,7 @@
 #' 
 #' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
 #'
-#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()].
+#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()] and markdown tables such as with [knitr::kable()].
 #' 
 #' All output [will be translated][translate] where possible.
 #'
@ -786,9 +786,9 @@ print.taxonomic_name <- function(x, ...) {
 as.data.frame.taxonomic_name <- function(x, ...) {
  nm <- deparse1(substitute(x))
  if (!"nm" %in% names(list(...))) {
-    as.data.frame(unclass(x), ..., nm = nm)
+    as.data.frame.vector(x, ..., nm = nm)
  } else {
-    as.data.frame(unclass(x), ...)
+    as.data.frame.vector(x, ...)
  }
 }

@ -801,12 +801,27 @@ type_sum.taxonomic_name <- function(x, ...) {
 pillar_shaft.taxonomic_name <- function(x, ...) {
  out <- format(x)
  hits <- tolower(x) %in% MO_lookup$fullname_lower | tolower(gsub("[^a-zA-Z ]", "", x)) %in% c(MO_lookup$g_species)
-  # grey out the kingdom (part until first "_")
  out[hits] <- font_italic(x[hits], collapse = NULL)
  out[is.na(x)] <- font_na(out[is.na(x)], collapse = NULL)
  create_pillar_column(out, align = "left")
 }

+#' @method format taxonomic_name
+#' @export
+#' @noRd
+format.taxonomic_name <- function(x, ...) {
+  # format only in case of markdown knitting
+  x <- unclass(x)
+  if (any(as.character(sys.calls()) %like% "(^|:| )kable\\(") ||
+      tryCatch(!is.null(knitr::opts_knit$get("out.format")), error = function(e) FALSE) ||
+      tryCatch(isTRUE(getOption('knitr.in.progress')), error = function(e) FALSE)) {
+    # perhaps this could be extended or better specified in the future?
+    hits <- tolower(x) %in% MO_lookup$fullname_lower | tolower(gsub("[^a-zA-Z ]", "", x)) %in% c(MO_lookup$g_species)
+    x[hits] <- paste0("*", x[hits], "*")
+  }
+  x
+}
+
 #' @method [ taxonomic_name
 #' @export
 #' @noRd
@ -856,3 +871,12 @@ unique.taxonomic_name <- function(x, incomparables = FALSE, ...) {
  attributes(y) <- attributes(x)
  y
 }
+
+#' @method rep taxonomic_name
+#' @export
+#' @noRd
+rep.taxonomic_name <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
--- a/R/rsi.R
+++ b/R/rsi.R
@ -1054,6 +1054,15 @@ unique.rsi <- function(x, incomparables = FALSE, ...) {
  y
 }

+#' @method rep rsi
+#' @export
+#' @noRd
+rep.rsi <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 check_reference_data <- function(reference_data) {
  if (!identical(reference_data, AMR::rsi_translation)) {
    class_rsi <- vapply(FUN.VALUE = character(1), rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/data-raw/translations.tsv
+++ b/data-raw/translations.tsv
@ -18,17 +18,17 @@ unknown subspecies	TRUE	TRUE	FALSE	TRUE	unbekannte Unterart	onbekende ondersoort
 unknown rank	TRUE	TRUE	FALSE	TRUE	unbekannter Rang	onbekende rang	rango desconocido	grado sconosciuto	rang inconnu	classificação desconhecido
 CoNS	FALSE	TRUE	FALSE	TRUE	KNS	CNS	SCN			
 CoPS	FALSE	TRUE	FALSE	TRUE	KPS	CPS	SCP			
-Gram-negative	TRUE	TRUE	FALSE	FALSE	Gramnegativ	Gram-negatief	Gram negativo	Gram negativo	Gram négatif	Gram negativo
-Gram-positive	TRUE	TRUE	FALSE	FALSE	Grampositiv	Gram-positief	Gram positivo	Gram positivo	Gram positif	Gram positivo
-^Bacteria$	TRUE	TRUE	FALSE	FALSE	Bakterien	Bacteriën	Bacterias	Batteri	Bactéries	Bactérias
-^Fungi$	TRUE	TRUE	FALSE	FALSE	Pilze	Schimmels	Hongos	Funghi	Champignons	Fungos
-^Yeasts$	TRUE	TRUE	FALSE	FALSE	Hefen	Gisten	Levaduras	Lieviti	Levures	Leveduras
-^Protozoa$	TRUE	TRUE	FALSE	FALSE	Protozoen	Protozoën	Protozoarios	Protozoi	Protozoaires	Protozoários
-biogroup	TRUE	TRUE	FALSE	FALSE	Biogruppe	biogroep	biogrupo	biogruppo	biogroupe	biogrupo
-biotype	TRUE	TRUE	FALSE	FALSE	Biotyp		biotipo	biotipo		biótipo
-vegetative	TRUE	TRUE	FALSE	FALSE	vegetativ	vegetatief	vegetativo	vegetativo	végétatif	vegetativo
-([([ ]*?)group	TRUE	TRUE	FALSE	FALSE	\\1Gruppe	\\1groep	\\1grupo	\\1gruppo	\\1groupe	\\1grupo
-([([ ]*?)Group	TRUE	TRUE	FALSE	FALSE	\\1Gruppe	\\1Groep	\\1Grupo	\\1Gruppo	\\1Groupe	\\1Grupo
+Gram-negative	TRUE	TRUE	FALSE	TRUE	Gramnegativ	Gram-negatief	Gram negativo	Gram negativo	Gram négatif	Gram negativo
+Gram-positive	TRUE	TRUE	FALSE	TRUE	Grampositiv	Gram-positief	Gram positivo	Gram positivo	Gram positif	Gram positivo
+^Bacteria$	TRUE	TRUE	FALSE	TRUE	Bakterien	Bacteriën	Bacterias	Batteri	Bactéries	Bactérias
+^Fungi$	TRUE	TRUE	FALSE	TRUE	Pilze	Schimmels	Hongos	Funghi	Champignons	Fungos
+^Yeasts$	TRUE	TRUE	FALSE	TRUE	Hefen	Gisten	Levaduras	Lieviti	Levures	Leveduras
+^Protozoa$	TRUE	TRUE	FALSE	TRUE	Protozoen	Protozoën	Protozoarios	Protozoi	Protozoaires	Protozoários
+biogroup	TRUE	TRUE	FALSE	TRUE	Biogruppe	biogroep	biogrupo	biogruppo	biogroupe	biogrupo
+biotype	TRUE	TRUE	FALSE	TRUE	Biotyp		biotipo	biotipo		biótipo
+vegetative	TRUE	TRUE	FALSE	TRUE	vegetativ	vegetatief	vegetativo	vegetativo	végétatif	vegetativo
+([([ ]*?)group	TRUE	TRUE	FALSE	TRUE	\\1Gruppe	\\1groep	\\1grupo	\\1gruppo	\\1groupe	\\1grupo
+([([ ]*?)Group	TRUE	TRUE	FALSE	TRUE	\\1Gruppe	\\1Groep	\\1Grupo	\\1Gruppo	\\1Groupe	\\1Grupo
 no .*growth	TRUE	FALSE	FALSE	FALSE	keine? .*wachstum	geen .*groei	no .*crecimientonon	sem .*crescimento	pas .*croissance	sem .*crescimento
 no|not	TRUE	FALSE	FALSE	FALSE	keine?	geen|niet	no|sin	sem	non	sem
 Susceptible	TRUE	FALSE	FALSE	FALSE	Empfindlich	Gevoelig	Susceptible			
--- a/docs/404.html
+++ b/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">1.7.1.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/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">1.7.1.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
      </span>
    </div>

--- a/docs/articles/AMR.html
+++ b/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">1.7.1.9013</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
      </span>
    </div>

@ -193,7 +193,7 @@
      <h1 data-toc-skip>How to conduct AMR data analysis</h1>
                        <h4 class="author">Matthijs S. Berends</h4>
            
-            <h4 class="date">04 July 2021</h4>
+            <h4 class="date">06 July 2021</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 04 July 2021.</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 06 July 2021.</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">2021-07-04</td>
+<td align="center">2021-07-06</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">2021-07-04</td>
+<td align="center">2021-07-06</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">2021-07-04</td>
+<td align="center">2021-07-06</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -344,32 +344,32 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-09-28</td>
-<td align="center">A1</td>
-<td align="center">Hospital A</td>
+<td align="center">2016-02-04</td>
+<td align="center">V9</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">M</td>
+<td align="center">S</td>
+<td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2012-09-28</td>
-<td align="center">J9</td>
+<td align="center">2011-09-24</td>
+<td align="center">D2</td>
 <td align="center">Hospital A</td>
 <td align="center">Streptococcus pneumoniae</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="odd">
-<td align="center">2011-10-02</td>
-<td align="center">S7</td>
-<td align="center">Hospital B</td>
-<td align="center">Klebsiella pneumoniae</td>
+<td align="center">2014-06-20</td>
+<td align="center">Z9</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>
@ -377,9 +377,9 @@
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2016-11-15</td>
-<td align="center">U6</td>
-<td align="center">Hospital A</td>
+<td align="center">2018-01-01</td>
+<td align="center">P4</td>
+<td align="center">Hospital C</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">S</td>
@ -388,26 +388,26 @@
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2016-12-08</td>
-<td align="center">B10</td>
+<td align="center">2014-12-14</td>
+<td align="center">W2</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2010-05-10</td>
-<td align="center">M2</td>
-<td align="center">Hospital D</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">2016-07-27</td>
+<td align="center">R6</td>
+<td align="center">Hospital B</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 </tr>
 </tbody>
 </table>
@ -441,16 +441,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,434</td>
-<td align="right">52.17%</td>
-<td align="right">10,434</td>
-<td align="right">52.17%</td>
+<td align="right">10,365</td>
+<td align="right">51.83%</td>
+<td align="right">10,365</td>
+<td align="right">51.83%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,566</td>
-<td align="right">47.83%</td>
+<td align="right">9,635</td>
+<td align="right">48.18%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -505,9 +505,9 @@ Longest: 1</p>
 <span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
 <span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="co"># 2</span>
-<span class="co"># =&gt; Found 10,702 first weighted isolates (phenotype-based, 53.5% of total</span>
+<span class="co"># =&gt; Found 10,656 first weighted isolates (phenotype-based, 53.3% of total</span>
 <span class="co">#    where a microbial ID was available)</span></code></pre></div>
-<p>So only 53.5% 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 53.3% 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>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -515,7 +515,7 @@ Longest: 1</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 10,702 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,656 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
 <table class="table">
@ -531,7 +531,7 @@ Longest: 1</p>
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="12%">
+<col width="13%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@ -553,99 +553,99 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2016-09-28</td>
-<td align="center">A1</td>
+<td align="left">2</td>
+<td align="center">2011-09-24</td>
+<td align="center">D2</td>
 <td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</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">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">Gram-positive</td>
+<td align="center"><em>Streptococcus</em></td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">2</td>
-<td align="center">2012-09-28</td>
-<td align="center">J9</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="left">3</td>
+<td align="center">2014-06-20</td>
+<td align="center">Z9</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">R</td>
-<td align="center">M</td>
+<td align="center">S</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"><em>Staphylococcus</em></td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">5</td>
-<td align="center">2016-12-08</td>
-<td align="center">B10</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="left">6</td>
+<td align="center">2016-07-27</td>
+<td align="center">R6</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">R</td>
 <td align="center">S</td>
+<td align="center">R</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">F</td>
+<td align="center">Gram-positive</td>
+<td align="center"><em>Staphylococcus</em></td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">7</td>
-<td align="center">2015-04-29</td>
-<td align="center">W8</td>
+<td align="center">2011-07-24</td>
+<td align="center">W2</td>
 <td align="center">Hospital A</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">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
+<td align="center"><em>Escherichia</em></td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">8</td>
-<td align="center">2010-06-19</td>
-<td align="center">Q5</td>
+<td align="left">9</td>
+<td align="center">2012-01-12</td>
+<td align="center">K9</td>
 <td align="center">Hospital C</td>
-<td align="center">B_STPHY_AURS</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">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">M</td>
+<td align="center">Gram-negative</td>
+<td align="center"><em>Escherichia</em></td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">9</td>
-<td align="center">2010-08-20</td>
-<td align="center">A8</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
-<td align="center">S</td>
+<td align="left">11</td>
+<td align="center">2013-03-11</td>
+<td align="center">B6</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">R</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"><em>Klebsiella</em></td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@ -669,8 +669,8 @@ Longest: 1</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,702<br>
-Available: 10,702 (100.0%, NA: 0 = 0.0%)<br>
+Length: 10,656<br>
+Available: 10,656 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -687,33 +687,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,661</td>
-<td align="right">43.55%</td>
-<td align="right">4,661</td>
-<td align="right">43.55%</td>
+<td align="right">4,664</td>
+<td align="right">43.77%</td>
+<td align="right">4,664</td>
+<td align="right">43.77%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,697</td>
-<td align="right">25.20%</td>
-<td align="right">7,358</td>
-<td align="right">68.75%</td>
+<td align="right">2,730</td>
+<td align="right">25.62%</td>
+<td align="right">7,394</td>
+<td align="right">69.39%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,145</td>
-<td align="right">20.04%</td>
-<td align="right">9,503</td>
-<td align="right">88.80%</td>
+<td align="right">2,093</td>
+<td align="right">19.64%</td>
+<td align="right">9,487</td>
+<td align="right">89.03%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,199</td>
-<td align="right">11.20%</td>
-<td align="right">10,702</td>
+<td align="right">1,169</td>
+<td align="right">10.97%</td>
+<td align="right">10,656</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -732,14 +732,14 @@ Longest: 24</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="11%">
+<col width="10%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="11%">
+<col width="13%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@ -760,23 +760,38 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-09-28</td>
-<td align="center">A1</td>
+<td align="center">2011-09-24</td>
+<td align="center">D2</td>
 <td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</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">R</td>
 <td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center"><em>Streptococcus</em></td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2011-07-24</td>
+<td align="center">W2</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">S</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"><em>Escherichia</em></td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="center">2012-09-28</td>
-<td align="center">J9</td>
+<tr class="odd">
+<td align="center">2011-03-17</td>
+<td align="center">D5</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
@ -785,67 +800,52 @@ Longest: 24</p>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
+<td align="center"><em>Streptococcus</em></td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="center">2015-04-29</td>
-<td align="center">W8</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<tr class="even">
+<td align="center">2011-06-13</td>
+<td align="center">X10</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STRPT_PNMN</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-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">Gram-positive</td>
+<td align="center"><em>Streptococcus</em></td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="center">2017-02-20</td>
-<td align="center">P2</td>
-<td align="center">Hospital C</td>
+<tr class="odd">
+<td align="center">2010-04-12</td>
+<td align="center">Z4</td>
+<td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</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">F</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
+<td align="center"><em>Streptococcus</em></td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="center">2010-09-14</td>
-<td align="center">T8</td>
-<td align="center">Hospital A</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">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="center">2011-01-26</td>
-<td align="center">K8</td>
+<td align="center">2017-02-25</td>
+<td align="center">B5</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">I</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
+<td align="center"><em>Streptococcus</em></td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
@ -868,52 +868,52 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">E. coli</td>
+<td align="center"><em>E. coli</em></td>
 <td align="center">AMX</td>
-<td align="center">2209</td>
-<td align="center">123</td>
-<td align="center">2329</td>
-<td align="center">4661</td>
+<td align="center">2180</td>
+<td align="center">145</td>
+<td align="center">2339</td>
+<td align="center">4664</td>
 </tr>
 <tr class="even">
-<td align="center">E. coli</td>
+<td align="center"><em>E. coli</em></td>
 <td align="center">AMC</td>
-<td align="center">3406</td>
-<td align="center">165</td>
-<td align="center">1090</td>
-<td align="center">4661</td>
+<td align="center">3360</td>
+<td align="center">176</td>
+<td align="center">1128</td>
+<td align="center">4664</td>
 </tr>
 <tr class="odd">
-<td align="center">E. coli</td>
+<td align="center"><em>E. coli</em></td>
 <td align="center">CIP</td>
-<td align="center">3416</td>
+<td align="center">3405</td>
 <td align="center">0</td>
-<td align="center">1245</td>
-<td align="center">4661</td>
+<td align="center">1259</td>
+<td align="center">4664</td>
 </tr>
 <tr class="even">
-<td align="center">E. coli</td>
+<td align="center"><em>E. coli</em></td>
 <td align="center">GEN</td>
-<td align="center">4086</td>
+<td align="center">4078</td>
 <td align="center">0</td>
-<td align="center">575</td>
-<td align="center">4661</td>
+<td align="center">586</td>
+<td align="center">4664</td>
 </tr>
 <tr class="odd">
-<td align="center">K. pneumoniae</td>
+<td align="center"><em>K. pneumoniae</em></td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1199</td>
-<td align="center">1199</td>
+<td align="center">1169</td>
+<td align="center">1169</td>
 </tr>
 <tr class="even">
-<td align="center">K. pneumoniae</td>
+<td align="center"><em>K. pneumoniae</em></td>
 <td align="center">AMC</td>
-<td align="center">933</td>
-<td align="center">39</td>
-<td align="center">227</td>
-<td align="center">1199</td>
+<td align="center">924</td>
+<td align="center">49</td>
+<td align="center">196</td>
+<td align="center">1169</td>
 </tr>
 </tbody>
 </table>
@ -934,36 +934,36 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">E. coli</td>
+<td align="center"><em>E. coli</em></td>
 <td align="center">GEN</td>
-<td align="center">4086</td>
+<td align="center">4078</td>
 <td align="center">0</td>
-<td align="center">575</td>
-<td align="center">4661</td>
+<td align="center">586</td>
+<td align="center">4664</td>
 </tr>
 <tr class="even">
-<td align="center">K. pneumoniae</td>
+<td align="center"><em>K. pneumoniae</em></td>
 <td align="center">GEN</td>
-<td align="center">1068</td>
+<td align="center">1042</td>
 <td align="center">0</td>
-<td align="center">131</td>
-<td align="center">1199</td>
+<td align="center">127</td>
+<td align="center">1169</td>
 </tr>
 <tr class="odd">
-<td align="center">S. aureus</td>
+<td align="center"><em>S. aureus</em></td>
 <td align="center">GEN</td>
-<td align="center">2407</td>
+<td align="center">2440</td>
 <td align="center">0</td>
 <td align="center">290</td>
-<td align="center">2697</td>
+<td align="center">2730</td>
 </tr>
 <tr class="even">
-<td align="center">S. pneumoniae</td>
+<td align="center"><em>S. pneumoniae</em></td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2145</td>
-<td align="center">2145</td>
+<td align="center">2093</td>
+<td align="center">2093</td>
 </tr>
 </tbody>
 </table>
@ -977,7 +977,7 @@ 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="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
-<span class="co"># [1] 0.5418613</span></code></pre></div>
+<span class="co"># [1] 0.5442005</span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@ -991,19 +991,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5276730</td>
+<td align="center">0.5512301</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5422819</td>
+<td align="center">0.5383792</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5609308</td>
+<td align="center">0.5587121</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5475970</td>
+<td align="center">0.5329877</td>
 </tr>
 </tbody>
 </table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5276730</td>
-<td align="center">3180</td>
+<td align="center">0.5512301</td>
+<td align="center">3211</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5422819</td>
-<td align="center">3725</td>
+<td align="center">0.5383792</td>
+<td align="center">3739</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5609308</td>
-<td align="center">1633</td>
+<td align="center">0.5587121</td>
+<td align="center">1584</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5475970</td>
-<td align="center">2164</td>
+<td align="center">0.5329877</td>
+<td align="center">2122</td>
 </tr>
 </tbody>
 </table>
@ -1058,28 +1058,28 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">Escherichia</td>
-<td align="center">0.7661446</td>
-<td align="center">0.8766359</td>
-<td align="center">0.9759708</td>
+<td align="center"><em>Escherichia</em></td>
+<td align="center">0.7581475</td>
+<td align="center">0.8743568</td>
+<td align="center">0.9762007</td>
 </tr>
 <tr class="even">
-<td align="center">Klebsiella</td>
-<td align="center">0.8106756</td>
-<td align="center">0.8907423</td>
-<td align="center">0.9833194</td>
+<td align="center"><em>Klebsiella</em></td>
+<td align="center">0.8323353</td>
+<td align="center">0.8913601</td>
+<td align="center">0.9760479</td>
 </tr>
 <tr class="odd">
-<td align="center">Staphylococcus</td>
-<td align="center">0.7942158</td>
-<td align="center">0.8924731</td>
-<td align="center">0.9818317</td>
+<td align="center"><em>Staphylococcus</em></td>
+<td align="center">0.7945055</td>
+<td align="center">0.8937729</td>
+<td align="center">0.9831502</td>
 </tr>
 <tr class="even">
-<td align="center">Streptococcus</td>
-<td align="center">0.5501166</td>
+<td align="center"><em>Streptococcus</em></td>
+<td align="center">0.5351171</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5501166</td>
+<td align="center">0.5351171</td>
 </tr>
 </tbody>
 </table>
@ -1104,23 +1104,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">52.8%</td>
-<td align="right">26.0%</td>
+<td align="right">55.1%</td>
+<td align="right">27.0%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">54.2%</td>
-<td align="right">26.5%</td>
+<td align="right">53.8%</td>
+<td align="right">26.2%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">56.1%</td>
-<td align="right">26.7%</td>
+<td align="right">55.9%</td>
+<td align="right">27.7%</td>
 </tr>
 <tr class="even">