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dr. M.S. (Matthijs) Berends 4 years ago
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  1. 2
      DESCRIPTION
  2. 1
      NEWS.md
  3. 21
      R/resistance_predict.R
  4. 11
      R/rsi.R
  5. 2
      README.md
  6. 428
      docs/articles/AMR.html
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  11. 4
      docs/articles/EUCAST.html
  12. 4
      docs/articles/G_test.html
  13. 162
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  19. 4
      docs/articles/ab_property.html
  20. 4
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  21. 44
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  22. 4
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  25. 10
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  26. 2
      docs/index.html
  27. 1
      docs/news/index.html
  28. 2
      docs/reference/AMR-deprecated.html
  29. 2
      docs/reference/AMR.html
  30. 2
      docs/reference/ITIS.html
  31. 2
      docs/reference/WHOCC.html
  32. 2
      docs/reference/WHONET.html
  33. 2
      docs/reference/abname.html
  34. 2
      docs/reference/age.html
  35. 2
      docs/reference/age_groups.html
  36. 2
      docs/reference/antibiotics.html
  37. 2
      docs/reference/as.atc.html
  38. 2
      docs/reference/as.mic.html
  39. 2
      docs/reference/as.mo.html
  40. 2
      docs/reference/as.rsi.html
  41. 2
      docs/reference/atc_online.html
  42. 2
      docs/reference/atc_property.html
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      docs/reference/availability.html
  44. 2
      docs/reference/count.html
  45. 2
      docs/reference/eucast_rules.html
  46. 2
      docs/reference/first_isolate.html
  47. 2
      docs/reference/freq.html
  48. 2
      docs/reference/g.test.html
  49. 2
      docs/reference/get_locale.html
  50. 2
      docs/reference/ggplot_rsi.html
  51. 2
      docs/reference/guess_ab_col.html
  52. 2
      docs/reference/join.html
  53. 2
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  60. 2
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  63. 2
      docs/reference/resistance_predict.html
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  65. 2
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  66. 2
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  67. 2
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  68. 2
      index.md
  69. 10
      man/resistance_predict.Rd
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  73. 92
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2
DESCRIPTION
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@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 0.5.0.9017
Date: 2019-02-08
Date: 2019-02-09
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

1
NEWS.md
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@ -87,6 +87,7 @@ @@ -87,6 +87,7 @@
* New colours for `scale_rsi_colours()`
* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
* Small text updates to summaries of class `rsi` and `mic`
* Function `as.rsi()` now gives a warning when inputting MIC values
* Frequency tables (`freq()` function):
* Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
```r

21
R/resistance_predict.R
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@ -30,11 +30,17 @@ @@ -30,11 +30,17 @@
#' @param year_max highest year to use in the prediction model, defaults to 10 years after today
#' @param year_every unit of sequence between lowest year found in the data and \code{year_max}
#' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
#' @param model the statistical model of choice. Valid values are \code{"binomial"} (or \code{"binom"} or \code{"logit"}) or \code{"loglin"} (or \code{"poisson"}) or \code{"linear"} (or \code{"lin"}).
#' @param model the statistical model of choice. Defaults to a generalised linear regression model with binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See Details for valid options.
#' @param I_as_R a logical to indicate whether values \code{I} should be treated as \code{R}
#' @param preserve_measurements a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be \code{NA}.
#' @param info a logical to indicate whether textual analysis should be printed with the name and \code{\link{summary}} of the statistical model.
#' @param main title of the plot
#' @details Valid options for the statistical model are:
#' \itemize{
#' \item{\code{"binomial"} or \code{"binom"} or \code{"logit"}: a generalised linear regression model with binomial distribution}
#' \item{\code{"loglin"} or \code{"poisson"}: a generalised log-linear regression model with poisson distribution}
#' \item{\code{"lin"} or \code{"linear"}: a linear regression model}
#' }
#' @return \code{data.frame} with extra class \code{"resistance_predict"} with columns:
#' \itemize{
#' \item{\code{year}}
@ -306,7 +312,9 @@ plot.resistance_predict <- function(x, main = paste("Resistance prediction of", @@ -306,7 +312,9 @@ plot.resistance_predict <- function(x, main = paste("Resistance prediction of",
ylab = paste0("Percentage (", ylab, ")"),
xlab = "Year",
main = main,
sub = paste0("(model: ", attributes(x)$model_title, ")"))
sub = paste0("(n = ", sum(x$observations, na.rm = TRUE),
", model: ", attributes(x)$model_title, ")"),
cex.sub = 0.75)
axis(side = 2, at = seq(0, 1, 0.1), labels = paste0(0:10 * 10, "%"))
@ -332,12 +340,13 @@ ggplot_rsi_predict <- function(x, main = paste("Resistance prediction of", attri @@ -332,12 +340,13 @@ ggplot_rsi_predict <- function(x, main = paste("Resistance prediction of", attri
}
suppressWarnings(
ggplot2::ggplot(x, ggplot2::aes(x = year, y = value)) +
ggplot2::geom_col() +
ggplot2::geom_errorbar(ggplot2::aes(ymin = se_min, ymax = se_max)) +
scale_y_percent() +
ggplot2::geom_point(size = 2) +
ggplot2::geom_errorbar(ggplot2::aes(ymin = se_min, ymax = se_max), na.rm = TRUE, width = 0.5) +
scale_y_percent(limits = c(0, 1)) +
ggplot2::labs(title = main,
y = paste0("Percentage (", ylab, ")"),
x = "Year",
caption = paste0("(model: ", attributes(x)$model_title, ")"))
caption = paste0("(n = ", sum(x$observations, na.rm = TRUE),
", model: ", attributes(x)$model_title, ")"))
)
}

11
R/rsi.R
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@ -64,6 +64,9 @@ as.rsi <- function(x) { @@ -64,6 +64,9 @@ as.rsi <- function(x) {
} else if (identical(levels(x), c("S", "I", "R"))) {
structure(x, class = c('rsi', 'ordered', 'factor'))
} else {
if (mic_like(x) > 0.5) {
warning("`as.rsi` is intended to clean antimicrobial interpretations - not to interpret MIC values.", call. = FALSE)
}
x <- x %>% unlist()
x.bak <- x
@ -103,6 +106,14 @@ as.rsi <- function(x) { @@ -103,6 +106,14 @@ as.rsi <- function(x) {
}
}
mic_like <- function(x) {
mic <- x %>%
gsub("[^0-9.,]+", "", .) %>%
unique()
mic_valid <- suppressWarnings(as.mic(mic))
sum(!is.na(mic_valid)) / length(mic)
}
#' @rdname as.rsi
#' @export
is.rsi <- function(x) {

2
README.md
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@ -54,7 +54,7 @@ This is the latest **development version**. Although it may contain bugfixes and @@ -54,7 +54,7 @@ This is the latest **development version**. Although it may contain bugfixes and
Development Test | Result | Reference
--- | :---: | ---
All functions checked on Linux | [![pipeline status](https://gitlab.com/msberends/AMR/badges/master/pipeline.svg)](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR/pipelines)
All functions checked on Linux | [![pipeline status](https://gitlab.com/msberends/AMR/badges/master/pipeline.svg)](https://gitlab.com/msberends/AMR/commits/master) | GitLab CI [[ref 1]](https://gitlab.com/msberends/AMR)
All functions checked on Windows | [![AppVeyor_Build](https://ci.appveyor.com/api/projects/status/gitlab/msberends/AMR?branch=master&svg=true)](https://ci.appveyor.com/project/msberends/amr-svxon) | Appveyor Systems Inc. [[ref 2]](https://ci.appveyor.com/project/msberends/amr-svxon)
Percentage of syntax lines checked | [![Code_Coverage](https://codecov.io/gl/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gl/msberends/AMR) | Codecov LLC [[ref 3]](https://codecov.io/gl/msberends/AMR)

428
docs/articles/AMR.html
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@ -40,7 +40,7 @@ @@ -40,7 +40,7 @@
</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="Released version">0.5.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
</span>
</div>
@ -185,7 +185,7 @@ @@ -185,7 +185,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 February 2019</h4>
<h4 class="date">09 February 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -194,7 +194,7 @@ @@ -194,7 +194,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 08 February 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 09 February 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@ @@ -210,21 +210,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-02-08</td>
<td align="center">2019-02-09</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">2019-02-08</td>
<td align="center">2019-02-09</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">2019-02-08</td>
<td align="center">2019-02-09</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -313,54 +313,54 @@ @@ -313,54 +313,54 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-10-06</td>
<td align="center">F7</td>
<td align="center">2012-10-05</td>
<td align="center">F3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</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">2015-07-29</td>
<td align="center">T1</td>
<td align="center">2012-11-18</td>
<td align="center">X7</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">F</td>
</tr>
<tr class="odd">
<td align="center">2017-10-20</td>
<td align="center">P2</td>
<td align="center">2012-04-27</td>
<td align="center">K2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</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">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-02-07</td>
<td align="center">Z6</td>
<td align="center">2014-09-03</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-06-26</td>
<td align="center">V4</td>
<td align="center">2015-09-13</td>
<td align="center">R4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -368,15 +368,15 @@ @@ -368,15 +368,15 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-02-08</td>
<td align="center">S2</td>
<td align="center">2011-09-19</td>
<td align="center">D6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -396,8 +396,8 @@ @@ -396,8 +396,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------ -------- ----------- -------------
# 1 M 2,551 51.0% 2,551 51.0%
# 2 F 2,449 49.0% 5,000 100.0%</code></pre>
# 1 M 2,565 51.3% 2,565 51.3%
# 2 F 2,435 48.7% 5,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -428,10 +428,10 @@ @@ -428,10 +428,10 @@
<a class="sourceLine" id="cb14-19" data-line-number="19"><span class="co"># Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb14-20" data-line-number="20"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-21" data-line-number="21"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-22" data-line-number="22"><span class="co"># Table 1: Intrinsic resistance in Enterobacteriaceae (345 changes)</span></a>
<a class="sourceLine" id="cb14-22" data-line-number="22"><span class="co"># Table 1: Intrinsic resistance in Enterobacteriaceae (306 changes)</span></a>
<a class="sourceLine" id="cb14-23" data-line-number="23"><span class="co"># Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-24" data-line-number="24"><span class="co"># Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 4: Intrinsic resistance in Gram-positive bacteria (673 changes)</span></a>
<a class="sourceLine" id="cb14-25" data-line-number="25"><span class="co"># Table 4: Intrinsic resistance in Gram-positive bacteria (681 changes)</span></a>
<a class="sourceLine" id="cb14-26" data-line-number="26"><span class="co"># Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-27" data-line-number="27"><span class="co"># Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-28" data-line-number="28"><span class="co"># Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
@ -447,9 +447,9 @@ @@ -447,9 +447,9 @@
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># =&gt; EUCAST rules affected 1,814 out of 5,000 rows</span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># =&gt; EUCAST rules affected 1,796 out of 5,000 rows</span></a>
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># -&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-43" data-line-number="43"><span class="co"># -&gt; changed 1,018 test results (0 to S; 0 to I; 1,018 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" data-line-number="43"><span class="co"># -&gt; changed 987 test results (0 to S; 0 to I; 987 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -474,8 +474,8 @@ @@ -474,8 +474,8 @@
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 2,939 first isolates (58.8% of total)</span></a></code></pre></div>
<p>So only 58.8% 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>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 2,948 first isolates (59.0% of total)</span></a></code></pre></div>
<p>So only 59% 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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -501,76 +501,76 @@ @@ -501,76 +501,76 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-03</td>
<td align="center">C3</td>
<td align="center">2010-05-12</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-10-31</td>
<td align="center">C3</td>
<td align="center">2010-05-12</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-11-12</td>
<td align="center">C3</td>
<td align="center">2010-07-18</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-21</td>
<td align="center">C3</td>
<td align="center">2011-01-18</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-12-01</td>
<td align="center">C3</td>
<td align="center">2011-11-20</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-10-22</td>
<td align="center">C3</td>
<td align="center">2011-12-03</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2012-03-22</td>
<td align="center">C3</td>
<td align="center">2012-09-09</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</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>
@ -578,40 +578,40 @@ @@ -578,40 +578,40 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2012-05-14</td>
<td align="center">C3</td>
<td align="center">2013-01-24</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<td align="center">2013-04-25</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2013-06-13</td>
<td align="center">C3</td>
<td align="center">2014-02-01</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Only 3 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 4 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -622,7 +622,7 @@ @@ -622,7 +622,7 @@
<a class="sourceLine" id="cb19-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 4,387 first weighted isolates (87.7% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 4,405 first weighted isolates (88.1% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -639,11 +639,11 @@ @@ -639,11 +639,11 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-03</td>
<td align="center">C3</td>
<td align="center">2010-05-12</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
@ -651,119 +651,119 @@ @@ -651,119 +651,119 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-10-31</td>
<td align="center">C3</td>
<td align="center">2010-05-12</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-11-12</td>
<td align="center">C3</td>
<td align="center">2010-07-18</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-11-21</td>
<td align="center">C3</td>
<td align="center">2011-01-18</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-12-01</td>
<td align="center">C3</td>
<td align="center">2011-11-20</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-10-22</td>
<td align="center">C3</td>
<td align="center">2011-12-03</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2012-03-22</td>
<td align="center">C3</td>
<td align="center">2012-09-09</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</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="even">
<td align="center">8</td>
<td align="center">2012-05-14</td>
<td align="center">C3</td>
<td align="center">2013-01-24</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-10-26</td>
<td align="center">C3</td>
<td align="center">2013-04-25</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2013-06-13</td>
<td align="center">C3</td>
<td align="center">2014-02-01</td>
<td align="center">B4</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 3, now 9 isolates are flagged. In total, 87.7% of all isolates are marked ‘first weighted’ - 29% 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 4, now 9 isolates are flagged. In total, 88.1% of all isolates are marked ‘first weighted’ - 29.1% 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>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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 4,387 isolates for analysis.</p>
<p>So we end up with 4,405 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -788,99 +788,99 @@ @@ -788,99 +788,99 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2010-10-06</td>
<td align="center">F7</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td>2</td>
<td align="center">2012-11-18</td>
<td align="center">X7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</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>
<tr class="even">
<td>2</td>
<td align="center">2015-07-29</td>
<td align="center">T1</td>
<td align="center">Hospital A</td>
<td>3</td>
<td align="center">2012-04-27</td>
<td align="center">K2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</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>3</td>
<td align="center">2017-10-20</td>
<td align="center">P2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td>4</td>
<td align="center">2014-09-03</td>
<td align="center">M6</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPTC_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">R</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>4</td>
<td align="center">2010-02-07</td>
<td align="center">Z6</td>
<td>5</td>
<td align="center">2015-09-13</td>
<td align="center">R4</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>
<tr class="odd">
<td>6</td>
<td align="center">2016-02-08</td>
<td align="center">S2</td>
<td align="center">2011-09-19</td>
<td align="center">D6</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">B_STRPTC_PNE</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</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">R</td>
<td align="center">M</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>9</td>
<td align="center">2016-10-31</td>
<td align="center">H3</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<td>7</td>
<td align="center">2013-01-13</td>
<td align="center">Q3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPTC_PNE</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">R</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -900,9 +900,9 @@ @@ -900,9 +900,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (4,387 x 13)</strong><br>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (4,405 x 13)</strong><br>
Columns: 2<br>
Length: 4,387 (of which NA: 0 = 0.00%)<br>
Length: 4,405 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -919,33 +919,33 @@ Longest: 24</p> @@ -919,33 +919,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">2,129</td>
<td align="right">48.5%</td>
<td align="right">2,129</td>
<td align="right">48.5%</td>
<td align="right">2,160</td>
<td align="right">49.0%</td>
<td align="right">2,160</td>
<td align="right">49.0%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">1,098</td>
<td align="right">25.0%</td>
<td align="right">3,227</td>
<td align="right">73.6%</td>
<td align="right">1,109</td>
<td align="right">25.2%</td>
<td align="right">3,269</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">688</td>
<td align="right">690</td>
<td align="right">15.7%</td>
<td align="right">3,915</td>
<td align="right">89.2%</td>
<td align="right">3,959</td>
<td align="right">89.9%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">472</td>
<td align="right">10.8%</td>
<td align="right">4,387</td>
<td align="right">446</td>
<td align="right">10.1%</td>
<td align="right">4,405</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -956,7 +956,7 @@ Longest: 24</p> @@ -956,7 +956,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code>portion_R</code>, <code>portion_RI</code>, <code>portion_I</code>, <code>portion_IS</code> and <code>portion_S</code> can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_IR</a></span>(amox)</a>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4700251</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4719637</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -969,19 +969,19 @@ Longest: 24</p> @@ -969,19 +969,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4544765</td>
<td align="center">0.4711316</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4920107</td>
<td align="center">0.4910714</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4686567</td>
<td align="center">0.4597701</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4570792</td>
<td align="center">0.4488698</td>
</tr>
</tbody>
</table>
@ -999,23 +999,23 @@ Longest: 24</p> @@ -999,23 +999,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4544765</td>
<td align="center">1318</td>
<td align="center">0.4711316</td>
<td align="center">1299</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4920107</td>
<td align="center">1502</td>
<td align="center">0.4910714</td>
<td align="center">1568</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4686567</td>
<td align="center">670</td>
<td align="center">0.4597701</td>
<td align="center">609</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4570792</td>
<td align="center">897</td>
<td align="center">0.4488698</td>
<td align="center">929</td>
</tr>
</tbody>
</table>
@ -1035,27 +1035,27 @@ Longest: 24</p> @@ -1035,27 +1035,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7491780</td>
<td align="center">0.9074683</td>
<td align="center">0.9798027</td>
<td align="center">0.7407407</td>
<td align="center">0.9000000</td>
<td align="center">0.9763889</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7521186</td>
<td align="center">0.9067797</td>
<td align="center">0.9745763</td>
<td align="center">0.7533632</td>
<td align="center">0.9147982</td>
<td align="center">0.9843049</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7349727</td>
<td align="center">0.9171220</td>
<td align="center">0.9708561</td>
<td align="center">0.7303877</td>
<td align="center">0.9305681</td>
<td align="center">0.9819657</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7398256</td>
<td align="center">0.7173913</td>
<td align="center">0.0000000</td>
<td align="center">0.7398256</td>
<td align="center">0.7173913</td>
</tr>
</tbody>
</table>

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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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</span>
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<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 February 2019</h4>
<h4 class="date">09 February 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

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<h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 February 2019</h4>
<h4 class="date">09 February 2019</h4>
<div class="hidden name"><code>G_test.Rmd</code></div>