P281424
/
AMR
mirror of https://github.com/msberends/AMR
1
0
Fork 0
Code Releases Activity

(v1.0.1) v 1.0.1

Browse Source
v1.8.2 v1.0.1
dr. M.S. (Matthijs) Berends 3 years ago
parent 0d5e78b2cf
commit f444c24ed3
69 changed files with 709 additions and 978 deletions
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Show Stats Download Patch File Download Diff File
  1. 2
      DESCRIPTION
  2. 7
      NEWS.md
  3. 2
      docs/404.html
  4. 2
      docs/LICENSE-text.html
  5. 450
      docs/articles/AMR.html
  6. BIN
      docs/articles/AMR_files/figure-html/plot 1-1.png
  7. BIN
      docs/articles/AMR_files/figure-html/plot 3-1.png
  8. BIN
      docs/articles/AMR_files/figure-html/plot 4-1.png
  9. BIN
      docs/articles/AMR_files/figure-html/plot 5-1.png
  10. 4
      docs/articles/EUCAST.html
  11. 208
      docs/articles/MDR.html
  12. 233
      docs/articles/SPSS.html
  13. 79
      docs/articles/WHONET.html
  14. 315
      docs/articles/benchmarks.html
  15. BIN
      docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
  16. BIN
      docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png
  17. 2
      docs/articles/index.html
  18. 208
      docs/articles/resistance_predict.html
  19. 2
      docs/authors.html
  20. 2
      docs/index.html
  21. 17
      docs/news/index.html
  22. 2
      docs/reference/AMR-deprecated.html
  23. 2
      docs/reference/AMR.html
  24. 2
      docs/reference/WHOCC.html
  25. 2
      docs/reference/WHONET.html
  26. 2
      docs/reference/ab_property.html
  27. 2
      docs/reference/age.html
  28. 2
      docs/reference/age_groups.html
  29. 2
      docs/reference/antibiotics.html
  30. 2
      docs/reference/as.ab.html
  31. 2
      docs/reference/as.disk.html
  32. 2
      docs/reference/as.mic.html
  33. 2
      docs/reference/as.mo.html
  34. 2
      docs/reference/as.rsi.html
  35. 2
      docs/reference/atc_online.html
  36. 2
      docs/reference/availability.html
  37. 2
      docs/reference/bug_drug_combinations.html
  38. 2
      docs/reference/catalogue_of_life.html
  39. 2
      docs/reference/catalogue_of_life_version.html
  40. 2
      docs/reference/count.html
  41. 2
      docs/reference/eucast_rules.html
  42. 2
      docs/reference/example_isolates.html
  43. 2
      docs/reference/example_isolates_unclean.html
  44. 2
      docs/reference/extended-functions.html
  45. 2
      docs/reference/filter_ab_class.html
  46. 2
      docs/reference/first_isolate.html
  47. 2
      docs/reference/g.test.html
  48. 2
      docs/reference/ggplot_rsi.html
  49. 2
      docs/reference/guess_ab_col.html
  50. 2
      docs/reference/index.html
  51. 2
      docs/reference/join.html
  52. 2
      docs/reference/key_antibiotics.html
  53. 2
      docs/reference/kurtosis.html
  54. 31
      docs/reference/lifecycle.html
  55. 2
      docs/reference/like.html
  56. 2
      docs/reference/mdro.html
  57. 2
      docs/reference/microorganisms.codes.html
  58. 2
      docs/reference/microorganisms.html
  59. 2
      docs/reference/microorganisms.old.html
  60. 2
      docs/reference/mo_property.html
  61. 2
      docs/reference/mo_source.html
  62. 2
      docs/reference/p_symbol.html
  63. 2
      docs/reference/proportion.html
  64. 2
      docs/reference/read.4D.html
  65. 31
      docs/reference/reexports.html
  66. 2
      docs/reference/resistance_predict.html
  67. 2
      docs/reference/rsi_translation.html
  68. 2
      docs/reference/skewness.html
  69. 2
      docs/reference/translate.html

2
DESCRIPTION
Unescape View File

@ -1,5 +1,5 @@
Package: AMR
Version: 1.0.0.9007
Version: 1.0.1
Date: 2020-02-22
Title: Antimicrobial Resistance Analysis
Authors@R: c(

7
NEWS.md
Unescape View File

@ -1,9 +1,8 @@
# AMR 1.0.0.9007
## <small>Last updated: 22-Feb-2020</small>
# AMR 1.0.1
### Changed
* Fixed floating point error for some MIC compa in EUCAST 2020 guideline
* Interpretation from MIC values to R/SI can now be used with `mutate_at()` of the dplyr package:
* Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
* Interpretation from MIC values (and disk zones) to R/SI can now be used with `mutate_at()` of the `dplyr` package:
```r
yourdata %>%
mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli")

2
docs/404.html
Unescape View File

@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>

2
docs/LICENSE-text.html
Unescape View File

@ -78,7 +78,7 @@
</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">1.0.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>

450
docs/articles/AMR.html
Unescape View File

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>
@ -179,7 +179,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 February 2020</h4>
<h4 class="date">23 February 2020</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -188,7 +188,7 @@
<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 20 February 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 23 February 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -219,21 +219,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-02-20</td>
<td align="center">2020-02-23</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">2020-02-20</td>
<td align="center">2020-02-23</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">2020-02-20</td>
<td align="center">2020-02-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -328,10 +328,10 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2014-10-31</td>
<td align="center">B4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -339,59 +339,59 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-08-23</td>
<td align="center">J5</td>
<td align="center">2012-02-24</td>
<td align="center">E10</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-06-20</td>
<td align="center">S1</td>
<td align="center">2017-11-04</td>
<td align="center">G1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-05-08</td>
<td align="center">J3</td>
<td align="center">Hospital A</td>
<td align="center">2011-10-08</td>
<td align="center">V4</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">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-12-28</td>
<td align="center">T8</td>
<td align="center">2016-02-16</td>
<td align="center">K6</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-11-05</td>
<td align="center">G9</td>
<td align="center">2014-05-28</td>
<td align="center">N6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -423,16 +423,16 @@ Unique: 2</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,402</td>
<td align="right">52.01%</td>
<td align="right">10,402</td>
<td align="right">52.01%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,598</td>
<td align="right">47.99%</td>
<td align="right">9,639</td>
<td align="right">48.20%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -447,65 +447,7 @@ Unique: 2</p>
<span id="cb12-2"><a href="#cb12-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMX<span class="op">:</span>GEN), as.rsi)</span></code></pre></div>
<p>Finally, we will apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Because the amoxicillin (column <code>AMX</code>) and amoxicillin/clavulanic acid (column <code>AMC</code>) in our data were generated randomly, some rows will undoubtedly contain AMX = S and AMC = R, which is technically impossible. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</span>
<span id="cb13-2"><a href="#cb13-2"></a><span class="co"># </span></span>
<span id="cb13-3"><a href="#cb13-3"></a><span class="co"># Other rules by this AMR package</span></span>
<span id="cb13-4"><a href="#cb13-4"></a><span class="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></span>
<span id="cb13-5"><a href="#cb13-5"></a><span class="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></span>
<span id="cb13-6"><a href="#cb13-6"></a><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,986 values changed)</span></span>
<span id="cb13-7"><a href="#cb13-7"></a><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (157 values changed)</span></span>
<span id="cb13-8"><a href="#cb13-8"></a><span class="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></span>
<span id="cb13-9"><a href="#cb13-9"></a><span class="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></span>
<span id="cb13-10"><a href="#cb13-10"></a><span class="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></span>
<span id="cb13-11"><a href="#cb13-11"></a><span class="co"># Non-EUCAST: set trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></span>
<span id="cb13-12"><a href="#cb13-12"></a><span class="co"># </span></span>
<span id="cb13-13"><a href="#cb13-13"></a><span class="co"># ----</span></span>
<span id="cb13-14"><a href="#cb13-14"></a><span class="co"># Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)</span></span>
<span id="cb13-15"><a href="#cb13-15"></a><span class="co"># http://eucast.org/</span></span>
<span id="cb13-16"><a href="#cb13-16"></a><span class="co"># </span></span>
<span id="cb13-17"><a href="#cb13-17"></a><span class="co"># EUCAST Clinical Breakpoints (v10.0, 2020)</span></span>
<span id="cb13-18"><a href="#cb13-18"></a><span class="co"># Aerococcus sanguinicola (no changes)</span></span>
<span id="cb13-19"><a href="#cb13-19"></a><span class="co"># Aerococcus urinae (no changes)</span></span>
<span id="cb13-20"><a href="#cb13-20"></a><span class="co"># Anaerobic Gram-negatives (no changes)</span></span>
<span id="cb13-21"><a href="#cb13-21"></a><span class="co"># Anaerobic Gram-positives (no changes)</span></span>
<span id="cb13-22"><a href="#cb13-22"></a><span class="co"># Burkholderia pseudomallei (no changes)</span></span>
<span id="cb13-23"><a href="#cb13-23"></a><span class="co"># Campylobacter coli (no changes)</span></span>
<span id="cb13-24"><a href="#cb13-24"></a><span class="co"># Campylobacter jejuni (no changes)</span></span>
<span id="cb13-25"><a href="#cb13-25"></a><span class="co"># Enterobacterales (Order) (no changes)</span></span>
<span id="cb13-26"><a href="#cb13-26"></a><span class="co"># Enterococcus (no changes)</span></span>
<span id="cb13-27"><a href="#cb13-27"></a><span class="co"># Haemophilus influenzae (no changes)</span></span>
<span id="cb13-28"><a href="#cb13-28"></a><span class="co"># Kingella kingae (no changes)</span></span>
<span id="cb13-29"><a href="#cb13-29"></a><span class="co"># Moraxella catarrhalis (no changes)</span></span>
<span id="cb13-30"><a href="#cb13-30"></a><span class="co"># Pasteurella multocida (no changes)</span></span>
<span id="cb13-31"><a href="#cb13-31"></a><span class="co"># Staphylococcus (no changes)</span></span>
<span id="cb13-32"><a href="#cb13-32"></a><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></span>
<span id="cb13-33"><a href="#cb13-33"></a><span class="co"># Streptococcus pneumoniae (1,017 values changed)</span></span>
<span id="cb13-34"><a href="#cb13-34"></a><span class="co"># Viridans group streptococci (no changes)</span></span>
<span id="cb13-35"><a href="#cb13-35"></a><span class="co"># </span></span>
<span id="cb13-36"><a href="#cb13-36"></a><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></span>
<span id="cb13-37"><a href="#cb13-37"></a><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,297 values changed)</span></span>
<span id="cb13-38"><a href="#cb13-38"></a><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></span>
<span id="cb13-39"><a href="#cb13-39"></a><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></span>
<span id="cb13-40"><a href="#cb13-40"></a><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,752 values changed)</span></span>
<span id="cb13-41"><a href="#cb13-41"></a><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></span>
<span id="cb13-42"><a href="#cb13-42"></a><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></span>
<span id="cb13-43"><a href="#cb13-43"></a><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></span>
<span id="cb13-44"><a href="#cb13-44"></a><span class="co"># Table 12: Interpretive rules for aminoglycosides (no changes)</span></span>
<span id="cb13-45"><a href="#cb13-45"></a><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></span>
<span id="cb13-46"><a href="#cb13-46"></a><span class="co"># </span></span>
<span id="cb13-47"><a href="#cb13-47"></a><span class="co"># -------------------------------------------------------------------------------</span></span>
<span id="cb13-48"><a href="#cb13-48"></a><span class="co"># EUCAST rules affected 6,502 out of 20,000 rows, making a total of 8,209 edits</span></span>
<span id="cb13-49"><a href="#cb13-49"></a><span class="co"># =&gt; added 0 test results</span></span>
<span id="cb13-50"><a href="#cb13-50"></a><span class="co"># </span></span>
<span id="cb13-51"><a href="#cb13-51"></a><span class="co"># =&gt; changed 8,209 test results</span></span>
<span id="cb13-52"><a href="#cb13-52"></a><span class="co"># - 124 test results changed from S to I</span></span>
<span id="cb13-53"><a href="#cb13-53"></a><span class="co"># - 4,743 test results changed from S to R</span></span>
<span id="cb13-54"><a href="#cb13-54"></a><span class="co"># - 1,209 test results changed from I to S</span></span>
<span id="cb13-55"><a href="#cb13-55"></a><span class="co"># - 356 test results changed from I to R</span></span>
<span id="cb13-56"><a href="#cb13-56"></a><span class="co"># - 1,777 test results changed from R to S</span></span>
<span id="cb13-57"><a href="#cb13-57"></a><span class="co"># -------------------------------------------------------------------------------</span></span>
<span id="cb13-58"><a href="#cb13-58"></a><span class="co"># </span></span>
<span id="cb13-59"><a href="#cb13-59"></a><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></span></code></pre></div>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</span></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -529,9 +471,8 @@ Unique: 2</p>
<span id="cb15-2"><a href="#cb15-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">first =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(.))</span>
<span id="cb15-3"><a href="#cb15-3"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></span>
<span id="cb15-4"><a href="#cb15-4"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span>
<span id="cb15-5"><a href="#cb15-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span>
<span id="cb15-6"><a href="#cb15-6"></a><span class="co"># =&gt; Found 5,695 first isolates (28.5% of total)</span></span></code></pre></div>
<p>So only 28.5% 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>
<span id="cb15-5"><a href="#cb15-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span></code></pre></div>
<p>So only 28.4% 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="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a>data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb16-2"><a href="#cb16-2"></a><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>)</span></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>
@ -541,7 +482,7 @@ Unique: 2</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 N2, 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 Q2, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -557,8 +498,8 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-09</td>
<td align="center">N2</td>
<td align="center">2010-02-26</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -568,98 +509,98 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-02</td>
<td align="center">N2</td>
<td align="center">2010-03-25</td>
<td align="center">Q2</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">N2</td>
<td align="center">2010-05-23</td>
<td align="center">Q2</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>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-19</td>
<td align="center">N2</td>
<td align="center">2010-05-24</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-08</td>
<td align="center">N2</td>
<td align="center">2010-09-08</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-09</td>
<td align="center">N2</td>
<td align="center">2011-03-19</td>
<td align="center">Q2</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-02</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-05</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-06-19</td>
<td align="center">N2</td>
<td align="center">2011-11-13</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-07-29</td>
<td align="center">N2</td>
<td align="center">2011-11-28</td>
<td align="center">Q2</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>
@ -676,9 +617,7 @@ Unique: 2</p>
<span id="cb18-5"><a href="#cb18-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></span>
<span id="cb18-6"><a href="#cb18-6"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span>
<span id="cb18-7"><a href="#cb18-7"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span>
<span id="cb18-8"><a href="#cb18-8"></a><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></span>
<span id="cb18-9"><a href="#cb18-9"></a><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></span>
<span id="cb18-10"><a href="#cb18-10"></a><span class="co"># =&gt; Found 15,096 first weighted isolates (75.5% of total)</span></span></code></pre></div>
<span id="cb18-8"><a href="#cb18-8"></a><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></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -695,8 +634,8 @@ Unique: 2</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-09</td>
<td align="center">N2</td>
<td align="center">2010-02-26</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -707,23 +646,23 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-02</td>
<td align="center">N2</td>
<td align="center">2010-03-25</td>
<td align="center">Q2</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-04-05</td>
<td align="center">N2</td>
<td align="center">2010-05-23</td>
<td align="center">Q2</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>
@ -731,11 +670,11 @@ Unique: 2</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-05-19</td>
<td align="center">N2</td>
<td align="center">2010-05-24</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -743,83 +682,83 @@ Unique: 2</p>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-08</td>
<td align="center">N2</td>
<td align="center">2010-09-08</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-09</td>
<td align="center">N2</td>
<td align="center">2011-03-19</td>
<td align="center">Q2</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">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-02</td>
<td align="center">Q2</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">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">8</td>
<td align="center">2011-05-26</td>
<td align="center">N2</td>
<td align="center">2011-04-05</td>
<td align="center">Q2</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-06-19</td>
<td align="center">N2</td>
<td align="center">2011-11-13</td>
<td align="center">Q2</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">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-07-29</td>
<td align="center">N2</td>
<td align="center">2011-11-28</td>
<td align="center">Q2</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>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 9 isolates are flagged. In total, 75.5% of all isolates are marked ‘first weighted’ - 47.0% 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 7 isolates are flagged. In total, 74.8% of all isolates are marked ‘first weighted’ - 46.4% 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="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a>data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</span></code></pre></div>
<p>So we end up with 15,096 isolates for analysis.</p>
<p>So we end up with 14,960 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb20-2"><a href="#cb20-2"></a><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://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</span></code></pre></div>
@ -827,7 +766,6 @@ Unique: 2</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(data_1st)</span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -844,30 +782,28 @@ Unique: 2</p>
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2014-10-31</td>
<td align="center">B4</td>
<td align="center">Hospital B</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">M</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>6</td>
<td align="center">2016-11-05</td>
<td align="center">G9</td>
<td align="center">Hospital C</td>
<td align="center">2012-02-24</td>
<td align="center">E10</td>
<td align="center">Hospital B</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -876,14 +812,13 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2016-05-20</td>
<td align="center">A10</td>
<td align="center">Hospital D</td>
<td align="center">2017-11-04</td>
<td align="center">G1</td>
<td align="center">Hospital B</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">M</td>
<td align="center">Gram-negative</td>
@ -892,10 +827,9 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2015-10-02</td>
<td align="center">R3</td>
<td align="center">Hospital C</td>
<td align="center">2011-10-08</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -908,35 +842,33 @@ Unique: 2</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>10</td>
<td align="center">2016-03-04</td>
<td align="center">B10</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">2016-02-16</td>
<td align="center">K6</td>
<td align="center">Hospital D</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">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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>11</td>
<td align="center">2013-09-10</td>
<td align="center">P4</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">2014-05-28</td>
<td align="center">N6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>
@ -958,8 +890,8 @@ Unique: 2</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,096<br>
Available: 15,096 (100%, NA: 0 = 0%)<br>
Length: 14,960<br>
Available: 14,960 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -976,33 +908,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,491</td>
<td align="right">49.62%</td>
<td align="right">7,491</td>
<td align="right">49.62%</td>
<td align="right">7,397</td>
<td align="right">49.45%</td>
<td align="right">7,397</td>
<td align="right">49.45%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,729</td>
<td align="right">24.70%</td>
<td align="right">11,220</td>
<td align="right">74.32%</td>
<td align="right">3,685</td>
<td align="right">24.63%</td>
<td align="right">11,082</td>
<td align="right">74.08%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,340</td>
<td align="right">15.50%</td>
<td align="right">13,560</td>
<td align="right">89.83%</td>
<td align="right">2,361</td>
<td align="right">15.78%</td>
<td align="right">13,443</td>
<td align="right">89.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,536</td>
<td align="right">10.17%</td>
<td align="right">15,096</td>
<td align="right">1,517</td>
<td align="right">10.14%</td>
<td align="right">14,960</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1014,7 +946,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</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="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</span>
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4681373</span></span></code></pre></div>
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4635695</span></span></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="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a>data_1st <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb25-2"><a href="#cb25-2"></a><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></span>
@ -1027,19 +959,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4648446</td>
<td align="center">0.4490022</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4689223</td>
<td align="center">0.4746786</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4656180</td>
<td align="center">0.4505104</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4734787</td>
<td align="center">0.4760039</td>
</tr>
</tbody>
</table>
@ -1057,23 +989,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4648446</td>
<td align="center">4537</td>
<td align="center">0.4490022</td>
<td align="center">4510</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4689223</td>
<td align="center">5261</td>
<td align="center">0.4746786</td>
<td align="center">5134</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4656180</td>
<td align="center">2225</td>
<td align="center">0.4505104</td>
<td align="center">2253</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4734787</td>
<td align="center">3073</td>
<td align="center">0.4760039</td>
<td align="center">3063</td>
</tr>
</tbody>
</table>
@ -1093,27 +1025,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9255106</td>
<td align="center">0.8972100</td>
<td align="center">0.9937258</td>
<td align="center">0.9251048</td>
<td align="center">0.8952278</td>
<td align="center">0.9928349</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9199219</td>
<td align="center">0.8932292</td>
<td align="center">0.9934896</td>
<td align="center">0.9169413</td>
<td align="center">0.9083718</td>
<td align="center">0.9947264</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9187450</td>
<td align="center">0.9133816</td>
<td align="center">0.9924913</td>
<td align="center">0.9305292</td>
<td align="center">0.9158752</td>
<td align="center">0.9937585</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6128205</td>
<td align="center">0.6027107</td>
<td align="center">0.0000000</td>
<td align="center">0.6128205</td>
<td align="center">0.6027107</td>
</tr>
</tbody>
</table>

BIN
docs/articles/AMR_files/figure-html/plot 1-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 64 KiB

After

Width:  |  Height:  |  Size: 64 KiB

BIN
docs/articles/AMR_files/figure-html/plot 3-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 51 KiB

After

Width:  |  Height:  |  Size: 51 KiB

BIN
docs/articles/AMR_files/figure-html/plot 4-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 102 KiB

After

Width:  |  Height:  |  Size: 102 KiB

BIN
docs/articles/AMR_files/figure-html/plot 5-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 83 KiB

After

Width:  |  Height:  |  Size: 83 KiB

4
docs/articles/EUCAST.html
Unescape View File

@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
</span>
</div>
@ -179,7 +179,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">20 February 2020</h4>
<h4 class="date">23 February 2020</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

208
docs/articles/MDR.html
Unescape View File

@ -16,9 +16,7 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons -