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  1. 2
      .github/workflows/check.yaml
  2. 4
      DESCRIPTION
  3. 14
      NEWS.md
  4. 27
      R/ab_property.R
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2
.github/workflows/check.yaml

@ -171,5 +171,5 @@ jobs: @@ -171,5 +171,5 @@ jobs:
if: always()
uses: actions/upload-artifact@v2
with:
name: artifacts-r-${{ matrix.config.r }}-${{ matrix.config.os }}
name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
path: AMR.Rcheck

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9029
Date: 2021-08-21
Version: 1.7.1.9030
Date: 2021-08-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

14
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# `AMR` 1.7.1.9029
## <small>Last updated: 21 August 2021</small>
# `AMR` 1.7.1.9030
## <small>Last updated: 29 August 2021</small>
### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@ -12,11 +12,12 @@ @@ -12,11 +12,12 @@
### Changed
* The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that:
* Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
* `antibiotics$atc` is now a `list` instead of a `character`, and this `atc` column was moved to the 5th position of the `antibiotics` data set
* `ab_atc()` does not always return a character vector with length 1, and returns a `list` if the input is larger than length 1
* `antibiotics$atc` is now a `list` containing `character` vectors, and this `atc` column was moved to the 5th position of the `antibiotics` data set
* `ab_atc()` does not always return a character vector of length 1, and returns a `list` if the input is larger than length 1
* `ab_info()` has a slightly different output
* Some DDDs (daily defined doses) were added or updated according to newly included ATC codes
* Antibiotic selectors
* They now also work in R-3.0 and R-3.1, supporting every version of R since 2013
* They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package
* Added more selectors for antibiotic classes: `aminopenicillins()`, `antifungals()`, `antimycobacterials()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()`, `trimethoprims()` and `ureidopenicillins()`
* Added specific selectors for certain types for treatment: `administrable_per_os()` and `administrable_iv()`, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):
```r
@ -30,8 +31,7 @@ @@ -30,8 +31,7 @@
```
* Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
* Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
* Fixed the Gram stain (`mo_gramstain()`) determination of the class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
* Fix for duplicate ATC codes in the `antibiotics` data set
* Fixed the Gram stain (`mo_gramstain()`) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`

27
R/ab_property.R

@ -288,7 +288,7 @@ ab_ddd <- function(x, administration = "oral", ...) { @@ -288,7 +288,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
units <- list(...)$units
if (!is.null(units) && isTRUE(units)) {
if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` instead. ",
warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
"This warning will be shown once per session.", call = FALSE)
}
ddd_prop <- paste0(ddd_prop, "_units")
@ -297,7 +297,7 @@ ab_ddd <- function(x, administration = "oral", ...) { @@ -297,7 +297,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
}
out <- ab_validate(x = x, property = ddd_prop)
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out)) ) {
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
@ -330,17 +330,18 @@ ab_info <- function(x, language = get_locale(), ...) { @@ -330,17 +330,18 @@ ab_info <- function(x, language = get_locale(), ...) {
x <- as.ab(x, ...)
list(ab = as.character(x),
atc = ab_atc(x),
cid = ab_cid(x),
name = ab_name(x, language = language),
group = ab_group(x, language = language),
atc_group1 = ab_atc_group1(x, language = language),
atc_group2 = ab_atc_group2(x, language = language),
tradenames = ab_tradenames(x),
ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"),
units = ab_ddd_units(x, administration = "oral")),
iv = list(amount = ab_ddd(x, administration = "iv"),
units = ab_ddd_units(x, administration = "iv"))))
cid = ab_cid(x),
name = ab_name(x, language = language),
group = ab_group(x, language = language),
atc = ab_atc(x),
atc_group1 = ab_atc_group1(x, language = language),
atc_group2 = ab_atc_group2(x, language = language),
tradenames = ab_tradenames(x),
loinc = ab_loinc(x),
ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"),
units = ab_ddd_units(x, administration = "oral")),
iv = list(amount = ab_ddd(x, administration = "iv"),
units = ab_ddd_units(x, administration = "iv"))))
}

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data-raw/AMR_latest.tar.gz

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9
docs/404.html

@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@ -173,13 +173,6 @@ @@ -173,13 +173,6 @@
Source Code
</a>
</li>
<li>
<a href="https://msberends.github.io/AMR/survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>

2
docs/LICENSE-text.html

@ -92,7 +92,7 @@ @@ -92,7 +92,7 @@
</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">1.7.1.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>

495
docs/articles/AMR.html

@ -44,7 +44,7 @@ @@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@ -174,13 +174,6 @@ @@ -174,13 +174,6 @@
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>
@ -198,7 +191,7 @@ @@ -198,7 +191,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">17 August 2021</h4>
<h4 data-toc-skip class="date">29 August 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -207,7 +200,7 @@ @@ -207,7 +200,7 @@
<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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 August 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/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 August 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -238,21 +231,21 @@ @@ -238,21 +231,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-08-17</td>
<td align="center">2021-08-29</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">2021-08-17</td>
<td align="center">2021-08-29</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">2021-08-17</td>
<td align="center">2021-08-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -349,68 +342,68 @@ @@ -349,68 +342,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2012-06-29</td>
<td align="center">E6</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-03</td>
<td align="center">D5</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">2014-08-25</td>
<td align="center">D8</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-03-20</td>
<td align="center">E3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">2017-01-14</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</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>
</tr>
<tr class="even">
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">2010-10-15</td>
<td align="center">X2</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-04-27</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">2011-04-05</td>
<td align="center">H6</td>
<td align="center">Hospital A</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>
<tr class="even">
<td align="center">2011-08-04</td>
<td align="center">O2</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -446,16 +439,16 @@ Longest: 1</p> @@ -446,16 +439,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,443</td>
<td align="right">52.22%</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,557</td>
<td align="right">47.79%</td>
<td align="right">9,674</td>
<td align="right">48.37%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -510,9 +503,9 @@ Longest: 1</p> @@ -510,9 +503,9 @@ 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 10,606 first weighted isolates (phenotype-based, 53.0% of total</span>
<span class="co"># =&gt; Found 10,571 first weighted isolates (phenotype-based, 52.9% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 53.0% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">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" class="external-link">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>
@ -520,7 +513,7 @@ Longest: 1</p> @@ -520,7 +513,7 @@ 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 10,606 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,571 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" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
@ -559,27 +552,11 @@ Longest: 1</p> @@ -559,27 +552,11 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2012-01-03</td>
<td align="center">D5</td>
<td align="center">Hospital B</td>
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -589,14 +566,14 @@ Longest: 1</p> @@ -589,14 +566,14 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2017-02-14</td>
<td align="center">L5</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-08-25</td>
<td align="center">D8</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
@ -605,52 +582,68 @@ Longest: 1</p> @@ -605,52 +582,68 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2012-03-07</td>
<td align="center">I8</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">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2010-12-20</td>
<td align="center">H10</td>
<td align="left">4</td>
<td align="center">2010-10-15</td>
<td align="center">X2</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">S</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">TRUE</td>
</tr>
<tr class="even">
<td align="left">11</td>
<td align="center">2014-01-24</td>
<td align="center">M2</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">6</td>
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2016-02-07</td>
<td align="center">V2</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</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">Escherichia</td>
<td align="center">coli</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2016-11-08</td>
<td align="center">D4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -674,8 +667,8 @@ Longest: 1</p> @@ -674,8 +667,8 @@ 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" class="external-link">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: 10,606<br>
Available: 10,606 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,571<br>
Available: 10,571 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -692,33 +685,33 @@ Longest: 24</p> @@ -692,33 +685,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,494</td>
<td align="right">42.37%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,785</td>
<td align="right">26.26%</td>
<td align="right">7,279</td>
<td align="right">68.63%</td>
<td align="right">2,799</td>
<td align="right">26.48%</td>
<td align="right">7,306</td>
<td align="right">69.11%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,106</td>
<td align="right">19.86%</td>
<td align="right">9,385</td>
<td align="right">88.49%</td>
<td align="right">2,087</td>
<td align="right">19.74%</td>
<td align="right">9,393</td>
<td align="right">88.86%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,221</td>
<td align="right">11.51%</td>
<td align="right">10,606</td>
<td align="right">1,178</td>
<td align="right">11.14%</td>
<td align="right">10,571</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -765,93 +758,93 @@ Longest: 24</p> @@ -765,93 +758,93 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-12-11</td>
<td align="center">B5</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2010-10-15</td>
<td align="center">X2</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">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-06-11</td>
<td align="center">L7</td>
<td align="center">Hospital C</td>
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-12-19</td>
<td align="center">A10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">2014-02-02</td>
<td align="center">K7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</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 align="center">2014-12-05</td>
<td align="center">M6</td>
<td align="center">2011-08-05</td>
<td align="center">V3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</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">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">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-05-14</td>
<td align="center">L8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2014-06-16</td>
<td align="center">Z8</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">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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-12-14</td>
<td align="center">Q1</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">2017-08-23</td>
<td align="center">J10</td>
<td align="center">Hospital D</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">F</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>
</tbody>
@ -875,50 +868,50 @@ Longest: 24</p> @@ -875,50 +868,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2137</td>
<td align="center">139</td>
<td align="center">2218</td>
<td align="center">4494</td>
<td align="center">2196</td>
<td align="center">119</td>
<td align="center">2192</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3298</td>
<td align="center">157</td>
<td align="center">1039</td>
<td align="center">4494</td>
<td align="center">3378</td>
<td align="center">151</td>
<td align="center">978</td>
<td align="center">4507</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3230</td>
<td align="center">3282</td>
<td align="center">0</td>
<td align="center">1264</td>
<td align="center">4494</td>
<td align="center">1225</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3946</td>
<td align="center">3929</td>
<td align="center">0</td>
<td align="center">548</td>
<td align="center">4494</td>
<td align="center">578</td>
<td align="center">4507</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1221</td>
<td align="center">1221</td>
<td align="center">1178</td>
<td align="center">1178</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">967</td>
<td align="center">44</td>
<td align="center">210</td>
<td align="center">1221</td>
<td align="center">930</td>
<td align="center">45</td>
<td align="center">203</td>
<td align="center">1178</td>
</tr>
</tbody>
</table>
@ -941,34 +934,34 @@ Longest: 24</p> @@ -941,34 +934,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3946</td>
<td align="center">3929</td>
<td align="center">0</td>
<td align="center">548</td>
<td align="center">4494</td>
<td align="center">578</td>
<td align="center">4507</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1088</td>
<td align="center">1052</td>
<td align="center">0</td>
<td align="center">133</td>
<td align="center">1221</td>
<td align="center">126</td>
<td align="center">1178</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2490</td>
<td align="center">2473</td>
<td align="center">0</td>
<td align="center">295</td>
<td align="center">2785</td>
<td align="center">326</td>
<td align="center">2799</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2106</td>
<td align="center">2106</td>
<td align="center">2087</td>
<td align="center">2087</td>
</tr>
</tbody>
</table>
@ -982,7 +975,7 @@ Longest: 24</p> @@ -982,7 +975,7 @@ 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] 0.5427117</span></code></pre></div>
<span class="co"># [1] 0.5403462</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">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>
@ -996,19 +989,19 @@ Longest: 24</p> @@ -996,19 +989,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5356582</td>
<td align="center">0.5487147</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5408108</td>
<td align="center">0.5436519</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5371153</td>
<td align="center">0.5257549</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5614714</td>
<td align="center">0.5338095</td>
</tr>
</tbody>
</table>
@ -1027,23 +1020,23 @@ Longest: 24</p> @@ -1027,23 +1020,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5356582</td>
<td align="center">3183</td>
<td align="center">0.5487147</td>
<td align="center">3151</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5408108</td>
<td align="center">3700</td>
<td align="center">0.5436519</td>
<td align="center">3631</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5371153</td>
<td align="center">1657</td>
<td align="center">0.5257549</td>
<td align="center">1689</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5614714</td>
<td align="center">2066</td>
<td align="center">0.5338095</td>
<td align="center">2100</td>
</tr>
</tbody>
</table>
@ -1064,27 +1057,27 @@ Longest: 24</p> @@ -1064,27 +1057,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7688028</td>
<td align="center">0.8780596</td>
<td align="center">0.9815309</td>
<td align="center">0.7830042</td>
<td align="center">0.8717550</td>
<td align="center">0.9764810</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8280098</td>
<td align="center">0.8910729</td>
<td align="center">0.9754300</td>
<td align="center">0.8276740</td>
<td align="center">0.8930390</td>
<td align="center">0.9787776</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7921005</td>
<td align="center">0.8940754</td>
<td align="center">0.9795332</td>
<td align="center">0.7874241</td>
<td align="center">0.8835298</td>
<td align="center">0.9828510</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5351377</td>
<td align="center">0.5318639</td>
<td align="center">0.0000000</td>
<td align="center">0.5351377</td>
<td align="center">0.5318639</td>
</tr>
</tbody>
</table>
@ -1109,23 +1102,23 @@ Longest: 24</p> @@ -1109,23 +1102,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">53.6%</td>
<td align="right">26.4%</td>
<td align="right">54.9%</td>
<td align="right">25.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.1%</td>
<td align="right">24.6%</td>
<td align="right">54.4%</td>
<td align="right">27.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.7%</td>
<td align="right">27.5%</td>
<td align="right">52.6%</td>
<td align="right">25.0%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">56.1%</td>
<td align="right">29.0%</td>
<td align="right">53.4%</td>
<td align="right">24.3%</td>
</tr>
</tbody>
</table>
@ -1209,16 +1202,16 @@ Longest: 24</p> @@ -1209,16 +1202,16 @@ Longest: 24</p>
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 0.25 16 0.0625 32 0.025 1 256 64 0.002 0.005 </span>
<span class="co"># [11] 0.01 0.005 8 0.01 0.025 128 0.01 8 0.005 256 </span>
<span class="co"># [21] 0.005 8 0.0625 0.125 0.005 16 8 2 0.5 4 </span>
<span class="co"># [31] 2 32 0.25 0.25 8 0.025 0.25 8 64 1 </span>
<span class="co"># [41] 0.005 0.01 0.005 256 0.025 0.5 2 0.025 0.5 0.005 </span>
<span class="co"># [51] 0.0625 128 4 1 0.0625 0.002 16 0.002 8 0.005 </span>
<span class="co"># [61] 1 1 8 32 0.002 32 0.25 8 4 0.001 </span>
<span class="co"># [71] 2 16 16 0.025 0.005 0.0625 2 128 0.001 2 </span>
<span class="co"># [81] 64 0.025 16 64 2 128 8 0.5 4 256 </span>
<span class="co"># [91] 0.5 32 0.001 0.01 2 64 4 32 4 0.0625</span></code></pre></div>
<span class="co"># [1] 1 128 0.01 0.25 0.01 16 0.001 0.125 0.25 0.01 </span>
<span class="co"># [11] 0.005 16 0.0625 64 &gt;=256 0.5 0.01 16 0.5 0.0625</span>
<span class="co"># [21] 0.001 0.5 0.0625 4 2 8 0.5 0.0625 0.125 128 </span>
<span class="co"># [31] 0.002 0.25 2 8 0.125 0.0625 0.125 16 128 0.002 </span>
<span class="co"># [41] 1 0.005 2 32 0.01 0.0625 &gt;=256 64 16 0.005 </span>
<span class="co"># [51] 2 0.001 &gt;=256 32 64 &gt;=256 128 0.01 0.005 0.001 </span>
<span class="co"># [61] 0.01 0.125 2 0.125 &gt;=256 32 64 0.01 2 0.25 </span>
<span class="co"># [71] 0.01 64 0.5 128 0.001 64 128 0.002 &gt;=256 64 </span>
<span class="co"># [81] 0.01 8 0.5 4 16 0.025 0.025 0.001 0.125 0.025 </span>
<span class="co"># [91] 2 64 64 128 32 128 0.001 32 2 0.005</span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@ -1247,10 +1240,10 @@ Longest: 24</p> @@ -1247,10 +1240,10 @@ Longest: 24</p>
<span class="co"># to review it.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 26 25 28 21 24 22 21 27 22 21 31 25 26 17 28 29 18 31 21 30 23 28 22 18 28</span>
<span class="co"># [26] 21 25 26 18 30 22 28 25 28 25 21 29 26 19 21 19 26 31 17 25 22 21 27 24 26</span>
<span class="co"># [51] 20 17 18 27 31 31 20 31 26 22 25 22 19 22 27 19 25 27 30 17 24 27 22 28 18</span>
<span class="co"># [76] 26 30 29 25 23 26 29 19 25 25 24 25 30 29 25 29 17 26 21 20 29 26 23 29 31</span></code></pre></div>
<span class="co"># [1] 30 29 25 23 27 18 23 21 31 26 17 30 18 31 30 25 22 19 18 26 31 19 21 25 29</span>
<span class="co"># [26] 22 26 30 20 20 18 19 18 29 22 17 27 21 24 18 17 23 27 18 19 31 18 29 30 25</span>
<span class="co"># [51] 27 23 21 20 31 19 19 25 25 23 23 19 17 25 21 30 20 31 26 23 29 27 30 29 24</span>
<span class="co"># [76] 20 23 23 27 20 24 19 28 24 31 29 26 23 20 29 23 18 17 27 21 28 28 17 23 17</span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>

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