P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-24 18:46:14 +01:00
Code Releases Activity

(v1.7.1) New CRAN release

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-06-03 15:19:21 +02:00
parent 279376fccb
commit 7e70403efb
94 changed files with 1709 additions and 543 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.0.9002
Date: 2021-06-01
Version: 1.7.1
Date: 2021-06-03
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@ -43,7 +43,6 @@ Depends:
R (>= 3.0.0)
Suggests:
cleaner,
covr,
curl,
dplyr,
ggplot2,

18
NEWS.md
View File

@ -1,18 +1,8 @@
# `AMR` 1.7.0.9002
## <small>Last updated: 1 June 2021</small>
### New
* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
### Changed
* `bug_drug_combinations()` now supports grouping using the `dplyr` package
* As requested by CRAN administrators: decreased package size by 3 MB in costs of a ~50 times slower loading time of the package (i.e., `library(AMR)`)
# `AMR` 1.7.0
# `AMR` 1.7.1
### Breaking change
* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.
* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
```r
# select columns with results for carbapenems
example_isolates[, carbapenems()] # base R
@ -45,6 +35,7 @@
### Changed
* `bug_drug_combinations()` now supports grouping using the `dplyr` package
* Custom MDRO guidelines (`mdro()`, `custom_mdro_guideline()`):
* Custom MDRO guidelines can now be combined with other custom MDRO guidelines using `c()`
* Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule
@ -77,6 +68,7 @@
* `age()` now vectorises over both `x` and `reference`
### Other
* As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package
* All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.

5
R/ab_class_selectors.R
View File

@ -73,6 +73,11 @@
#' \donttest{
#' if (require("dplyr")) {
#'
#' # get AMR for all aminoglycosides e.g., per hospital:
#' example_isolates %>%
#' group_by(hospital_id) %>%
#' summarise(across(aminoglycosides(), resistance))
#'
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
#' example_isolates %>%
#' select(carbapenems())

BIN
R/sysdata.rda
View File

Binary file not shown.

9
README.md
View File

@ -23,14 +23,7 @@ This is the development source of the `AMR` package for R. Not a developer? Then
### How to get this package
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
You have to add [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'), by running:
```r
options(repos = c(getOption("repos"),
msberends = "https://msberends.r-universe.dev"))
```
You can now install or update the `AMR` package in the same way you are used to:
You can install or update the `AMR` package from CRAN using:
```r
install.packages("AMR")

2
cran-comments.md
View File

@ -1 +1 @@
* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. The package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software earlier this year. We will add the paper as a vignette after publication in a next version. All data sets were compressed using `compression = "xz"` to make them as small as possible. We try to update as infrequent as possible.
* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, following 15 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.

BIN
data-raw/AMR_latest.tar.gz
View File

Binary file not shown.

1
data-raw/_internals.R
View File

@ -146,7 +146,6 @@ usethis::use_data(eucast_rules_file,
LANGUAGES_SUPPORTED,
MO_CONS,
MO_COPS,
AB_lookup,
AMINOGLYCOSIDES,
AMINOPENICILLINS,
CARBAPENEMS,

2
docs/404.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

488
docs/articles/AMR.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 May 2021</h4>
<h4 class="date">03 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 26 May 2021.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 03 June 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-05-26</td>
<td align="center">2021-06-03</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2021-05-26</td>
<td align="center">2021-06-03</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2021-05-26</td>
<td align="center">2021-06-03</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -344,52 +344,52 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-04-02</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">2014-11-23</td>
<td align="center">A2</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-07-17</td>
<td align="center">X6</td>
<td align="center">Hospital A</td>
<td align="center">2013-08-17</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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>
</tr>
<tr class="odd">
<td align="center">2012-09-03</td>
<td align="center">C4</td>
<td align="center">2011-02-20</td>
<td align="center">B1</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">Streptococcus pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2010-02-11</td>
<td align="center">D2</td>
<td align="center">Hospital B</td>
<td align="center">2016-10-04</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-12-14</td>
<td align="center">L5</td>
<td align="center">2010-04-22</td>
<td align="center">F1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -399,12 +399,12 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-01-30</td>
<td align="center">S3</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">2013-01-15</td>
<td align="center">W4</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -441,16 +441,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
<td align="right">10,416</td>
<td align="right">52.08%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,625</td>
<td align="right">48.13%</td>
<td align="right">9,584</td>
<td align="right">47.92%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -505,9 +505,9 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,550 first weighted isolates (phenotype-based, 52.8% of total</span>
<span class="co"># =&gt; Found 10,645 first weighted isolates (phenotype-based, 53.2% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 52.8% 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>
<p>So only 53.2% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -515,7 +515,7 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,550 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,645 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table class="table">
@ -553,89 +553,25 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-04-02</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2015-07-17</td>
<td align="center">X6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2010-02-11</td>
<td align="center">D2</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="even">
<td align="left">6</td>
<td align="center">2016-01-30</td>
<td align="center">S3</td>
<td align="center">2013-08-17</td>
<td align="center">V3</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2012-10-20</td>
<td align="center">D10</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2016-03-28</td>
<td align="center">K7</td>
<td align="left">3</td>
<td align="center">2011-02-20</td>
<td align="center">B1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -648,6 +584,70 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="center">2010-04-22</td>
<td align="center">F1</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="even">
<td align="left">7</td>
<td align="center">2014-07-28</td>
<td align="center">W5</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2015-01-06</td>
<td align="center">V3</td>
<td align="center">Hospital A</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">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2014-03-16</td>
<td align="center">H4</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">R</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>
</table>
<p>Time for the analysis!</p>
@ -669,8 +669,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,550<br>
Available: 10,550 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,645<br>
Available: 10,645 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -687,33 +687,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,566</td>
<td align="right">43.28%</td>
<td align="right">4,566</td>
<td align="right">43.28%</td>
<td align="right">4,652</td>
<td align="right">43.70%</td>
<td align="right">4,652</td>
<td align="right">43.70%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,786</td>
<td align="right">26.41%</td>
<td align="right">7,352</td>
<td align="right">69.69%</td>
<td align="right">2,744</td>
<td align="right">25.78%</td>
<td align="right">7,396</td>
<td align="right">69.48%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,025</td>
<td align="right">19.19%</td>
<td align="right">9,377</td>
<td align="right">88.88%</td>
<td align="right">2,052</td>
<td align="right">19.28%</td>
<td align="right">9,448</td>
<td align="right">88.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,173</td>
<td align="right">11.12%</td>
<td align="right">10,550</td>
<td align="right">1,197</td>
<td align="right">11.24%</td>
<td align="right">10,645</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -760,8 +760,8 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-03-28</td>
<td align="center">K7</td>
<td align="center">2011-02-20</td>
<td align="center">B1</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -775,44 +775,14 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2010-01-30</td>
<td align="center">A1</td>
<td align="center">Hospital A</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="odd">
<td align="center">2012-12-10</td>
<td align="center">M7</td>
<td align="center">2015-01-06</td>
<td align="center">V3</td>
<td align="center">Hospital A</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">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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-08-04</td>
<td align="center">Y7</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -820,13 +790,28 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-08-05</td>
<td align="center">I4</td>
<td align="center">Hospital A</td>
<td align="center">2012-05-03</td>
<td align="center">B2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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="center">2017-03-18</td>
<td align="center">K10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -834,14 +819,14 @@ Longest: 24</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-15</td>
<td align="center">H2</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2010-12-15</td>
<td align="center">H3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
@ -849,6 +834,21 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-08-10</td>
<td align="center">N2</td>
<td align="center">Hospital C</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">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">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -870,50 +870,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2148</td>
<td align="center">153</td>
<td align="center">2265</td>
<td align="center">4566</td>
<td align="center">2232</td>
<td align="center">119</td>
<td align="center">2301</td>
<td align="center">4652</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3344</td>
<td align="center">157</td>
<td align="center">1065</td>
<td align="center">4566</td>
<td align="center">3424</td>
<td align="center">165</td>
<td align="center">1063</td>
<td align="center">4652</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3356</td>
<td align="center">3386</td>
<td align="center">0</td>
<td align="center">1210</td>
<td align="center">4566</td>
<td align="center">1266</td>
<td align="center">4652</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3983</td>
<td align="center">4062</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4566</td>
<td align="center">590</td>
<td align="center">4652</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">1173</td>
<td align="center">1173</td>
<td align="center">1197</td>
<td align="center">1197</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">930</td>
<td align="center">43</td>
<td align="center">200</td>
<td align="center">1173</td>
<td align="center">932</td>
<td align="center">60</td>
<td align="center">205</td>
<td align="center">1197</td>
</tr>
</tbody>
</table>
@ -936,34 +936,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3983</td>
<td align="center">4062</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4566</td>
<td align="center">590</td>
<td align="center">4652</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1063</td>
<td align="center">1069</td>
<td align="center">0</td>
<td align="center">110</td>
<td align="center">1173</td>
<td align="center">128</td>
<td align="center">1197</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2490</td>
<td align="center">2444</td>
<td align="center">0</td>
<td align="center">296</td>
<td align="center">2786</td>
<td align="center">300</td>
<td align="center">2744</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">2025</td>
<td align="center">2025</td>
<td align="center">2052</td>
<td align="center">2052</td>
</tr>
</tbody>
</table>
@ -977,7 +977,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
<span class="co"># [1] 0.5443602</span></code></pre></div>
<span class="co"># [1] 0.5431658</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -991,19 +991,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5542598</td>
<td align="center">0.5461634</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5400160</td>
<td align="center">0.5394702</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5508217</td>
<td align="center">0.5609756</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5322972</td>
<td align="center">0.5316215</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5542598</td>
<td align="center">3087</td>
<td align="center">0.5461634</td>
<td align="center">3206</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5400160</td>
<td align="center">3761</td>
<td align="center">0.5394702</td>
<td align="center">3737</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5508217</td>
<td align="center">1643</td>
<td align="center">0.5609756</td>
<td align="center">1599</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5322972</td>
<td align="center">2059</td>
<td align="center">0.5316215</td>
<td align="center">2103</td>
</tr>
</tbody>
</table>
@ -1059,27 +1059,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7667543</td>
<td align="center">0.8723171</td>
<td align="center">0.9770039</td>
<td align="center">0.7714961</td>
<td align="center">0.8731728</td>
<td align="center">0.9776440</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8294970</td>
<td align="center">0.9062234</td>
<td align="center">0.9795396</td>
<td align="center">0.8287385</td>
<td align="center">0.8930660</td>
<td align="center">0.9824561</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7910983</td>
<td align="center">0.8937545</td>
<td align="center">0.9852836</td>
<td align="center">0.7882653</td>
<td align="center">0.8906706</td>
<td align="center">0.9839650</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5387654</td>
<td align="center">0.5414230</td>
<td align="center">0.0000000</td>
<td align="center">0.5387654</td>
<td align="center">0.5414230</td>
</tr>
</tbody>
</table>
@ -1163,16 +1163,16 @@ 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] 2 2 16 4 0.125 0.5 64 16 128 32 </span>
<span class="co"># [11] 4 32 1 0.125 128 2 8 64 64 2 </span>
<span class="co"># [21] 8 0.125 0.25 1 16 64 0.25 0.5 0.25 4 </span>
<span class="co"># [31] 16 32 0.25 1 0.5 8 64 2 0.25 0.0625</span>
<span class="co"># [41] 128 1 2 2 0.0625 0.125 64 8 8 8 </span>
<span class="co"># [51] 4 8 0.125 1 128 1 128 2 2 0.5 </span>
<span class="co"># [61] 32 64 16 32 32 16 4 1 16 2 </span>
<span class="co"># [71] 1 0.125 2 4 0.125 32 2 0.125 8 0.25 </span>
<span class="co"># [81] 0.0625 4 0.5 16 128 8 128 0.125 0.0625 1 </span>
<span class="co"># [91] 1 0.25 0.0625 128 128 8 0.0625 32 128 0.25</span></code></pre></div>
<span class="co"># [1] 4 4 0.25 &gt;=512 0.0625 2 128 2 64 1 </span>
<span class="co"># [11] 64 256 32 2 2 256 0.125 128 16 32 </span>
<span class="co"># [21] 1 2 0.0625 32 16 16 0.0625 0.125 0.0625 2 </span>
<span class="co"># [31] 128 8 0.0625 0.25 4 16 1 0.0625 1 16 </span>
<span class="co"># [41] 4 0.0625 2 4 0.0625 256 16 0.5 1 1 </span>
<span class="co"># [51] 16 64 &gt;=512 64 64 1 4 0.5 16 1 </span>
<span class="co"># [61] 16 256 8 256 256 &gt;=512 8 0.5 2 2 </span>
<span class="co"># [71] &gt;=512 8 64 4 8 0.25 2 4 16 0.125 </span>
<span class="co"># [81] 0.25 4 0.125 8 0.125 0.0625 &gt;=512 0.125 64 1 </span>
<span class="co"># [91] 16 2 0.5 16 0.0625 128 2 0.0625 128 2</span></code></pre></div>
<div class="sourceCode" id="cb36"><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>
@ -1201,10 +1201,10 @@ 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] 31 27 25 19 19 17 23 24 30 28 22 26 18 29 25 24 22 30 17 20 23 24 26 24 27</span>
<span class="co"># [26] 22 27 22 17 26 22 31 27 31 31 25 21 18 26 22 21 25 21 26 22 21 20 20 24 19</span>
<span class="co"># [51] 25 17 29 26 28 30 30 29 30 28 19 28 22 21 26 25 24 23 21 18 27 20 17 29 30</span>
<span class="co"># [76] 17 25 19 30 22 26 22 31 18 19 26 20 18 23 17 30 30 22 21 25 21 17 30 30 24</span></code></pre></div>
<span class="co"># [1] 27 28 23 21 23 21 28 31 26 17 23 23 24 29 20 18 27 24 26 24 27 23 30 18 26</span>
<span class="co"># [26] 31 19 26 21 27 29 29 19 19 31 25 23 19 26 21 21 20 23 29 22 18 27 28 21 27</span>
<span class="co"># [51] 21 18 19 28 26 26 29 20 31 28 30 30 21 21 25 29 28 29 30 25 27 19 23 26 24</span>
<span class="co"># [76] 20 21 25 19 26 22 19 30 28 27 18 19 18 25 31 20 19 29 31 31 29 22 20 17 31</span></code></pre></div>
<div class="sourceCode" id="cb42"><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>

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

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 41 KiB

After

Width:  |  Height:  |  Size: 41 KiB

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

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 51 KiB

After

Width:  |  Height:  |  Size: 52 KiB

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

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 29 KiB

After

Width:  |  Height:  |  Size: 30 KiB

BIN
docs/articles/AMR_files/figure-html/mic_plots-2.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 36 KiB

After

Width:  |  Height:  |  Size: 34 KiB

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

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 41 KiB

After

Width:  |  Height:  |  Size: 41 KiB

BIN
docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 52 KiB

After

Width:  |  Height:  |  Size: 52 KiB

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: 39 KiB

After

Width:  |  Height:  |  Size: 39 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: 27 KiB

After

Width:  |  Height:  |  Size: 27 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: 69 KiB

After

Width:  |  Height:  |  Size: 69 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: 46 KiB

After

Width:  |  Height:  |  Size: 46 KiB

2
docs/articles/EUCAST.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

58
docs/articles/MDR.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -339,19 +339,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I I I I S S</span>
<span class="co"># 2 R I S I I I</span>
<span class="co"># 3 S R R R R I</span>
<span class="co"># 4 S R S S R S</span>
<span class="co"># 5 R S I R S R</span>
<span class="co"># 6 R R R R I I</span>
<span class="co"># 1 S I R R R S</span>
<span class="co"># 2 I R R R R R</span>
<span class="co"># 3 S S S R I R</span>
<span class="co"># 4 R I R R S S</span>
<span class="co"># 5 I R S S R I</span>
<span class="co"># 6 I S S R R R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 I</span>
<span class="co"># 3 S</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 I</span>
<span class="co"># 6 I</span></code></pre></div>
<span class="co"># 5 S</span>
<span class="co"># 6 S</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
@ -382,40 +382,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3271</td>
<td align="right">65.42%</td>
<td align="right">3271</td>
<td align="right">65.42%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">949</td>
<td align="right">18.98%</td>
<td align="right">4220</td>
<td align="right">84.40%</td>
<td align="right">1027</td>
<td align="right">20.54%</td>
<td align="right">4214</td>
<td align="right">84.28%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">449</td>
<td align="right">8.98%</td>
<td align="right">4669</td>
<td align="right">93.38%</td>
<td align="right">430</td>
<td align="right">8.60%</td>
<td align="right">4644</td>
<td align="right">92.88%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">240</td>
<td align="right">4.80%</td>
<td align="right">4909</td>
<td align="right">98.18%</td>
<td align="right">245</td>
<td align="right">4.90%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">91</td>
<td align="right">1.82%</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
docs/articles/PCA.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

6
docs/articles/SPSS.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -193,7 +193,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">26 May 2021</h4>
<h4 class="date">03 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -228,7 +228,7 @@
</li>
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">403,383 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">404,559 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
</li>
<li>
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>

2
docs/articles/WHONET.html
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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

72
docs/articles/benchmarks.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -227,18 +227,18 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 10.0 11.0 16.0 11.0 13.0 50 25</span>
<span class="co"># as.mo("stau") 54.0 58.0 72.0 61.0 89.0 99 25</span>
<span class="co"># as.mo("STAU") 53.0 55.0 67.0 56.0 91.0 95 25</span>
<span class="co"># as.mo("staaur") 10.0 11.0 16.0 11.0 13.0 47 25</span>
<span class="co"># as.mo("STAAUR") 10.0 11.0 17.0 12.0 13.0 58 25</span>
<span class="co"># as.mo("S. aureus") 26.0 27.0 36.0 31.0 33.0 70 25</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 40.0 29.0 61.0 68 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.6 3.2 6.5 3.5 3.8 42 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 260.0 260.0 270.0 290 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 190.0 190.0 200.0 200.0 210.0 300 25</span>
<span class="co"># as.mo("MRSA") 10.0 11.0 13.0 12.0 13.0 40 25</span>
<span class="co"># as.mo("VISA") 18.0 19.0 32.0 20.0 24.0 130 25</span></code></pre></div>
<span class="co"># as.mo("sau") 13.0 13.0 16.0 15.0 16.0 44 25</span>
<span class="co"># as.mo("stau") 55.0 58.0 75.0 62.0 94.0 110 25</span>
<span class="co"># as.mo("STAU") 55.0 59.0 77.0 89.0 94.0 100 25</span>
<span class="co"># as.mo("staaur") 11.0 13.0 20.0 14.0 16.0 48 25</span>
<span class="co"># as.mo("STAAUR") 11.0 13.0 17.0 15.0 16.0 49 25</span>
<span class="co"># as.mo("S. aureus") 26.0 30.0 41.0 32.0 60.0 68 25</span>
<span class="co"># as.mo("S aureus") 27.0 29.0 44.0 32.0 58.0 160 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.3 3.9 5.5 4.2 4.7 37 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 280.0 280.0 290.0 320 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170.0 200.0 210.0 200.0 220.0 250 25</span>
<span class="co"># as.mo("MRSA") 12.0 14.0 21.0 15.0 17.0 56 25</span>
<span class="co"># as.mo("VISA") 20.0 23.0 33.0 25.0 51.0 59 25</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -260,8 +260,8 @@
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># Class &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_EPDR B_STRPT_GRPA B_STPHY_AURS B_BCTRD_FRGL B_STPHY_HMNS</span>
<span class="co"># [6] B_STPHY_CONS</span>
<span class="co"># [1] B_STPHY_CONS B_ESCHR_COLI B_STPHY_AURS B_STRPT_PYGN B_ESCHR_COLI</span>
<span class="co"># [6] B_HMPHL_INFL</span>
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -277,8 +277,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 187 223 233 226 229 318 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.226 seconds. That is 113 nanoseconds on average. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 165 238 258 246 253 369 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.246 seconds. That is 123 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -292,10 +292,10 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.28 7.59 8.01 8.03 8.45 8.66 10</span>
<span class="co"># B 23.00 24.10 30.30 25.50 27.30 75.30 10</span>
<span class="co"># C 1.55 1.74 7.31 1.95 2.01 56.10 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<span class="co"># A 8.20 8.33 13.30 8.53 9.71 53.2 10</span>
<span class="co"># B 22.80 23.50 29.20 24.60 26.80 69.3 10</span>
<span class="co"># C 1.82 2.04 2.25 2.16 2.38 2.9 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -309,14 +309,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.42 1.45 1.56 1.50 1.57 2.00 10</span>
<span class="co"># B 1.43 1.46 1.49 1.47 1.55 1.59 10</span>
<span class="co"># C 1.41 1.43 1.58 1.49 1.57 2.19 10</span>
<span class="co"># D 1.41 1.48 1.61 1.54 1.63 2.33 10</span>
<span class="co"># E 1.41 1.45 1.64 1.51 1.56 2.68 10</span>
<span class="co"># F 1.42 1.52 1.63 1.57 1.71 1.99 10</span>
<span class="co"># G 1.41 1.46 1.65 1.56 1.90 1.98 10</span>
<span class="co"># H 1.42 1.46 1.59 1.55 1.70 1.88 10</span></code></pre></div>
<span class="co"># A 1.66 1.70 1.86 1.77 1.90 2.41 10</span>
<span class="co"># B 1.61 1.71 1.99 1.84 2.37 2.56 10</span>
<span class="co"># C 1.64 1.72 1.79 1.74 1.77 2.14 10</span>
<span class="co"># D 1.68 1.71 2.06 2.06 2.23 2.77 10</span>
<span class="co"># E 1.63 1.71 1.85 1.75 1.92 2.43 10</span>
<span class="co"># F 1.61 1.67 1.80 1.75 1.86 2.22 10</span>
<span class="co"># G 1.63 1.67 4.37 1.96 2.58 25.70 10</span>
<span class="co"># H 1.67 1.73 1.88 1.83 2.01 2.28 10</span></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -344,13 +344,13 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 17.81 18.24 21.93 18.78 19.44 60.56 100</span>
<span class="co"># de 28.82 29.53 37.92 30.33 32.62 81.75 100</span>
<span class="co"># nl 32.65 33.61 44.22 34.43 37.44 193.90 100</span>
<span class="co"># es 32.51 32.95 41.88 33.70 36.39 80.63 100</span>
<span class="co"># it 22.00 22.57 27.98 23.15 25.14 67.04 100</span>
<span class="co"># fr 21.71 22.22 27.20 22.83 24.41 66.08 100</span>
<span class="co"># pt 21.71 22.54 26.97 23.06 23.94 67.41 100</span></code></pre></div>
<span class="co"># en 19.99 20.43 25.64 21.15 22.38 82.52 100</span>
<span class="co"># de 31.03 31.96 38.34 32.88 35.27 82.31 100</span>
<span class="co"># nl 35.25 36.19 43.25 37.63 39.66 85.19 100</span>
<span class="co"># es 35.01 35.85 40.89 36.91 38.58 83.68 100</span>
<span class="co"># it 24.35 24.90 30.43 25.81 28.03 78.90 100</span>
<span class="co"># fr 23.87 25.02 31.72 26.03 27.46 83.88 100</span>
<span class="co"># pt 24.00 24.99 31.16 26.05 28.06 80.74 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

BIN
docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 82 KiB

After

Width:  |  Height:  |  Size: 82 KiB

6
docs/articles/datasets.html
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">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">01 June 2021</h4>
<h4 class="date">03 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -1007,7 +1007,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 21,996 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 1 June 2021 14:31:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 1 June 2021 14:47:11 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>

2
docs/articles/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/articles/resistance_predict.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/articles/welcome_to_AMR.html
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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

28
docs/index.html
View File

@ -42,7 +42,7 @@
</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">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -376,13 +376,9 @@
<div id="latest-released-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p>This package is <a href="https://msberends.r-universe.dev">available here</a> on the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, as CRAN does not allow frequent updates of large packages (though the <code>AMR</code> package is only 7-9 MB). We are working on splitting this package into two: a new data package containing the microbial taxonomy, and the <code>AMR</code> package that only contains all functions.</p>
<p>In the meanwhile, you have to add <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’), by running:</p>
<p><a href="https://cran.r-project.org/package=AMR"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>You can now install or update the <code>AMR</code> package in the same way you are used to:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
@ -390,11 +386,23 @@
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><img src="https://www.codefactor.io/repository/github/msberends/amr" alt="CodeFactor"><img src="https://codecov.io/gh/msberends/AMR?branch=master" alt="Codecov"></p>
<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
<ol>
<li>
<p>Directly, using:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><img src="https://www.codefactor.io/repository/github/msberends/amr" alt="CodeFactor"><img src="https://codecov.io/gh/msberends/AMR?branch=master" alt="Codecov"></p>
</li>
<li>
<p>From the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>After this, you can install and update this <code>AMR</code> package like any official release (using <code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages("AMR")</a></code> or in RStudio via <em>Tools</em> &gt; <em>Check of Package Updates…</em>).</p>
</li>
</ol>
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
</div>
</div>

171
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>
@ -236,40 +236,16 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1709002" class="section level1">
<h1 class="page-header" data-toc-text="1.7.0.9002">
<a href="#amr-1709002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0.9002</h1>
<div id="last-updated-1-june-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-1-june-2021" class="anchor"></a><small>Last updated: 1 June 2021</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
</ul>
</div>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>
<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
<li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a ~50 times slower loading time of the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>)</li>
</ul>
</div>
</div>
</div>
<div id="amr-170" class="section level1">
<h1 class="page-header" data-toc-text="1.7.0">
<a href="#amr-170" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.0</h1>
<div id="amr-171" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1">
<a href="#amr-171" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1</h1>
<div id="breaking-change" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
<ul>
<li><p>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</p></li>
<li>
<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release.</p>
<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># select columns with results for carbapenems</span>
@ -289,9 +265,9 @@
</li>
</ul>
</div>
<div id="new-1" class="section level3">
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3>
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
@ -313,10 +289,12 @@
</li>
</ul>
</div>
<div id="changed-1" class="section level3">
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-1" class="anchor"></a>Changed</h3>
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>
<code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now supports grouping using the <code>dplyr</code> package</li>
<li>Custom MDRO guidelines (<code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code>):
<ul>
<li>Custom MDRO guidelines can now be combined with other custom MDRO guidelines using <code><a href="https://rdrr.io/r/base/c.html">c()</a></code>
@ -365,6 +343,7 @@
<h3 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h3>
<ul>
<li>As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package</li>
<li>All unit tests are now processed by the <code>tinytest</code> package, instead of the <code>testthat</code> package. The <code>testthat</code> package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the <code>tinytest</code> package is very lightweight and dependency-free.</li>
</ul>
</div>
@ -372,9 +351,9 @@
<div id="amr-160" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0">
<a href="#amr-160" class="anchor"></a><small> 2021-03-14 </small><code>AMR</code> 1.6.0</h1>
<div id="new-2" class="section level3">
<div id="new-1" class="section level3">
<h3 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h3>
<a href="#new-1" class="anchor"></a>New</h3>
<ul>
<li>
<p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p>
@ -448,9 +427,9 @@
</li>
</ul>
</div>
<div id="changed-2" class="section level3">
<div id="changed-1" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-2" class="anchor"></a>Changed</h3>
<a href="#changed-1" class="anchor"></a>Changed</h3>
<ul>
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
<ul>
@ -509,9 +488,9 @@
<div id="amr-150" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0">
<a href="#amr-150" class="anchor"></a><small> 2021-01-06 </small><code>AMR</code> 1.5.0</h1>
<div id="new-3" class="section level3">
<div id="new-2" class="section level3">
<h3 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h3>
<a href="#new-2" class="anchor"></a>New</h3>
<ul>
<li>
<p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
@ -527,9 +506,9 @@
<li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
</ul>
</div>
<div id="changed-3" class="section level3">
<div id="changed-2" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-3" class="anchor"></a>Changed</h3>
<a href="#changed-2" class="anchor"></a>Changed</h3>
<ul>
<li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
<li>
@ -622,9 +601,9 @@
<div id="amr-140" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0">
<a href="#amr-140" class="anchor"></a><small> 2020-10-08 </small><code>AMR</code> 1.4.0</h1>
<div id="new-4" class="section level3">
<div id="new-3" class="section level3">
<h3 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h3>
<a href="#new-3" class="anchor"></a>New</h3>
<ul>
<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics and the <code><a href="../reference/mdro.html">mdro()</a></code> function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the arguments <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2. The <code><a href="../reference/mdro.html">mdro()</a></code> function now accepts <code>guideline == "EUCAST3.1"</code> and <code>guideline == "EUCAST3.2"</code>.</p></li>
<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
@ -644,9 +623,9 @@
<li><p>Support for skimming classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;mo&gt;</code> with the <code>skimr</code> package</p></li>
</ul>
</div>
<div id="changed-4" class="section level3">
<div id="changed-3" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-4" class="anchor"></a>Changed</h3>
<a href="#changed-3" class="anchor"></a>Changed</h3>
<ul>
<li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
<li>
@ -725,9 +704,9 @@
<div id="amr-130" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a><small> 2020-07-31 </small><code>AMR</code> 1.3.0</h1>
<div id="new-5" class="section level3">
<div id="new-4" class="section level3">
<h3 class="hasAnchor">
<a href="#new-5" class="anchor"></a>New</h3>
<a href="#new-4" class="anchor"></a>New</h3>
<ul>
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
@ -749,9 +728,9 @@
<li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
</ul>
</div>
<div id="changed-5" class="section level3">
<div id="changed-4" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-5" class="anchor"></a>Changed</h3>
<a href="#changed-4" class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
@ -824,9 +803,9 @@
</li>
</ul>
</div>
<div id="changed-6" class="section level3">
<div id="changed-5" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-6" class="anchor"></a>Changed</h3>
<a href="#changed-5" class="anchor"></a>Changed</h3>
<ul>
<li>Taxonomy:
<ul>
@ -870,17 +849,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-110" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a><small> 2020-04-15 </small><code>AMR</code> 1.1.0</h1>
<div id="new-6" class="section level3">
<div id="new-5" class="section level3">
<h3 class="hasAnchor">
<a href="#new-6" class="anchor"></a>New</h3>
<a href="#new-5" class="anchor"></a>New</h3>
<ul>
<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
</ul>
</div>
<div id="changed-7" class="section level3">
<div id="changed-6" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h3>
<a href="#changed-6" class="anchor"></a>Changed</h3>
<ul>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
@ -911,9 +890,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-101" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
<div id="changed-8" class="section level3">
<div id="changed-7" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-8" class="anchor"></a>Changed</h3>
<a href="#changed-7" class="anchor"></a>Changed</h3>
<ul>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
@ -936,9 +915,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h1 class="page-header" data-toc-text="1.0.0">
<a href="#amr-100" class="anchor"></a><small> 2020-02-17 </small><code>AMR</code> 1.0.0</h1>
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
<div id="new-7" class="section level3">
<div id="new-6" class="section level3">
<h3 class="hasAnchor">
<a href="#new-7" class="anchor"></a>New</h3>
<a href="#new-6" class="anchor"></a>New</h3>
<ul>
<li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
@ -1033,9 +1012,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="new-8" class="section level3">
<div id="new-7" class="section level3">
<h3 class="hasAnchor">
<a href="#new-8" class="anchor"></a>New</h3>
<a href="#new-7" class="anchor"></a>New</h3>
<ul>
<li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
@ -1152,9 +1131,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
<div id="new-9" class="section level3">
<div id="new-8" class="section level3">
<h3 class="hasAnchor">
<a href="#new-9" class="anchor"></a>New</h3>
<a href="#new-8" class="anchor"></a>New</h3>
<ul>
<li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
@ -1219,9 +1198,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="changed-9" class="section level3">
<div id="changed-8" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-9" class="anchor"></a>Changed</h3>
<a href="#changed-8" class="anchor"></a>Changed</h3>
<ul>
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<ul>
@ -1285,9 +1264,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-071" class="section level1">
<h1 class="page-header" data-toc-text="0.7.1">
<a href="#amr-071" class="anchor"></a><small> 2019-06-23 </small><code>AMR</code> 0.7.1</h1>
<div id="new-10" class="section level4">
<div id="new-9" class="section level4">
<h4 class="hasAnchor">
<a href="#new-10" class="anchor"></a>New</h4>
<a href="#new-9" class="anchor"></a>New</h4>
<ul>
<li>
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
@ -1331,9 +1310,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
</ul>
</div>
<div id="changed-10" class="section level4">
<div id="changed-9" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-10" class="anchor"></a>Changed</h4>
<a href="#changed-9" class="anchor"></a>Changed</h4>
<ul>
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li>
@ -1369,9 +1348,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-070" class="section level1">
<h1 class="page-header" data-toc-text="0.7.0">
<a href="#amr-070" class="anchor"></a><small> 2019-06-03 </small><code>AMR</code> 0.7.0</h1>
<div id="new-11" class="section level4">
<div id="new-10" class="section level4">
<h4 class="hasAnchor">
<a href="#new-11" class="anchor"></a>New</h4>
<a href="#new-10" class="anchor"></a>New</h4>
<ul>
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
@ -1379,9 +1358,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
</ul>
</div>
<div id="changed-11" class="section level4">
<div id="changed-10" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-11" class="anchor"></a>Changed</h4>
<a href="#changed-10" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
@ -1465,9 +1444,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-061" class="section level1">
<h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
<div id="changed-12" class="section level4">
<div id="changed-11" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-12" class="anchor"></a>Changed</h4>
<a href="#changed-11" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
</li>
@ -1484,9 +1463,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Contains the complete manual of this package and all of its functions with an explanation of their arguments</li>
<li>Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<div id="new-12" class="section level4">
<div id="new-11" class="section level4">
<h4 class="hasAnchor">
<a href="#new-12" class="anchor"></a>New</h4>
<a href="#new-11" class="anchor"></a>New</h4>
<ul>
<li><p><strong>BREAKING</strong>: removed deprecated functions, arguments and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
<li>
@ -1584,9 +1563,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
</div>
<div id="changed-13" class="section level4">
<div id="changed-12" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-13" class="anchor"></a>Changed</h4>
<a href="#changed-12" class="anchor"></a>Changed</h4>
<ul>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
@ -1729,9 +1708,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-050" class="section level1">
<h1 class="page-header" data-toc-text="0.5.0">
<a href="#amr-050" class="anchor"></a><small> 2018-11-30 </small><code>AMR</code> 0.5.0</h1>
<div id="new-13" class="section level4">
<div id="new-12" class="section level4">
<h4 class="hasAnchor">
<a href="#new-13" class="anchor"></a>New</h4>
<a href="#new-12" class="anchor"></a>New</h4>
<ul>
<li>Repository moved to GitLab</li>
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
@ -1742,9 +1721,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
</ul>
</div>
<div id="changed-14" class="section level4">
<div id="changed-13" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-14" class="anchor"></a>Changed</h4>
<a href="#changed-13" class="anchor"></a>Changed</h4>
<ul>
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
@ -1852,9 +1831,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-040" class="section level1">
<h1 class="page-header" data-toc-text="0.4.0">
<a href="#amr-040" class="anchor"></a><small> 2018-10-01 </small><code>AMR</code> 0.4.0</h1>
<div id="new-14" class="section level4">
<div id="new-13" class="section level4">
<h4 class="hasAnchor">
<a href="#new-14" class="anchor"></a>New</h4>
<a href="#new-13" class="anchor"></a>New</h4>
<ul>
<li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
<li>
@ -1932,9 +1911,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
</ul>
</div>
<div id="changed-15" class="section level4">
<div id="changed-14" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-15" class="anchor"></a>Changed</h4>
<a href="#changed-14" class="anchor"></a>Changed</h4>
<ul>
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
@ -2000,9 +1979,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-030" class="section level1">
<h1 class="page-header" data-toc-text="0.3.0">
<a href="#amr-030" class="anchor"></a><small> 2018-08-14 </small><code>AMR</code> 0.3.0</h1>
<div id="new-15" class="section level4">
<div id="new-14" class="section level4">
<h4 class="hasAnchor">
<a href="#new-15" class="anchor"></a>New</h4>
<a href="#new-14" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
@ -2073,9 +2052,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="changed-16" class="section level4">
<div id="changed-15" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-16" class="anchor"></a>Changed</h4>
<a href="#changed-15" class="anchor"></a>Changed</h4>
<ul>
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
<li>More antibiotics added as arguments for EUCAST rules</li>
@ -2136,9 +2115,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div id="amr-020" class="section level1">
<h1 class="page-header" data-toc-text="0.2.0">
<a href="#amr-020" class="anchor"></a><small> 2018-05-03 </small><code>AMR</code> 0.2.0</h1>
<div id="new-16" class="section level4">
<div id="new-15" class="section level4">
<h4 class="hasAnchor">
<a href="#new-16" class="anchor"></a>New</h4>
<a href="#new-15" class="anchor"></a>New</h4>
<ul>
<li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
@ -2158,9 +2137,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul>
</div>
<div id="changed-17" class="section level4">
<div id="changed-16" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-17" class="anchor"></a>Changed</h4>
<a href="#changed-16" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-06-01T14:35Z
last_built: 2021-06-03T13:04Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/AMR-deprecated.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/AMR.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/WHOCC.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/WHONET.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/ab_from_text.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/ab_property.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/age.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/age_groups.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

1207
docs/reference/antibiotic_class_selectors.html
View File

File diff suppressed because it is too large Load Diff

2
docs/reference/antibiotics.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/as.ab.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/as.disk.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/as.mic.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/as.mo.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/as.rsi.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/atc_online.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/availability.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/count.html
View File

@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/custom_eucast_rules.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/dosage.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/eucast_rules.html
View File

@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/example_isolates.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/example_isolates_unclean.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/first_isolate.html
View File

@ -83,7 +83,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/g.test.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/get_episode.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/ggplot_pca.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/intrinsic_resistant.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/italicise_taxonomy.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/join.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/key_antimicrobials.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/kurtosis.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/lifecycle.html
View File

@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/like.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/mdro.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/microorganisms.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/mo_matching_score.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/mo_source.html
View File

@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/pca.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/plot.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/proportion.html
View File

@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/random.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/resistance_predict.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/rsi_translation.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/skewness.html
View File

@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/reference/translate.html
View File

@ -82,7 +82,7 @@
</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">1.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
</span>
</div>

29
index.md
View File

@ -98,16 +98,10 @@ This package can be used for:
#### Latest released version
This package is [available here](https://msberends.r-universe.dev) on the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), as CRAN does not allow frequent updates of large packages (though the `AMR` package is only 7-9 MB). We are working on splitting this package into two: a new data package containing the microbial taxonomy, and the `AMR` package that only contains all functions.
[![CRAN](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.r-project.org/package=AMR)
[![CRANlogs](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.r-project.org/package=AMR)
In the meanwhile, you have to add [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'), by running:
```r
options(repos = c(getOption("repos"),
msberends = "https://msberends.r-universe.dev"))
```
You can now install or update the `AMR` package in the same way you are used to:
This package is available [here on the official R network (CRAN)](https://cran.r-project.org/package=AMR). Install this package in R from CRAN by using the command:
```r
install.packages("AMR")
@ -117,18 +111,27 @@ It will be downloaded and installed automatically. For RStudio, click on the men
**Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.
#### Latest development version
The latest and unpublished development version can be installed from GitHub using:
![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)
![[CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
![[Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
The latest and unpublished development version can be installed from GitHub in two ways:
1. Directly, using:
```r
install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")
```
![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)
![[CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
![[Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
2. From the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
```r
options(repos = c(getOption("repos"),
msberends = "https://msberends.r-universe.dev"))
```
After this, you can install and update this `AMR` package like any official release (e.g., using `install.packages("AMR")` or in RStudio via *Tools* > *Check for Package Updates...*).
You can also download the latest build from our repository: <https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz>

5
man/antibiotic_class_selectors.Rd
View File

@ -118,6 +118,11 @@ example_isolates[any(carbapenems() == "R"), penicillins()]
\donttest{
if (require("dplyr")) {
# get AMR for all aminoglycosides e.g., per hospital:
example_isolates \%>\%
group_by(hospital_id) \%>\%
summarise(across(aminoglycosides(), resistance))
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
example_isolates \%>\%
select(carbapenems())