Browse Source

(v1.7.1.9075) assignment operator

development
parent
commit
d9274bcd0a
  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. 2
      R/mo.R
  4. BIN
      data-raw/AMR_latest.tar.gz
  5. 102
      docs/articles/datasets.html
  6. 2
      docs/articles/index.html
  7. 16
      docs/news/index.html
  8. 10
      vignettes/datasets.Rmd

2
DESCRIPTION

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9074
Version: 1.7.1.9075
Date: 2021-12-14
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md

@ -1,4 +1,4 @@ @@ -1,4 +1,4 @@
# `AMR` 1.7.1.9074
# `AMR` 1.7.1.9075
## <small>Last updated: 14 December 2021</small>
All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.

2
R/mo.R

@ -613,8 +613,6 @@ exec_as.mo <- function(x, @@ -613,8 +613,6 @@ exec_as.mo <- function(x,
on.exit(close(progress))
}
xx <<- x_backup[!already_known]
for (i in which(!already_known)) {
if (initial_search == TRUE) {

BIN
data-raw/AMR_latest.tar.gz

Binary file not shown.

102
docs/articles/datasets.html

@ -44,7 +44,7 @@ @@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9073</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9075</span>
</span>
</div>
@ -788,7 +788,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -788,7 +788,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div class="section level2">
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 December 2021 17:16:54 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
@ -808,7 +808,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -808,7 +808,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2</a> (2020).</p>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
</div>
<div class="section level3">
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@ -826,14 +826,6 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -826,14 +826,6 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Acetylspiramycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Amoxicillin/clavulanic acid</td>
</tr>
<tr class="odd">
@ -842,19 +834,19 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -842,19 +834,19 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Ampicillin/sulbactam</td>
<td align="center">Amoxicillin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Avoparcin</td>
<td align="center">Acetylspiramycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Azithromycin</td>
<td align="center">Avoparcin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Benzylpenicillin</td>
<td align="center">Azithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
@ -862,23 +854,15 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -862,23 +854,15 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefadroxil</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefazolin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cefoxitin</td>
<td align="center">Cephalothin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cephalexin</td>
<td align="center">Cefadroxil</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cephalothin</td>
<td align="center">Clindamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
@ -886,11 +870,11 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -886,11 +870,11 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Clindamycin</td>
<td align="center">Cycloserine</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Cycloserine</td>
<td align="center">Cefazolin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
@ -910,19 +894,27 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -910,19 +894,27 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Fusidic acid</td>
<td align="center">Cefoxitin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Gamithromycin</td>
<td align="center">Fusidic acid</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Gamithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Josamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Kitasamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Kitasamycin (Leucomycin)</td>
<td align="center">Cephalexin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
@ -934,43 +926,43 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -934,43 +926,43 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Meleumycin</td>
<td align="center">Miocamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Midecamycin</td>
<td align="center">Meleumycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Miocamycin</td>
<td align="center">Midecamycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Nafithromycin</td>
<td align="center">Norvancomycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Norvancomycin</td>
<td align="center">Oleandomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oleandomycin</td>
<td align="center">Oritavancin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Oritavancin</td>
<td align="center">Benzylpenicillin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pirlimycin</td>
<td align="center">Pristinamycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Primycin</td>
<td align="center">Pirlimycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pristinamycin</td>
<td align="center">Primycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
@ -994,15 +986,15 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -994,15 +986,15 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Solithromycin</td>
<td align="center">Ampicillin/sulbactam</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Spiramycin</td>
<td align="center">Solithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tedizolid</td>
<td align="center">Spiramycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
@ -1010,23 +1002,23 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -1010,23 +1002,23 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Telavancin</td>
<td align="center">Thiacetazone</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Telithromycin</td>
<td align="center">Tilmicosin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Thiacetazone</td>
<td align="center">Tildipirosin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tildipirosin</td>
<td align="center">Telithromycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tilmicosin</td>
<td align="center">Telavancin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
@ -1046,8 +1038,16 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -1046,8 +1038,16 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Tedizolid</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Vancomycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Nafithromycin</td>
</tr>
</tbody>
</table>
</div>
@ -1057,7 +1057,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -1057,7 +1057,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</h2>
<p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</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 13 December 2021 10:53:42 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 14 December 2021 21:17:09 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/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
@ -1070,7 +1070,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi @@ -1070,7 +1070,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.4 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>

2
docs/articles/index.html

@ -17,7 +17,7 @@ @@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9074</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9075</span>
</span>
</div>

16
docs/news/index.html

@ -17,7 +17,7 @@ @@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9074</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9075</span>
</span>
</div>
@ -157,13 +157,13 @@ @@ -157,13 +157,13 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.7.1.9074" id="amr-1719074">
<code>AMR</code> 1.7.1.9074<a class="anchor" aria-label="anchor" href="#amr-1719074"></a></h2>
<h2 class="page-header" data-toc-text="1.7.1.9075" id="amr-1719075">
<code>AMR</code> 1.7.1.9075<a class="anchor" aria-label="anchor" href="#amr-1719075"></a></h2>
<div class="section level3">
<h3 id="last-updated-december-1-7-1-9074"><small>Last updated: 14 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9074"></a></h3>
<h3 id="last-updated-december-1-7-1-9075"><small>Last updated: 14 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9075"></a></h3>
<p>All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</p>
<div class="section level4">
<h4 id="breaking-changes-1-7-1-9074">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9074"></a></h4>
<h4 id="breaking-changes-1-7-1-9075">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9075"></a></h4>
<ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
<li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code>
</li>
@ -171,7 +171,7 @@ @@ -171,7 +171,7 @@
<li>Renamed function <code>get_locale()</code> to <code><a href="../reference/translate.html">get_AMR_locale()</a></code> to prevent conflicts with other packages</li>
</ul></div>
<div class="section level4">
<h4 id="new-1-7-1-9074">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9074"></a></h4>
<h4 id="new-1-7-1-9075">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9075"></a></h4>
<ul><li><p>Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the <code>rsi_translation</code> data set. This data set now more strictly follows the WHONET software as well.</p></li>
<li><p>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>. The <code>intrinsic_resistant</code> data set was also updated accordingly.</p></li>
<li><p>Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish</p></li>
@ -186,7 +186,7 @@ @@ -186,7 +186,7 @@
<li><p>Function <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> to get units of DDDs (daily defined doses), deprecating the use of <code>ab_ddd(..., units = TRUE)</code> to be more consistent in data types of function output</p></li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-7-1-9074">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9074"></a></h4>
<h4 id="changed-1-7-1-9075">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9075"></a></h4>
<ul><li>Updated the bacterial taxonomy to 5 October 2021 (according to <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>), including all 11 new staphylococcal species named since 1 January last year</li>
<li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <a href="https://www.whocc.no" class="external-link">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that:
<ul><li>Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)</li>
@ -258,7 +258,7 @@ @@ -258,7 +258,7 @@
<code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> can now cope with <code>NA</code>s</li>
</ul></div>
<div class="section level4">
<h4 id="other-1-7-1-9074">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9074"></a></h4>
<h4 id="other-1-7-1-9075">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9075"></a></h4>
<ul><li>This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations.</li>
</ul></div>
</div>

10
vignettes/datasets.Rmd vendored

@ -120,10 +120,8 @@ Included (sub)species per taxonomic kingdom: @@ -120,10 +120,8 @@ Included (sub)species per taxonomic kingdom:
```{r, echo = FALSE}
microorganisms %>%
pull(kingdom) %>%
table() %>%
as.data.frame() %>%
mutate(Freq = format(Freq, big.mark = ",")) %>%
count(kingdom) %>%
mutate(n = format(n, big.mark = ",")) %>%
setNames(c("Kingdom", "Number of (sub)species")) %>%
print_df()
```
@ -222,7 +220,7 @@ This data set is in R available as `intrinsic_resistant`, after you load the `AM @@ -222,7 +220,7 @@ This data set is in R available as `intrinsic_resistant`, after you load the `AM
### Source
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on `r AMR:::format_eucast_version_nr("3.2")`.
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on `r AMR:::format_eucast_version_nr("3.3")`.
### Example content
@ -230,6 +228,8 @@ Example rows when filtering on *Enterobacter cloacae*: @@ -230,6 +228,8 @@ Example rows when filtering on *Enterobacter cloacae*:
```{r, echo = FALSE}
intrinsic_resistant %>%
transmute(microorganism = mo_name(mo),
antibiotic = ab_name(ab)) %>%
filter(microorganism == "Enterobacter cloacae") %>%
print_df(rows = Inf)
```

Loading…
Cancel
Save