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

(v1.7.1.9072) as.rsi() fix for UTIs

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-12-14 12:33:29 +01:00
parent 0cbf8f48b6
commit 5eef01165e
12 changed files with 1779 additions and 1778 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9071
Date: 2021-12-13
Version: 1.7.1.9072
Date: 2021-12-14
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

4
NEWS.md
View File

@ -1,5 +1,5 @@
# `AMR` 1.7.1.9071
## <small>Last updated: 13 December 2021</small>
# `AMR` 1.7.1.9072
## <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.

3
R/rsi.R
View File

@ -799,7 +799,8 @@ exec_as.rsi <- function(method,
lookup_lancefield <- paste(mo_lancefield, ab)
lookup_other <- paste(mo_other, ab)
if (all(trans$uti == TRUE, na.rm = TRUE) & all(uti == FALSE)) {
if (length(unique(paste(trans$mo, trans$ab))) == length(unique(paste(trans$mo, trans$ab, trans$uti))) &&
any(trans$uti == TRUE, na.rm = TRUE) && all(uti == FALSE)) {
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
warning_("Introducing NA: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI). Use argument `uti` to set which isolates are from urine. See ?as.rsi.", call = FALSE)
warned <- TRUE

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

Binary file not shown.

2
data-raw/rsi.md5
View File

@ -1 +1 @@
2d5adb3d28ff14e0ce09b391b4a55768
0ee01887dda2f9f829a0f1f60196cd4e

BIN
data-raw/rsi_translation.dta
View File

Binary file not shown.

BIN
data-raw/rsi_translation.rds
View File

Binary file not shown.

BIN
data-raw/rsi_translation.sas
View File

Binary file not shown.

BIN
data-raw/rsi_translation.sav
View File

Binary file not shown.

3522
data-raw/rsi_translation.txt
View File

File diff suppressed because it is too large Load Diff

6
docs/articles/datasets.html
View File

@ -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">1.7.1.9071</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9072</span>
</span>
</div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">13 December 2021</h4>
<h4 data-toc-skip class="date">14 December 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@ -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 10:08:29 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 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><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>

16
docs/news/index.html
View File

@ -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">1.7.1.9071</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9072</span>
</span>
</div>
@ -157,13 +157,13 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.7.1.9071" id="amr-1719071">
<code>AMR</code> 1.7.1.9071<a class="anchor" aria-label="anchor" href="#amr-1719071"></a></h2>
<h2 class="page-header" data-toc-text="1.7.1.9072" id="amr-1719072">
<code>AMR</code> 1.7.1.9072<a class="anchor" aria-label="anchor" href="#amr-1719072"></a></h2>
<div class="section level3">
<h3 id="last-updated-december-1-7-1-9071"><small>Last updated: 13 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9071"></a></h3>
<h3 id="last-updated-december-1-7-1-9072"><small>Last updated: 14 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9072"></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-1-7-1-9071">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9071"></a></h4>
<h4 id="breaking-changes-1-7-1-9072">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9072"></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 @@
<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-1-7-1-9071">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9071"></a></h4>
<h4 id="new-1-7-1-9072">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9072"></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 @@
<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-1-7-1-9071">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9071"></a></h4>
<h4 id="changed-1-7-1-9072">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9072"></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>
@ -256,7 +256,7 @@
<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-1-7-1-9071">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9071"></a></h4>
<h4 id="other-1-7-1-9072">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9072"></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>