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(v1.7.1.9052) eucast-update

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dr. M.S. (Matthijs) Berends 2021-10-06 16:22:36 +02:00
parent 37e6e35ec4
commit 91149d6d35
8 changed files with 9 additions and 9 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.7.1.9051 Version: 1.7.1.9052
Date: 2021-10-06 Date: 2021-10-06
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# `AMR` 1.7.1.9051 # `AMR` 1.7.1.9052
## <small>Last updated: 6 October 2021</small> ## <small>Last updated: 6 October 2021</small>
### Breaking changes ### Breaking changes

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R/aa_helper_functions.R
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@ -303,7 +303,7 @@ pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
out <- requireNamespace(pkg, quietly = TRUE) out <- requireNamespace(pkg, quietly = TRUE)
} }
if (!is.null(min_version)) { if (!is.null(min_version)) {
out <- out && packageVersion(pkg) >= min_version out <- out && utils::packageVersion(pkg) >= min_version
} }
isTRUE(out) isTRUE(out)
} }

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R/sysdata.rda
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data-raw/AMR_latest.tar.gz
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data-raw/eucast_rules.tsv
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@ -367,7 +367,7 @@ genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rule
genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.2 genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.2
fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.2 fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.2
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.2 fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.2
genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Metakosakonia, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp. genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp.
fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.2 fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.2
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2 genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2 genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2

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docs/articles/datasets.html
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@ -44,7 +44,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9052</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -92,7 +92,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9052</span>
</span> </span>
</div> </div>
@ -240,9 +240,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1719051" class="section level1"> <div id="amr-1719052" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9051"> <h1 class="page-header" data-toc-text="1.7.1.9052">
<a href="#amr-1719051" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9051</h1> <a href="#amr-1719052" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9052</h1>
<div id="last-updated-6-october-2021" class="section level2"> <div id="last-updated-6-october-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-6-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 6 October 2021</small> <a href="#last-updated-6-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 6 October 2021</small>