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(v1.7.1.9052) eucast-update

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  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. 2
      R/aa_helper_functions.R
  4. BIN
      R/sysdata.rda
  5. BIN
      data-raw/AMR_latest.tar.gz
  6. 2
      data-raw/eucast_rules.tsv
  7. 2
      docs/articles/datasets.html
  8. 8
      docs/news/index.html

2
DESCRIPTION

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9051
Version: 1.7.1.9052
Date: 2021-10-06
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` 1.7.1.9051
# `AMR` 1.7.1.9052
## <small>Last updated: 6 October 2021</small>
### Breaking changes

2
R/aa_helper_functions.R

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

@ -367,7 +367,7 @@ genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rule @@ -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
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
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
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

Can't render this file because it contains an unexpected character in line 6 and column 96.

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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="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>
</div>

8
docs/news/index.html

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

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