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(v0.7.1.9095) get_column_abx() fix

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dr. M.S. (Matthijs) Berends 2019-10-06 22:19:26 +02:00
parent 3d5692219e
commit 1e260d85c8
10 changed files with 20 additions and 15 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.7.1.9094
Version: 0.7.1.9095
Date: 2019-10-06
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9094
# AMR 0.7.1.9095
<small>Last updated: 06-Oct-2019</small>
### Breaking

11
R/guess_ab_col.R
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@ -129,9 +129,14 @@ get_column_abx <- function(x,
x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode
# remove the ones that do not already have the rsi class (as.rsi) and that have >50% invalid values
x <- sapply(x, function(col = x, df = x_bak) {
ifelse(is.rsi(as.data.frame(df)[, col]) |
# remove the ones that are not a valid AB code, ATC code, name, abbreviation or synonym,
# and do not already have the rsi class (as.rsi)
# and that have >50% invalid values
vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[,c("ab", "atc", "name", "abbreviations", "synonyms")])))
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x <- sapply(x, function(col = x, df = x_bak) {
ifelse(toupper(col) %in% vectr_antibiotics |
is.rsi(as.data.frame(df)[, col]) |
is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5),
col,
NA)

2
docs/404.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>

8
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>
@ -231,9 +231,9 @@
</div>
<div id="amr-0-7-1-9094" class="section level1">
<div id="amr-0-7-1-9095" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9094" class="anchor"></a>AMR 0.7.1.9094<small> Unreleased </small>
<a href="#amr-0-7-1-9095" class="anchor"></a>AMR 0.7.1.9095<small> Unreleased </small>
</h1>
<p><small>Last updated: 06-Oct-2019</small></p>
<div id="breaking" class="section level3">
@ -1289,7 +1289,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9094">0.7.1.9094</a></li>
<li><a href="#amr-0-7-1-9095">0.7.1.9095</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9094</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
</span>
</div>