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(v0.7.1.9095) get_column_abx() fix
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Package: AMR
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Version: 0.7.1.9094
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Version: 0.7.1.9095
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Date: 2019-10-06
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9094
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# AMR 0.7.1.9095
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<small>Last updated: 06-Oct-2019</small>
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### Breaking
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@ -129,9 +129,14 @@ get_column_abx <- function(x,
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x <- as.character(df_trans$colnames)
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names(x) <- df_trans$abcode
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# remove the ones that do not already have the rsi class (as.rsi) and that have >50% invalid values
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# remove the ones that are not a valid AB code, ATC code, name, abbreviation or synonym,
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# and do not already have the rsi class (as.rsi)
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# and that have >50% invalid values
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vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[,c("ab", "atc", "name", "abbreviations", "synonyms")])))
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vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
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x <- sapply(x, function(col = x, df = x_bak) {
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ifelse(is.rsi(as.data.frame(df)[, col]) |
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ifelse(toupper(col) %in% vectr_antibiotics |
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is.rsi(as.data.frame(df)[, col]) |
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is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5),
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col,
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NA)
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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@ -231,9 +231,9 @@
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</div>
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<div id="amr-0-7-1-9094" class="section level1">
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<div id="amr-0-7-1-9095" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9094" class="anchor"></a>AMR 0.7.1.9094<small> Unreleased </small>
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<a href="#amr-0-7-1-9095" class="anchor"></a>AMR 0.7.1.9095<small> Unreleased </small>
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</h1>
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<p><small>Last updated: 06-Oct-2019</small></p>
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<div id="breaking" class="section level3">
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@ -1289,7 +1289,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9094">0.7.1.9094</a></li>
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<li><a href="#amr-0-7-1-9095">0.7.1.9095</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9094</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9095</span>
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</span>
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</div>
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