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(v0.8.0.9011) col guess update

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dr. M.S. (Matthijs) Berends 2019-11-04 12:08:08 +01:00
parent 9060233953
commit fe606e287b
10 changed files with 20 additions and 14 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.8.0.9010 Version: 0.8.0.9011
Date: 2019-11-04 Date: 2019-11-04
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.8.0.9010 # AMR 0.8.0.9011
<small>Last updated: 04-Nov-2019</small> <small>Last updated: 04-Nov-2019</small>
### New ### New

10
R/misc.R
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@ -36,11 +36,17 @@ search_type_in_df <- function(x, type) {
found <- NULL found <- NULL
colnames(x) <- trimws(colnames(x)) colnames(x) <- trimws(colnames(x))
# -- mo # -- mo
if (type == "mo") { if (type == "mo") {
if ("mo" %in% lapply(x, class)) { if ("mo" %in% lapply(x, class)) {
found <- colnames(x)[lapply(x, class) == "mo"][1] found <- colnames(x)[lapply(x, class) == "mo"][1]
} else if ("mo" %in% colnames(x) &
suppressWarnings(
all(x$mo %in% c(NA,
microorganisms$mo,
microorganisms.translation$mo_old)))) {
found <- "mo"
} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$")) { } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$")) {
found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$"][1] found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$"][1]
} else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)")) { } else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)")) {
@ -48,7 +54,7 @@ search_type_in_df <- function(x, type) {
} else if (any(colnames(x) %like% "species")) { } else if (any(colnames(x) %like% "species")) {
found <- colnames(x)[colnames(x) %like% "species"][1] found <- colnames(x)[colnames(x) %like% "species"][1]
} }
} }
# -- key antibiotics # -- key antibiotics
if (type == "keyantibiotics") { if (type == "keyantibiotics") {

2
docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -45,7 +45,7 @@
</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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0-8-0-9010" class="section level1"> <div id="amr-0-8-0-9011" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-8-0-9010" class="anchor"></a>AMR 0.8.0.9010<small> Unreleased </small> <a href="#amr-0-8-0-9011" class="anchor"></a>AMR 0.8.0.9011<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 04-Nov-2019</small></p> <p><small>Last updated: 04-Nov-2019</small></p>
<div id="new" class="section level3"> <div id="new" class="section level3">
@ -1333,7 +1333,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-8-0-9010">0.8.0.9010</a></li> <li><a href="#amr-0-8-0-9011">0.8.0.9011</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li> <li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</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-0-7-0">0.7.0</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9011</span>
</span> </span>
</div> </div>