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AMR
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(v0.7.0.9002) scale fix

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dr. M.S. (Matthijs) Berends 2019-06-08 15:00:28 +02:00
parent f02679fb63
commit f50d3a5ba1
11 changed files with 13 additions and 16 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.0.9001
Date: 2019-06-07
Version: 0.7.0.9002
Date: 2019-06-08
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

2
NAMESPACE
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@ -173,8 +173,6 @@ export(resistance_predict)
export(right_join_microorganisms)
export(rsi_predict)
export(scale_rsi_colours)
export(scale_type.ab)
export(scale_type.mo)
export(scale_y_percent)
export(semi_join_microorganisms)
export(set_mo_source)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.0.9001
# AMR 0.7.0.9002
#### New
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:

1
R/ab.R
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@ -260,7 +260,6 @@ pull.ab <- function(.data, ...) {
}
#' @exportMethod scale_type.ab
#' @export
#' @noRd
scale_type.ab <- function(x) {
# fix for:

2
R/mo.R
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@ -1486,7 +1486,7 @@ translate_allow_uncertain <- function(allow_uncertain) {
}
#' @exportMethod scale_type.mo
#' @export
# @export
#' @noRd
scale_type.mo <- function(x) {
# fix for:

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
</span>
</div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
</span>
</div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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="Released version">0.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
</span>
</div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
</span>
</div>
@ -239,9 +239,9 @@
</div>
<div id="amr-0709001" class="section level1">
<div id="amr-0709002" class="section level1">
<h1 class="page-header">
<a href="#amr-0709001" class="anchor"></a>AMR 0.7.0.9001<small> Unreleased </small>
<a href="#amr-0709002" class="anchor"></a>AMR 0.7.0.9002<small> Unreleased </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
@ -1108,7 +1108,7 @@ 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-0709001">0.7.0.9001</a></li>
<li><a href="#amr-0709002">0.7.0.9002</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>

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docs/reference/index.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
</span>
</div>