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(v0.7.0.9002) scale fix
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Package: AMR
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Package: AMR
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Version: 0.7.0.9001
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Version: 0.7.0.9002
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Date: 2019-06-07
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Date: 2019-06-08
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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person(
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person(
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@ -173,8 +173,6 @@ export(resistance_predict)
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export(right_join_microorganisms)
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export(right_join_microorganisms)
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export(rsi_predict)
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export(rsi_predict)
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export(scale_rsi_colours)
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export(scale_rsi_colours)
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export(scale_type.ab)
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export(scale_type.mo)
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export(scale_y_percent)
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export(scale_y_percent)
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export(semi_join_microorganisms)
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export(semi_join_microorganisms)
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export(set_mo_source)
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export(set_mo_source)
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.0.9001
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# AMR 0.7.0.9002
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#### New
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#### New
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* 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*:
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* 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*:
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1
R/ab.R
1
R/ab.R
@ -260,7 +260,6 @@ pull.ab <- function(.data, ...) {
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}
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}
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#' @exportMethod scale_type.ab
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#' @exportMethod scale_type.ab
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#' @export
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#' @noRd
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#' @noRd
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scale_type.ab <- function(x) {
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scale_type.ab <- function(x) {
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# fix for:
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# fix for:
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2
R/mo.R
2
R/mo.R
@ -1486,7 +1486,7 @@ translate_allow_uncertain <- function(allow_uncertain) {
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}
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}
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#' @exportMethod scale_type.mo
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#' @exportMethod scale_type.mo
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#' @export
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# @export
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#' @noRd
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#' @noRd
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scale_type.mo <- function(x) {
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scale_type.mo <- function(x) {
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# fix for:
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# fix for:
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.7.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.7.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.7.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -42,7 +42,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.7.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.7.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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@ -239,9 +239,9 @@
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</div>
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</div>
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<div id="amr-0709001" class="section level1">
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<div id="amr-0709002" class="section level1">
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<h1 class="page-header">
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<h1 class="page-header">
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<a href="#amr-0709001" class="anchor"></a>AMR 0.7.0.9001<small> Unreleased </small>
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<a href="#amr-0709002" class="anchor"></a>AMR 0.7.0.9002<small> Unreleased </small>
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</h1>
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</h1>
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<div id="new" class="section level4">
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<div id="new" class="section level4">
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<h4 class="hasAnchor">
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<h4 class="hasAnchor">
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@ -1108,7 +1108,7 @@ 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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<div id="tocnav">
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<h2>Contents</h2>
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0709001">0.7.0.9001</a></li>
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<li><a href="#amr-0709002">0.7.0.9002</a></li>
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<li><a href="#amr-070">0.7.0</a></li>
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<li><a href="#amr-070">0.7.0</a></li>
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<li><a href="#amr-061">0.6.1</a></li>
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<li><a href="#amr-061">0.6.1</a></li>
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<li><a href="#amr-060">0.6.0</a></li>
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<li><a href="#amr-060">0.6.0</a></li>
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@ -78,7 +78,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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="Released version">0.7.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
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</span>
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</span>
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</div>
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</div>
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