mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 07:26:13 +01:00
(v0.7.0.9002) scale fix
This commit is contained in:
parent
f02679fb63
commit
f50d3a5ba1
@ -1,6 +1,6 @@
|
|||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 0.7.0.9001
|
Version: 0.7.0.9002
|
||||||
Date: 2019-06-07
|
Date: 2019-06-08
|
||||||
Title: Antimicrobial Resistance Analysis
|
Title: Antimicrobial Resistance Analysis
|
||||||
Authors@R: c(
|
Authors@R: c(
|
||||||
person(
|
person(
|
||||||
|
|||||||
@ -173,8 +173,6 @@ export(resistance_predict)
|
|||||||
export(right_join_microorganisms)
|
export(right_join_microorganisms)
|
||||||
export(rsi_predict)
|
export(rsi_predict)
|
||||||
export(scale_rsi_colours)
|
export(scale_rsi_colours)
|
||||||
export(scale_type.ab)
|
|
||||||
export(scale_type.mo)
|
|
||||||
export(scale_y_percent)
|
export(scale_y_percent)
|
||||||
export(semi_join_microorganisms)
|
export(semi_join_microorganisms)
|
||||||
export(set_mo_source)
|
export(set_mo_source)
|
||||||
|
|||||||
2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
|
|||||||
# AMR 0.7.0.9001
|
# AMR 0.7.0.9002
|
||||||
|
|
||||||
#### New
|
#### 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*:
|
* 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
1
R/ab.R
@ -260,7 +260,6 @@ pull.ab <- function(.data, ...) {
|
|||||||
}
|
}
|
||||||
|
|
||||||
#' @exportMethod scale_type.ab
|
#' @exportMethod scale_type.ab
|
||||||
#' @export
|
|
||||||
#' @noRd
|
#' @noRd
|
||||||
scale_type.ab <- function(x) {
|
scale_type.ab <- function(x) {
|
||||||
# fix for:
|
# fix for:
|
||||||
|
|||||||
2
R/mo.R
2
R/mo.R
@ -1486,7 +1486,7 @@ translate_allow_uncertain <- function(allow_uncertain) {
|
|||||||
}
|
}
|
||||||
|
|
||||||
#' @exportMethod scale_type.mo
|
#' @exportMethod scale_type.mo
|
||||||
#' @export
|
# @export
|
||||||
#' @noRd
|
#' @noRd
|
||||||
scale_type.mo <- function(x) {
|
scale_type.mo <- function(x) {
|
||||||
# fix for:
|
# fix for:
|
||||||
|
|||||||
@ -78,7 +78,7 @@
|
|||||||
</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="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>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -78,7 +78,7 @@
|
|||||||
</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="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>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -78,7 +78,7 @@
|
|||||||
</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="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>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -42,7 +42,7 @@
|
|||||||
</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="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>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -78,7 +78,7 @@
|
|||||||
</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="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>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -239,9 +239,9 @@
|
|||||||
|
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div id="amr-0709001" class="section level1">
|
<div id="amr-0709002" class="section level1">
|
||||||
<h1 class="page-header">
|
<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>
|
</h1>
|
||||||
<div id="new" class="section level4">
|
<div id="new" class="section level4">
|
||||||
<h4 class="hasAnchor">
|
<h4 class="hasAnchor">
|
||||||
@ -1108,7 +1108,7 @@ 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-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-070">0.7.0</a></li>
|
||||||
<li><a href="#amr-061">0.6.1</a></li>
|
<li><a href="#amr-061">0.6.1</a></li>
|
||||||
<li><a href="#amr-060">0.6.0</a></li>
|
<li><a href="#amr-060">0.6.0</a></li>
|
||||||
|
|||||||
@ -78,7 +78,7 @@
|
|||||||
</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="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>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user