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(v0.8.0.9010) mdro bug fix

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dr. M.S. (Matthijs) Berends 2019-11-04 11:35:34 +01:00
parent 0bb531f3e0
commit 9060233953
12 changed files with 29 additions and 19 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.8.0.9009 Version: 0.8.0.9010
Date: 2019-11-03 Date: 2019-11-04
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -25,6 +25,8 @@ Authors@R: c(
family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"), family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"),
person(role = "ctb", person(role = "ctb",
family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"), family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"),
person(role = "ctb",
family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
person(role = "ctb", person(role = "ctb",
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl")) family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"))
Description: Functions to simplify the analysis and prediction of Antimicrobial Description: Functions to simplify the analysis and prediction of Antimicrobial

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.8.0.9009 # AMR 0.8.0.9010
<small>Last updated: 03-Nov-2019</small> <small>Last updated: 04-Nov-2019</small>
### New ### New
* Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012). * Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012).
@ -18,6 +18,7 @@
### Other ### Other
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
* Added Dr. Sofia Ny as contributor
# AMR 0.8.0 # AMR 0.8.0

8
R/mdro.R
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@ -48,7 +48,7 @@
#' \item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests} #' \item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests}
#' } #' }
#' @rdname mdro #' @rdname mdro
#' @importFrom dplyr %>% filter_all #' @importFrom dplyr %>% filter_at vars all_vars pull
#' @importFrom crayon blue bold italic #' @importFrom crayon blue bold italic
#' @importFrom cleaner percentage #' @importFrom cleaner percentage
#' @export #' @export
@ -474,8 +474,8 @@ mdro <- function(x,
function(row, group_tbl = lst) { function(row, group_tbl = lst) {
sum(sapply(group_tbl, sum(sapply(group_tbl,
function(group) { function(group) {
any(x[row, group[!is.na(group)]] == "R") | any(x[row, group[!is.na(group)]] == "R", na.rm = TRUE) |
any(x[row, group[!is.na(group)]] == "I") any(x[row, group[!is.na(group)]] == "I", na.rm = TRUE)
}), }),
na.rm = TRUE) na.rm = TRUE)
}) })
@ -975,7 +975,7 @@ mdro <- function(x,
# Results ---- # Results ----
if (guideline$code == "cmi2012") { if (guideline$code == "cmi2012") {
if (any(x$MDRO == -1)) { if (any(x$MDRO == -1, na.rm = TRUE)) {
warning("NA introduced for isolates where the available percentage of antimicrobial classes was below ", warning("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)") percentage(pct_required_classes), " (set with `pct_required_classes`)")
# set these -1s to NA # set these -1s to NA

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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</span>
</span> </span>
</div> </div>

6
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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</span>
</span> </span>
</div> </div>
@ -275,6 +275,10 @@
<p><strong>Bart C. Meijer</strong>. Contributor. <p><strong>Bart C. Meijer</strong>. Contributor.
</p> </p>
</li> </li>
<li>
<p><strong>Sofia Ny</strong>. Contributor.
</p>
</li>
<li> <li>
<p><strong>Dennis Souverein</strong>. Contributor. <p><strong>Dennis Souverein</strong>. Contributor.
</p> </p>

1
docs/extra.js
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@ -87,6 +87,7 @@ $( document ).ready(function() {
x = x.replace("Corinna", "Dr. Corinna"); x = x.replace("Corinna", "Dr. Corinna");
// others // others
x = x.replace("Bart", "Dr. Bart"); x = x.replace("Bart", "Dr. Bart");
x = x.replace("Sofia", "Dr. Sofia");
x = x.replace("Dennis", "Dr. Dennis"); x = x.replace("Dennis", "Dr. Dennis");
x = x.replace("Judith", "Dr. Judith"); x = x.replace("Judith", "Dr. Judith");
} }

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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</span>
</span> </span>
</div> </div>

11
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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</span>
</span> </span>
</div> </div>
@ -231,11 +231,11 @@
</div> </div>
<div id="amr-0-8-0-9009" class="section level1"> <div id="amr-0-8-0-9010" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-8-0-9009" class="anchor"></a>AMR 0.8.0.9009<small> Unreleased </small> <a href="#amr-0-8-0-9010" class="anchor"></a>AMR 0.8.0.9010<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 03-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">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3> <a href="#new" class="anchor"></a>New</h3>
@ -269,6 +269,7 @@
<a href="#other" class="anchor"></a>Other</h3> <a href="#other" class="anchor"></a>Other</h3>
<ul> <ul>
<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li> <li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
<li>Added Dr. Sofia Ny as contributor</li>
</ul> </ul>
</div> </div>
</div> </div>
@ -1332,7 +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-0-8-0-9009">0.8.0.9009</a></li> <li><a href="#amr-0-8-0-9010">0.8.0.9010</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>

2
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">0.8.0.9009</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9010</span>
</span> </span>
</div> </div>

1
pkgdown/extra.js
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@ -87,6 +87,7 @@ $( document ).ready(function() {
x = x.replace("Corinna", "Dr. Corinna"); x = x.replace("Corinna", "Dr. Corinna");
// others // others
x = x.replace("Bart", "Dr. Bart"); x = x.replace("Bart", "Dr. Bart");
x = x.replace("Sofia", "Dr. Sofia");
x = x.replace("Dennis", "Dr. Dennis"); x = x.replace("Dennis", "Dr. Dennis");
x = x.replace("Judith", "Dr. Judith"); x = x.replace("Judith", "Dr. Judith");
} }