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(v0.7.1.9061) mo_property improvement

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dr. M.S. (Matthijs) Berends 2019-08-26 10:03:37 +02:00
parent 05dcb43660
commit 13d4fef801
12 changed files with 26 additions and 21 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9060
Date: 2019-08-25
Version: 0.7.1.9061
Date: 2019-08-26
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9060
# AMR 0.7.1.9061
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). The `freq()` function still works, since it is re-exported from the `clean` package to this `AMR` package. Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

13
R/mo_property.R
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@ -144,7 +144,6 @@ mo_name <- function(x, language = get_locale(), ...) {
mo_fullname <- mo_name
#' @rdname mo_property
#' @importFrom dplyr %>% mutate pull
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
x.mo <- AMR::as.mo(x, ...)
@ -417,9 +416,15 @@ mo_validate <- function(x, property, ...) {
tryCatch(x[1L] %in% AMR::microorganisms[1, property],
error = function(e) stop(e$message, call. = FALSE))
if (!all(x %in% pull(AMR::microorganisms, property))
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
if (is.mo(x)
& !Becker %in% c(TRUE, "all")
& !Lancefield %in% c(TRUE, "all")) {
# this will not reset mo_uncertainties and mo_failures
# because it's already a valid MO
x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
} else if (!all(x %in% pull(AMR::microorganisms, property))
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
x <- exec_as.mo(x, property = property, ...)
}

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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
</span>
</div>
@ -225,9 +225,9 @@
</div>
<div id="amr-0-7-1-9059" class="section level1">
<div id="amr-0-7-1-9061" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9059" class="anchor"></a>AMR 0.7.1.9059<small> Unreleased </small>
<a href="#amr-0-7-1-9061" class="anchor"></a>AMR 0.7.1.9061<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -1252,7 +1252,7 @@ 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-0-7-1-9059">0.7.1.9059</a></li>
<li><a href="#amr-0-7-1-9061">0.7.1.9061</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-0-6-1">0.6.1</a></li>

2
docs/reference/availability.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html
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@ -80,7 +80,7 @@
</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
</span>
</div>

2
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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
</span>
</div>

2
docs/reference/reexports.html
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@ -84,7 +84,7 @@ below to see their documentation.
</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="Latest development version">0.7.1.9059</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9061</span>
</span>
</div>