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(v0.7.1.9057) get_column_abx() improvement
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Package: AMR
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Version: 0.7.1.9056
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Date: 2019-08-14
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Version: 0.7.1.9057
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Date: 2019-08-15
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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3
NEWS.md
3
NEWS.md
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# AMR 0.7.1.9056
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# AMR 0.7.1.9057
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### Breaking
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* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). 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.
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@ -46,6 +46,7 @@
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* Printed info now distinguishes between added and changes values
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* Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output
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* Using factors as input now adds missing factors levels when the function changes antibiotic results
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* Improved the internal auto-guessing function for determining antibiotics in your data set (`AMR:::get_column_abx()`)
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* Added tibble printing support for classes `rsi`, `mic`, `disk`, `ab` `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red. Microbial IDs (class `mo`) will emphasise on the genus and species, not on the kingdom.
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```r
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# (run this on your own console, as this page does not support colour printing)
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@ -148,27 +148,21 @@ get_column_abx <- function(x,
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}
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# sort on name
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x <- x[sort(names(x))]
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dupes <- x[base::duplicated(x)]
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x <- x[order(names(x), x)]
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duplicates <- x[base::duplicated(x)]
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x <- x[!names(x) %in% names(duplicates)]
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if (verbose == TRUE) {
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for (i in 1:length(x)) {
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if (x[i] %in% dupes) {
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message(red(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
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"` (", ab_name(names(x)[i], language = "en", tolower = TRUE), ") [DUPLICATED USE].")))
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} else {
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message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
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"` (", ab_name(names(x)[i], language = "en", tolower = TRUE), ").")))
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}
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message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
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"` (", ab_name(names(x)[i], tolower = TRUE), ").")))
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}
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}
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if (n_distinct(x) != length(x)) {
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msg_txt <- paste("Column(s)", paste0("`", dupes, "`", collapse = " and "), "used for more than one antibiotic.")
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if (verbose == FALSE) {
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msg_txt <- paste(msg_txt, "Use verbose = TRUE to see which antibiotics are used by which columns.")
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} else if (length(duplicates) > 0) {
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for (i in 1:length(duplicates)) {
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warning(red(paste0("Using column `", bold(duplicates[i]), "` as input for `", names(x[which(x == duplicates[i])]),
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"` (", ab_name(names(x[names(which(x == duplicates))[i]]), tolower = TRUE),
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"), although it was matched for multiple antibiotics or columns.")), call. = FALSE)
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}
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stop(msg_txt, call. = FALSE)
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}
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if (!is.null(hard_dependencies)) {
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@ -78,7 +78,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -225,9 +225,9 @@
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</div>
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<div id="amr-0-7-1-9056" class="section level1">
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<div id="amr-0-7-1-9057" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9056" class="anchor"></a>AMR 0.7.1.9056<small> Unreleased </small>
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<a href="#amr-0-7-1-9057" class="anchor"></a>AMR 0.7.1.9057<small> Unreleased </small>
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</h1>
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<div id="breaking" class="section level3">
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<h3 class="hasAnchor">
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@ -288,6 +288,7 @@
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<li>Using factors as input now adds missing factors levels when the function changes antibiotic results</li>
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</ul>
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</li>
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<li>Improved the internal auto-guessing function for determining antibiotics in your data set (<code>AMR:::get_column_abx()</code>)</li>
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<li>
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<p>Added tibble printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using tibbles containing antibiotic columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
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<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
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@ -1237,7 +1238,7 @@ 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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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9056">0.7.1.9056</a></li>
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<li><a href="#amr-0-7-1-9057">0.7.1.9057</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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@ -80,7 +80,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -476,7 +476,7 @@ To conduct an analysis of antimicrobial resistance, you should only include the
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<footer>
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<div class="copyright">
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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</div>
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<div class="pkgdown">
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@ -78,7 +78,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9056</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -80,7 +80,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9057</span>
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</span>
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</div>
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@ -388,7 +388,7 @@
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<footer>
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<div class="copyright">
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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</div>
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<div class="pkgdown">
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@ -44,6 +44,6 @@ test_that("looking up ab columns works", {
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expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
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expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
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expect_message(get_column_abx(septic_patients, soft_dependencies = "FUS"))
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expect_error(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
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expect_error(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
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expect_message(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
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expect_warning(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
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})
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