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(v0.7.1.9066) bug-drug fix
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Package: AMR
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Version: 0.7.1.9065
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Version: 0.7.1.9066
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Date: 2019-08-27
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9065
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# AMR 0.7.1.9066
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### Breaking
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* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
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#' @inheritParams eucast_rules
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#' @param combine_IR logical to indicate whether values R and I should be summed
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#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
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#' @param ... argumments passed on to \code{\link{mo_name}}
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#' @inheritParams rsi_df
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#' @importFrom dplyr rename
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#' @importFrom tidyr spread
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@ -75,14 +76,14 @@ bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
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#' @exportMethod format.bug_drug_combinations
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#' @export
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#' @rdname bug_drug_combinations
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format.bug_drug_combinations <- function(x, combine_IR = FALSE, add_ab_group = TRUE) {
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format.bug_drug_combinations <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) {
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if (combine_IR == FALSE) {
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x$isolates <- x$R
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} else {
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x$isolates <- x$R + x$I
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}
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y <- x %>%
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mutate(mo = mo_name(mo),
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mutate(mo = mo_name(mo, ...),
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txt = paste0(percent(isolates / total, force_zero = TRUE),
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" (", trimws(format(isolates, big.mark = ",")), "/",
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trimws(format(total, big.mark = ",")), ")")) %>%
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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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</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-0-7-1-9065" class="section level1">
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<div id="amr-0-7-1-9066" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9065" class="anchor"></a>AMR 0.7.1.9065<small> Unreleased </small>
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<a href="#amr-0-7-1-9066" class="anchor"></a>AMR 0.7.1.9066<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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@ -1258,7 +1258,7 @@ 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-0-7-1-9065">0.7.1.9065</a></li>
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<li><a href="#amr-0-7-1-9066">0.7.1.9066</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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</span>
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</span>
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</div>
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@ -238,7 +238,7 @@
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<span class='co'># S3 method for bug_drug_combinations</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
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<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<th>add_ab_group</th>
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<td><p>logical to indicate where the group of the antimicrobials must be included as a first column</p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>argumments passed on to <code><a href='mo_property.html'>mo_name</a></code></p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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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">0.7.1.9065</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9066</span>
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</span>
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</div>
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bug_drug_combinations(x, col_mo = NULL, minimum = 30)
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\method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
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add_ab_group = TRUE)
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add_ab_group = TRUE, ...)
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}
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\arguments{
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\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
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\item{combine_IR}{logical to indicate whether values R and I should be summed}
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\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
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\item{...}{argumments passed on to \code{\link{mo_name}}}
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}
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\description{
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Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
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test_that("bug_drug_combinations works", {
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b <- suppressWarnings(bug_drug_combinations(example_isolates))
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expect_s3_class(b, "bugdrug")
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expect_s3_class(b, "bug_drug_combinations")
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expect_message(print(b))
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expect_true(is.data.frame(format(b)))
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})
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