mirror of https://github.com/msberends/AMR.git
(v1.0.0.9003) prepare for short update
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Package: AMR
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Version: 1.0.0.9002
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Date: 2020-02-20
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Version: 1.0.0.9003
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Date: 2020-02-21
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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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6
NEWS.md
6
NEWS.md
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@ -1,8 +1,7 @@
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# AMR 1.0.0.9002
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## <small>Last updated: 20-Feb-2020</small>
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# AMR 1.0.0.9003
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## <small>Last updated: 21-Feb-2020</small>
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### Changed
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* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
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* Fixed floating point error for some MIC compa in EUCAST 2020 guideline
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* Interpretation from MIC values to R/SI can now be used with `mutate_at()` of the dplyr package:
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```r
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@ -12,6 +11,7 @@
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yourdata %>%
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mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = .$mybacteria)
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```
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* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
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* Added `uti` (as abbreviation of urinary tract infections) as parameter to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
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# AMR 1.0.0
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25
R/rsi.R
25
R/rsi.R
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@ -67,6 +67,8 @@
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#' NIT = as.mic(32))
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#' as.rsi(df)
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#'
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#' \donttest{
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#'
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#' # the dplyr way
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#' library(dplyr)
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#' df %>%
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@ -88,7 +90,8 @@
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#'
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#' df %>%
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#' mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
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#'
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#' }
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#'
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#' # for single values
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#' as.rsi(x = as.mic(2),
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#' mo = as.mo("S. pneumoniae"),
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@ -199,20 +202,6 @@ as.rsi.default <- function(x, ...) {
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}
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}
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#' @importFrom dplyr %>%
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input_resembles_mic <- function(x) {
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mic <- x %>%
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gsub("[^0-9.,]+", "", .) %>%
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unique()
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mic_valid <- suppressWarnings(as.mic(mic))
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result <- sum(!is.na(mic_valid)) / length(mic)
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if (is.na(result)) {
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0
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} else {
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result
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}
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}
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#' @rdname as.rsi
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#' @export
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as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, ...) {
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@ -402,10 +391,14 @@ get_guideline <- function(guideline) {
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rev() %>%
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.[1]
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}
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if (!guideline_param %like% " ") {
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# like 'EUCAST2020', should be 'EUCAST 2020'
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guideline_param <- gsub("([a-z]+)([0-9]+)", "\\1 \\2", guideline_param, ignore.case = TRUE)
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}
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if (!guideline_param %in% rsi_translation$guideline) {
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stop(paste0("invalid guideline: '", guideline,
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"'.\nValid guidelines are: ", paste0("'", rev(sort(unique(rsi_translation$guideline))), "'", collapse = ", ")),
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"'.\nValid guidelines are: ", paste0("'", unique(rsi_translation$guideline), "'", collapse = ", "), "."),
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call. = FALSE)
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}
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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="https://msberends.gitlab.io/AMR/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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
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</span>
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</div>
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@ -219,19 +219,18 @@
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</div>
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<div id="amr-1009002" class="section level1">
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<div id="amr-1009003" class="section level1">
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<h1 class="page-header">
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<a href="#amr-1009002" class="anchor"></a>AMR 1.0.0.9002<small> Unreleased </small>
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<a href="#amr-1009003" class="anchor"></a>AMR 1.0.0.9003<small> Unreleased </small>
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</h1>
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<div id="last-updated-20-feb-2020" class="section level2">
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<div id="last-updated-21-feb-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-20-feb-2020" class="anchor"></a><small>Last updated: 20-Feb-2020</small>
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<a href="#last-updated-21-feb-2020" class="anchor"></a><small>Last updated: 21-Feb-2020</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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<a href="#changed" class="anchor"></a>Changed</h3>
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<ul>
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<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
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<li><p>Fixed floating point error for some MIC compa in EUCAST 2020 guideline</p></li>
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<li>
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<p>Interpretation from MIC values to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the dplyr package:</p>
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@ -241,6 +240,7 @@
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<span id="cb1-4"><a href="#cb1-4"></a>yourdata <span class="op">%>%</span><span class="st"> </span></span>
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<span id="cb1-5"><a href="#cb1-5"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(antibiotic1<span class="op">:</span>antibiotic25), as.rsi, <span class="dt">mo =</span> .<span class="op">$</span>mybacteria)</span></code></pre></div>
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</li>
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<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
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<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
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</ul>
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</div>
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@ -1473,7 +1473,7 @@
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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-1009002">1.0.0.9002</a></li>
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<li><a href="#amr-1009003">1.0.0.9003</a></li>
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<li><a href="#amr-100">1.0.0</a></li>
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<li><a href="#amr-090">0.9.0</a></li>
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<li><a href="#amr-080">0.8.0</a></li>
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@ -79,7 +79,7 @@
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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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
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</span>
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</div>
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@ -342,6 +342,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='kw'>NIT</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>32</span>))
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<span class='fu'>as.rsi</span>(<span class='no'>df</span>)
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<span class='co'># \donttest{</span>
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<span class='co'># the dplyr way</span>
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>df</span> <span class='kw'>%>%</span>
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@ -363,6 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='no'>df</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>NIT</span>), <span class='no'>as.rsi</span>, <span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
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<span class='co'># }</span>
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<span class='co'># for single values</span>
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<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
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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">1.0.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9003</span>
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</span>
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</div>
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@ -108,6 +108,8 @@ df <- data.frame(microorganism = "E. coli",
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NIT = as.mic(32))
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as.rsi(df)
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\donttest{
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# the dplyr way
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library(dplyr)
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df \%>\%
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df \%>\%
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mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
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}
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# for single values
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as.rsi(x = as.mic(2),
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mo = as.mo("S. pneumoniae"),
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barplot(as.rsi(c("S", "I", "R")))
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plot(as.rsi(c("S", "I", "R")))
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print(as.rsi(c("S", "I", "R")))
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expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
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expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
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as.logical() %>%
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sum(),
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40)
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expect_output(tibble(ab = as.rsi("S")))
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expect_error(as.rsi.mic(as.mic(16)))
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expect_error(as.rsi.disk(as.disk(16)))
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expect_error(get_guideline("this one does not exist"))
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})
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test_that("mic2rsi works", {
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skip_on_cran()
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