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(v1.0.0.9001) add uti to as.rsi()
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Package: AMR
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Version: 1.0.0.9000
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Version: 1.0.0.9001
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Date: 2020-02-20
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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4
NEWS.md
4
NEWS.md
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# AMR 1.0.0.9000
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## <small>Last updated: 20-Feb-2020</small>
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# AMR 1.0.0.9001
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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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27
R/rsi.R
27
R/rsi.R
@ -87,10 +87,8 @@
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#' as.rsi() # automatically determines urine isolates
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#'
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#' df %>%
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#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
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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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@ -139,18 +137,25 @@ as.rsi.default <- function(x, ...) {
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x
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} else if (identical(levels(x), c("S", "I", "R"))) {
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structure(x, class = c("rsi", "ordered", "factor"))
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} else if (all_valid_mics(x) & !all(is.na(x))) {
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as.rsi(as.mic(x), ab = deparse(substitute(x)), ...)
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} else if (all_valid_disks(x) & !all(is.na(x))) {
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#message("These values seem to be disk diffusion diameters and were treated as such.")
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as.rsi(as.disk(x), ab = deparse(substitute(x)), ...)
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} else if (identical(class(x), "integer") & all(x %in% c(1:3, NA))) {
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} else if (inherits(x, "integer") & all(x %in% c(1:3, NA))) {
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x[x == 1] <- "S"
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x[x == 2] <- "I"
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x[x == 3] <- "R"
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structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
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class = c("rsi", "ordered", "factor"))
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} else {
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ab <- deparse(substitute(x))
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if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
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if (!is.na(suppressWarnings(as.ab(ab)))) {
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# check if they are actually MICs or disks now that the antibiotic name is valid
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if (all_valid_mics(x)) {
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as.rsi(as.mic(x), ab = ab, ...)
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} else if (all_valid_disks(x)) {
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as.rsi(as.disk(x), ab = ab, ...)
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}
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}
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}
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x <- x %>% unlist()
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x.bak <- x
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@ -632,9 +637,9 @@ plot.rsi <- function(x,
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#' @importFrom graphics barplot axis par
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#' @noRd
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barplot.rsi <- function(height,
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col = c("green3", "orange2", "red3"),
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col = c("chartreuse4", "chartreuse3", "brown3"),
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xlab = ifelse(beside, "Antimicrobial Interpretation", ""),
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main = paste("Susceptibility Analysis of", deparse(substitute(height))),
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main = paste("Antimicrobial resistance of", deparse(substitute(height))),
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ylab = "Frequency",
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beside = TRUE,
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axes = beside,
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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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
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</span>
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</div>
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@ -219,14 +219,10 @@
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</div>
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<div id="amr-1009000" class="section level1">
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<div id="amr-1009001" class="section level1">
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<h1 class="page-header">
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<a href="#amr-1009000" class="anchor"></a>AMR 1.0.0.9000<small> Unreleased </small>
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<a href="#amr-1009001" class="anchor"></a>AMR 1.0.0.9001<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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<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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</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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@ -244,7 +240,6 @@
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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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</div>
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</div>
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<div id="amr-100" class="section level1">
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<h1 class="page-header">
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@ -1473,7 +1468,7 @@
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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-1009000">1.0.0.9000</a></li>
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<li><a href="#amr-1009001">1.0.0.9001</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">0.9.0.9029</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
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</span>
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</div>
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@ -362,9 +362,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
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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'>TOB</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='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'># 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">1.0.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
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</span>
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</div>
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@ -128,10 +128,8 @@ data.frame(mo = "E. coli",
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as.rsi() # automatically determines urine isolates
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df \%>\%
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mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
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mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
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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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