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(v1.0.0.9001) add uti to as.rsi()

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dr. M.S. (Matthijs) Berends 2020-02-20 17:21:01 +01:00
parent c6184a0fb8
commit bdb26f624f
12 changed files with 32 additions and 36 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.0.0.9000
Version: 1.0.0.9001
Date: 2020-02-20
Title: Antimicrobial Resistance Analysis
Authors@R: c(

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.0.0.9000
## <small>Last updated: 20-Feb-2020</small>
# AMR 1.0.0.9001
### Changed
* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole

27
R/rsi.R
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@ -87,9 +87,7 @@
#' as.rsi() # automatically determines urine isolates
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
#'
#'
#' mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
#'
#' # for single values
#' as.rsi(x = as.mic(2),
@ -139,12 +137,7 @@ as.rsi.default <- function(x, ...) {
x
} else if (identical(levels(x), c("S", "I", "R"))) {
structure(x, class = c("rsi", "ordered", "factor"))
} else if (all_valid_mics(x) & !all(is.na(x))) {
as.rsi(as.mic(x), ab = deparse(substitute(x)), ...)
} else if (all_valid_disks(x) & !all(is.na(x))) {
#message("These values seem to be disk diffusion diameters and were treated as such.")
as.rsi(as.disk(x), ab = deparse(substitute(x)), ...)
} else if (identical(class(x), "integer") & all(x %in% c(1:3, NA))) {
} else if (inherits(x, "integer") & all(x %in% c(1:3, NA))) {
x[x == 1] <- "S"
x[x == 2] <- "I"
x[x == 3] <- "R"
@ -152,6 +145,18 @@ as.rsi.default <- function(x, ...) {
class = c("rsi", "ordered", "factor"))
} else {
ab <- deparse(substitute(x))
if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
if (!is.na(suppressWarnings(as.ab(ab)))) {
# check if they are actually MICs or disks now that the antibiotic name is valid
if (all_valid_mics(x)) {
as.rsi(as.mic(x), ab = ab, ...)
} else if (all_valid_disks(x)) {
as.rsi(as.disk(x), ab = ab, ...)
}
}
}
x <- x %>% unlist()
x.bak <- x
@ -632,9 +637,9 @@ plot.rsi <- function(x,
#' @importFrom graphics barplot axis par
#' @noRd
barplot.rsi <- function(height,
col = c("green3", "orange2", "red3"),
col = c("chartreuse4", "chartreuse3", "brown3"),
xlab = ifelse(beside, "Antimicrobial Interpretation", ""),
main = paste("Susceptibility Analysis of", deparse(substitute(height))),
main = paste("Antimicrobial resistance of", deparse(substitute(height))),
ylab = "Frequency",
beside = TRUE,
axes = beside,

2
docs/404.html
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
</span>
</div>

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">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</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">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
</span>
</div>

13
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">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
</span>
</div>
@ -219,14 +219,10 @@
</div>
<div id="amr-1009000" class="section level1">
<div id="amr-1009001" class="section level1">
<h1 class="page-header">
<a href="#amr-1009000" class="anchor"></a>AMR 1.0.0.9000<small> Unreleased </small>
<a href="#amr-1009001" class="anchor"></a>AMR 1.0.0.9001<small> Unreleased </small>
</h1>
<div id="last-updated-20-feb-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-20-feb-2020" class="anchor"></a><small>Last updated: 20-Feb-2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
@ -244,7 +240,6 @@
<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>
</ul>
</div>
</div>
</div>
<div id="amr-100" class="section level1">
<h1 class="page-header">
@ -1473,7 +1468,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-1009000">1.0.0.9000</a></li>
<li><a href="#amr-1009001">1.0.0.9001</a></li>
<li><a href="#amr-100">1.0.0</a></li>
<li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li>

6
docs/reference/as.rsi.html
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@ -79,7 +79,7 @@
</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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
</span>
</div>
@ -362,9 +362,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
<span class='no'>df</span> <span class='kw'>%&gt;%</span>
<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>)
<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>)
<span class='co'># for single values</span>
<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>),

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">1.0.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9001</span>
</span>
</div>

4
man/as.rsi.Rd
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@ -128,9 +128,7 @@ data.frame(mo = "E. coli",
as.rsi() # automatically determines urine isolates
df \%>\%
mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
# for single values
as.rsi(x = as.mic(2),