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(v1.2.0.9039) conserve_capped_values for as.rsi()

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dr. M.S. (Matthijs) Berends 2020-07-29 11:46:59 +02:00
parent 453f7f210b
commit e7def0aa4c
14 changed files with 84 additions and 31 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.2.0.9038 Version: 1.2.0.9039
Date: 2020-07-29 Date: 2020-07-29
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.2.0.9038 # AMR 1.2.0.9039
## <small>Last updated: 29 July 2020</small> ## <small>Last updated: 29 July 2020</small>
### New ### New
@ -17,6 +17,7 @@
* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()` * Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set * Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
* Added Monuril as trade name for fosfomycin * Added Monuril as trade name for fosfomycin
* Added parameter `conserve_capped_values` to `as.rsi()` for interpreting MIC values - it makes sure that values starting with "<" (but not "<=") will always return "S" and values starting with ">" (but not ">=") will always return "R". The default behaviour of `as.rsi()` has not changed, so you need to specifically do `as.rsi(..., conserve_capped_values = TRUE)`.
### Changed ### Changed
* Big speed improvement for using any function on microorganism codes from earlier package versions (prior to `AMR` v1.2.0), such as `as.mo()`, `mo_name()`, `first_isolate()`, `eucast_rules()`, `mdro()`, etc. * Big speed improvement for using any function on microorganism codes from earlier package versions (prior to `AMR` v1.2.0), such as `as.mo()`, `mo_name()`, `first_isolate()`, `eucast_rules()`, `mdro()`, etc.

42
R/rsi.R
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@ -21,7 +21,7 @@
#' Class 'rsi' #' Class 'rsi'
#' #'
#' Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning. #' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
#' @inheritSection lifecycle Stable lifecycle #' @inheritSection lifecycle Stable lifecycle
#' @rdname as.rsi #' @rdname as.rsi
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres) #' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
@ -30,6 +30,7 @@
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See *Examples*. #' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate #' @inheritParams first_isolate
#' @param guideline defaults to the latest included EUCAST guideline, see Details for all options #' @param guideline defaults to the latest included EUCAST guideline, see Details for all options
#' @param conserve_capped_values a logical to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples* #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
#' @param ... parameters passed on to methods #' @param ... parameters passed on to methods
#' @details #' @details
@ -37,6 +38,8 @@
#' #'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline. #' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline.
#' #'
#' When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and will in this case return "S" or "I".
#'
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. #' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
#' #'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism. #' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
@ -210,7 +213,13 @@ as.rsi.default <- function(x, ...) {
#' @rdname as.rsi #' @rdname as.rsi
#' @export #' @export
as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, ...) { as.rsi.mic <- function(x,
mo,
ab = deparse(substitute(x)),
guideline = "EUCAST",
uti = FALSE,
conserve_capped_values = FALSE,
...) {
stop_if(missing(mo), stop_if(missing(mo),
'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n', 'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use\n", "To transform certain columns with e.g. mutate_at(), use\n",
@ -240,13 +249,20 @@ as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST",
mo = mo_coerced, mo = mo_coerced,
ab = ab_coerced, ab = ab_coerced,
guideline = guideline_coerced, guideline = guideline_coerced,
uti = uti) # exec_as.rsi will return message(font_blue(" OK.")) uti = uti,
conserve_capped_values = conserve_capped_values) # exec_as.rsi will return message(font_blue(" OK."))
result result
} }
#' @rdname as.rsi #' @rdname as.rsi
#' @export #' @export
as.rsi.disk <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, ...) { as.rsi.disk <- function(x,
mo,
ab = deparse(substitute(x)),
guideline = "EUCAST",
uti = FALSE,
conserve_capped_values = FALSE,
...) {
stop_if(missing(mo), stop_if(missing(mo),
'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n', 'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use\n", "To transform certain columns with e.g. mutate_at(), use\n",
@ -282,7 +298,12 @@ as.rsi.disk <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST"
#' @rdname as.rsi #' @rdname as.rsi
#' @export #' @export
as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL, ...) { as.rsi.data.frame <- function(x,
col_mo = NULL,
guideline = "EUCAST",
uti = NULL,
conserve_capped_values = FALSE,
...) {
# try to find columns based on type # try to find columns based on type
# -- mo # -- mo
if (is.null(col_mo)) { if (is.null(col_mo)) {
@ -368,7 +389,8 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL
mo = x %>% pull(col_mo), mo = x %>% pull(col_mo),
ab = ab_cols[i], ab = ab_cols[i],
guideline = guideline, guideline = guideline,
uti = uti) uti = uti,
conserve_capped_values = conserve_capped_values)
} else if (types[i] == "disk") { } else if (types[i] == "disk") {
x[, ab_cols[i]] <- as.rsi.disk(x = x %>% pull(ab_cols[i]), x[, ab_cols[i]] <- as.rsi.disk(x = x %>% pull(ab_cols[i]),
mo = x %>% pull(col_mo), mo = x %>% pull(col_mo),
@ -399,7 +421,7 @@ get_guideline <- function(guideline) {
} }
exec_as.rsi <- function(method, x, mo, ab, guideline, uti) { exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_values) {
if (method == "mic") { if (method == "mic") {
x <- as.mic(x) # when as.rsi.mic is called directly x <- as.mic(x) # when as.rsi.mic is called directly
} else if (method == "disk") { } else if (method == "disk") {
@ -471,10 +493,12 @@ exec_as.rsi <- function(method, x, mo, ab, guideline, uti) {
mic_input <- x[i] mic_input <- x[i]
mic_S <- as.mic(get_record$breakpoint_S) mic_S <- as.mic(get_record$breakpoint_S)
mic_R <- as.mic(get_record$breakpoint_R) mic_R <- as.mic(get_record$breakpoint_R)
new_rsi[i] <- ifelse(isTRUE(which(levels(mic_input) == mic_input) <= which(levels(mic_S) == mic_S)), "S", new_rsi[i] <- ifelse(isTRUE(conserve_capped_values) & mic_input %like% "^<[0-9]", "S",
ifelse(isTRUE(conserve_capped_values) & mic_input %like% "^>[0-9]", "R",
ifelse(isTRUE(which(levels(mic_input) == mic_input) <= which(levels(mic_S) == mic_S)), "S",
ifelse(isTRUE(which(levels(mic_input) == mic_input) >= which(levels(mic_R) == mic_R)), "R", ifelse(isTRUE(which(levels(mic_input) == mic_input) >= which(levels(mic_R) == mic_R)), "R",
ifelse(!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R), "I", ifelse(!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R), "I",
NA_character_))) NA_character_)))))
} else if (method == "disk") { } else if (method == "disk") {
new_rsi[i] <- ifelse(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)), "S", new_rsi[i] <- ifelse(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)), "S",
ifelse(isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)), "R", ifelse(isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)), "R",

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209038" class="section level1"> <div id="amr-1209039" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9038"> <h1 class="page-header" data-toc-text="1.2.0.9039">
<a href="#amr-1209038" class="anchor"></a>AMR 1.2.0.9038<small> Unreleased </small> <a href="#amr-1209039" class="anchor"></a>AMR 1.2.0.9039<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-29-july-2020" class="section level2"> <div id="last-updated-29-july-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -256,6 +256,7 @@
<li><p>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code></p></li> <li><p>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code></p></li>
<li><p>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</p></li> <li><p>Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the <code>antibiotics</code> data set</p></li>
<li><p>Added Monuril as trade name for fosfomycin</p></li> <li><p>Added Monuril as trade name for fosfomycin</p></li>
<li><p>Added parameter <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “&lt;” (but not “&lt;=”) will always return “S” and values starting with “&gt;” (but not “&gt;=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
</ul> </ul>
</div> </div>
<div id="changed" class="section level3"> <div id="changed" class="section level3">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-07-29T08:31Z last_built: 2020-07-29T09:46Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

22
docs/reference/as.rsi.html
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@ -49,7 +49,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Class 'rsi' — as.rsi" /> <meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." /> <meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>
@ -232,7 +232,7 @@
</div> </div>
<div class="ref-description"> <div class="ref-description">
<p>Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p> <p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
</div> </div>
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>) <pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -244,6 +244,7 @@
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)), <span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span> <span class='no'>...</span>
) )
@ -254,11 +255,19 @@
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)), <span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span> <span class='no'>...</span>
) )
<span class='co'># S3 method for data.frame</span> <span class='co'># S3 method for data.frame</span>
<span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>) <span class='fu'>as.rsi</span>(
<span class='no'>x</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
)
<span class='fu'>is.rsi</span>(<span class='no'>x</span>) <span class='fu'>is.rsi</span>(<span class='no'>x</span>)
@ -291,6 +300,10 @@
<th>uti</th> <th>uti</th>
<td><p>(Urinary Tract Infection) A vector with <a href='https://rdrr.io/r/base/logical.html'>logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, this can also be a column containing <a href='https://rdrr.io/r/base/logical.html'>logical</a>s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See <em>Examples</em>.</p></td> <td><p>(Urinary Tract Infection) A vector with <a href='https://rdrr.io/r/base/logical.html'>logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, this can also be a column containing <a href='https://rdrr.io/r/base/logical.html'>logical</a>s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See <em>Examples</em>.</p></td>
</tr> </tr>
<tr>
<th>conserve_capped_values</th>
<td><p>a logical to indicate that MIC values starting with <code>"&gt;"</code> (but not <code>"&gt;="</code>) must always return "R" , and that MIC values starting with <code>"&lt;"</code> (but not <code>"&lt;="</code>) must always return "S"</p></td>
</tr>
<tr> <tr>
<th>col_mo</th> <th>col_mo</th>
<td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td> <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
@ -308,6 +321,7 @@
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p> <p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p> <p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
<p>When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and will in this case return "S" or "I".</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p> <p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p> <p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p> <p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span>
</span> </span>
</div> </div>

17
man/as.rsi.Rd
View File

@ -18,6 +18,7 @@ as.rsi(x, ...)
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
conserve_capped_values = FALSE,
... ...
) )
@ -27,10 +28,18 @@ as.rsi(x, ...)
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
conserve_capped_values = FALSE,
... ...
) )
\method{as.rsi}{data.frame}(x, col_mo = NULL, guideline = "EUCAST", uti = NULL, ...) \method{as.rsi}{data.frame}(
x,
col_mo = NULL,
guideline = "EUCAST",
uti = NULL,
conserve_capped_values = FALSE,
...
)
is.rsi(x) is.rsi(x)
@ -49,6 +58,8 @@ is.rsi.eligible(x, threshold = 0.05)
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See \emph{Examples}.} \item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See \emph{Examples}.}
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}} \item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
@ -57,13 +68,15 @@ is.rsi.eligible(x, threshold = 0.05)
Ordered factor with new class \code{\link{rsi}} Ordered factor with new class \code{\link{rsi}}
} }
\description{ \description{
Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning. Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
} }
\details{ \details{
When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class \code{\link{mic}} (using \code{\link[=as.mic]{as.mic()}}) or class \code{\link{disk}} (using \code{\link[=as.disk]{as.disk()}}), the data will be interpreted based on the guideline set with the \code{guideline} parameter. When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class \code{\link{mic}} (using \code{\link[=as.mic]{as.mic()}}) or class \code{\link{disk}} (using \code{\link[=as.disk]{as.disk()}}), the data will be interpreted based on the guideline set with the \code{guideline} parameter.
Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline. Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline.
When using \code{conserve_capped_values = TRUE}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{conserve_capped_values = FALSE}) considers ">2" to be lower than ">=4" and will in this case return "S" or "I".
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism. After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.