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(v1.5.0.9004) custom MDRO guideline

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dr. M.S. (Matthijs) Berends 2021-01-17 00:26:48 +01:00
parent 7ebc534ccd
commit e699de955c
17 changed files with 272 additions and 54 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.5.0.9003
Date: 2021-01-15
Version: 1.5.0.9004
Date: 2021-01-17
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

2
NAMESPACE
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@ -52,6 +52,7 @@ S3method(plot,rsi)
S3method(print,ab)
S3method(print,bug_drug_combinations)
S3method(print,catalogue_of_life_version)
S3method(print,custom_mdro_guideline)
S3method(print,disk)
S3method(print,isolate_identifier)
S3method(print,mic)
@ -120,6 +121,7 @@ export(count_all)
export(count_df)
export(count_resistant)
export(count_susceptible)
export(custom_mdro_guideline)
export(eucast_dosage)
export(eucast_exceptional_phenotypes)
export(eucast_rules)

5
NEWS.md
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@ -1,10 +1,11 @@
# AMR 1.5.0.9003
## <small>Last updated: 15 January 2021</small>
# AMR 1.5.0.9004
## <small>Last updated: 17 January 2021</small>
### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
* Data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
* Function `eucast_dosage()` to get a `data.frame` with advised dosages of a certain bug-drug combination, which is based on the new `dosage` data set
* Support for custom MDRO guidelines, using the new `custom_mdro_guideline()` function, please see `mdro()` for additional info
* Function `isolate_identifier()`, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
* Function `mo_is_yeast()`, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
```r

185
R/mdro.R
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@ -25,10 +25,10 @@
#' Determine multidrug-resistant organisms (MDRO)
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank for automatic determination.
#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
#' @param guideline a specific guideline to follow. Can also have [custom_mdro_guideline()] as input. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
#' @inheritParams eucast_rules
#' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
@ -39,6 +39,10 @@
#'
#' For the `pct_required_classes` argument, values above 1 will be divided by 100. This is to support both fractions (`0.75` or `3/4`) and percentages (`75`).
#'
#' **Note:** Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named *order* Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu *et al.* in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this [mdro()] function makes sure that results from before 2016 and after 2016 are identical.
#'
#' ### International / National guidelines
#'
#' Currently supported guidelines are (case-insensitive):
#'
#' * `guideline = "CMI2012"` (default)
@ -67,7 +71,40 @@
#'
#' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
#'
#' **Note:** Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named *order* Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu *et al.* in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this [mdro()] function makes sure that results from before 2016 and after 2016 are identical.
#'
#' ### Custom guidelines
#'
#' Custom guidelines can be set with the [custom_mdro_guideline()] function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
#'
#' If you are familiar with `case_when()` of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation':
#'
#' ```
#' custom <- custom_mdro_guideline("CIP == 'R' & age > 60" ~ "Elderly Type A",
#' "ERY == 'R' & age > 60" ~ "Elderly Type B")
#' ```
#'
#' If a row/an isolate matches the first rule, the value after the first `~` (in this case *'Elderly Type A'*) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.
#'
#' You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.
#'
#' ```
#' custom
#' #> A set of custom MDRO rules:
#' #> 1. CIP == "R" & age > 60 -> "Elderly Type A"
#' #> 2. ERY == "R" & age > 60 -> "Elderly Type B"
#' #> 3. Otherwise -> "Negative"
#' #>
#' #> Unmatched rows will return NA.
#' ```
#'
#' The outcome of the function can be used for the `guideline` argument in the [mdro()] function:
#'
#' ```
#' x <- mdro(example_isolates, guideline = custom)
#' table(x)
#' ```
#'
#' The rules set (the `custom` object in this case) could be exported to a shared file location using [saveRDS()] if you collaborate with multiple users. The custom rules set could then be imported using [readRDS()],
#' @inheritSection as.rsi Interpretation of R and S/I
#' @return
#' - CMI 2012 paper - function [mdr_cmi2012()] or [mdro()]:\cr
@ -76,7 +113,7 @@
#' Ordered [factor] with levels `Negative` < `Mono-resistant` < `Poly-resistant` < `Multi-drug-resistant` < `Extensively drug-resistant`
#' - German guideline - function [mrgn()] or [`mdro(..., guideline = "MRGN")`][mdro()]:\cr
#' Ordered [factor] with levels `Negative` < `3MRGN` < `4MRGN`
#' - Everything else:\cr
#' - Everything else, except for custom guidelines:\cr
#' Ordered [factor] with levels `Negative` < `Positive, unconfirmed` < `Positive`. The value `"Positive, unconfirmed"` means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests
#' @rdname mdro
#' @aliases MDR XDR PDR BRMO 3MRGN 4MRGN
@ -87,6 +124,10 @@
#' @examples
#' mdro(example_isolates, guideline = "EUCAST")
#'
#' mdro(example_isolates,
#' guideline = custom_mdro_guideline("AMX == 'R'" ~ "Custom MDRO 1",
#' "VAN == 'R'" ~ "Custom MDRO 2"))
#'
#' \donttest{
#' if (require("dplyr")) {
#' example_isolates %>%
@ -113,7 +154,7 @@ mdro <- function(x,
x <- get_current_data(arg_name = "x", call = -2)
}
meet_criteria(x, allow_class = "data.frame")
meet_criteria(guideline, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(guideline, allow_class = c("list", "character"), allow_NULL = TRUE)
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
meet_criteria(info, allow_class = "logical", has_length = 1)
meet_criteria(pct_required_classes, allow_class = "numeric", has_length = 1)
@ -153,6 +194,30 @@ mdro <- function(x,
}
guideline.bak <- guideline
if (is.list(guideline)) {
# Custom MDRO guideline ---------------------------------------------------
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use `custom_mdro_guideline()` to create custom guidelines")
if (info == TRUE) {
cat("Determining MDROs based on custom rules.\n")
}
x <- run_custom_mdro_guideline(x, guideline)
if (info == TRUE) {
if (sum(!is.na(x$MDRO)) == 0) {
cat(font_bold(paste0("=> Found 0 MDROs since no isolates are covered by the custom guideline")))
} else {
cat(font_bold(paste0("=> Found ", sum(x$MDRO != "Negative", na.rm = TRUE), " custom defined MDROs out of ", sum(!is.na(x$MDRO)),
" isolates (", trimws(percentage(sum(x$MDRO != "Negative", na.rm = TRUE) / sum(!is.na(x$MDRO)))), ")\n")))
}
}
if (verbose == TRUE) {
return(x[, c("row_number",
"MDRO",
"reason",
"columns_nonsusceptible")])
} else {
return(x$MDRO)
}
}
guideline <- tolower(gsub("[^a-zA-Z0-9.]+", "", guideline))
if (is.null(guideline)) {
# default to the paper by Magiorakos et al. (2012)
@ -583,6 +648,11 @@ mdro <- function(x,
ab_NA <- function(x) {
x[!is.na(x)]
}
try_ab <- function(expr) {
out <- tryCatch(expr, error = function(e) FALSE)
out[is.na(out)] <- FALSE
out
}
# antibiotic classes
# nolint start
@ -1041,52 +1111,52 @@ mdro <- function(x,
if (guideline$code == "mrgn") {
# Germany -----------------------------------------------------------------
CTX_or_CAZ <- CTX %or% CAZ
IPM_or_MEM <- IPM %or% MEM
# Table 1
trans_tbl(2, # 3MRGN
which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
(x$genus == "Acinetobacter" & x$species == "baumannii")) &
x[, PIP, drop = TRUE] == "R" &
x[, CTX_or_CAZ, drop = TRUE] == "R" &
x[, IPM_or_MEM, drop = TRUE] == "S" &
x[, CIP, drop = TRUE] == "R"),
try_ab(x[, PIP, drop = TRUE] == "R") &
(try_ab(x[, CTX, drop = TRUE] == "R") | try_ab(x[, CAZ, drop = TRUE] == "R")) &
(try_ab(x[, IPM, drop = TRUE] != "R") | try_ab(x[, MEM, drop = TRUE] != "R")) &
try_ab(x[, CIP, drop = TRUE] == "R")),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
trans_tbl(3, # 4MRGN, overwrites 3MRGN if applicable
which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
(x$genus == "Acinetobacter" & x$species == "baumannii")) &
x[, PIP, drop = TRUE] == "R" &
x[, CTX_or_CAZ, drop = TRUE] == "R" &
x[, IPM_or_MEM, drop = TRUE] == "R" &
x[, CIP, drop = TRUE] == "R"),
try_ab(x[, PIP, drop = TRUE] == "R") &
(try_ab(x[, CTX, drop = TRUE] == "R") | try_ab(x[, CAZ, drop = TRUE] == "R")) &
(try_ab(x[, IPM, drop = TRUE] == "R") | try_ab(x[, MEM, drop = TRUE] == "R")) &
try_ab(x[, CIP, drop = TRUE] == "R")),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
trans_tbl(3, # 4MRGN, overwrites 3MRGN if applicable
which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
(x$genus == "Acinetobacter" & x$species == "baumannii")) &
(x[, IPM, drop = TRUE] == "R" | x[, MEM, drop = TRUE] == "R")),
(try_ab(x[, IPM, drop = TRUE] == "R") | try_ab(x[, MEM, drop = TRUE] == "R"))),
c(IPM, MEM),
"any")
trans_tbl(2, # 3MRGN, if only 1 group is S
which(x$genus == "Pseudomonas" & x$species == "aeruginosa" &
(x[, PIP, drop = TRUE] == "S") +
(x[, CTX_or_CAZ, drop = TRUE] == "S") +
(x[, IPM_or_MEM, drop = TRUE] == "S") +
(x[, CIP, drop = TRUE] == "S") == 1),
try_ab(x[, PIP, drop = TRUE] == "S") +
try_ab(x[, CTX, drop = TRUE] == "S") +
try_ab(x[, CAZ, drop = TRUE] == "S") +
try_ab(x[, IPM, drop = TRUE] == "S") +
try_ab(x[, MEM, drop = TRUE] == "S") +
try_ab(x[, CIP, drop = TRUE] == "S") == 1),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
trans_tbl(3, # 4MRGN otherwise
which((x$genus == "Pseudomonas" & x$species == "aeruginosa") &
(x[, PIP, drop = TRUE] == "R" | x[, TZP, drop = TRUE] == "R") &
x[, CTX_or_CAZ, drop = TRUE] == "R" &
x[, IPM_or_MEM, drop = TRUE] == "R" &
x[, CIP, drop = TRUE] == "R"),
try_ab(x[, PIP, drop = TRUE] == "R") &
(try_ab(x[, CTX, drop = TRUE] == "R") | try_ab(x[, CAZ, drop = TRUE] == "R")) &
(try_ab(x[, IPM, drop = TRUE] == "R") | try_ab(x[, MEM, drop = TRUE] == "R")) &
try_ab(x[, CIP, drop = TRUE] == "R")),
c(PIP, CTX, CAZ, IPM, MEM, CIP),
"any")
@ -1237,7 +1307,7 @@ mdro <- function(x,
}
if (info == TRUE) {
if (sum(!is.na(x$MDRO) == 0)) {
if (sum(!is.na(x$MDRO)) == 0) {
cat(font_bold(paste0("=> Found 0 MDROs since no isolates are covered by the guideline")))
} else {
cat(font_bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " ", guideline$type, " out of ", sum(!is.na(x$MDRO)),
@ -1298,6 +1368,71 @@ mdro <- function(x,
}
#' @rdname mdro
#' @export
custom_mdro_guideline <- function(...) {
dots <- list(...)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?mdro`.")
out <- vector("list", n_dots)
for (i in seq_len(n_dots)) {
stop_ifnot(inherits(dots[[i]], "formula"),
"element ", i, " must be a valid formula input (e.g., using '~'), please see `?mdro`")
qry <- as.character(dots[[i]][[2]])
val <- tryCatch(eval(dots[[i]][[3]]), error = function(e) NULL)
stop_if(is.null(val), "element ", i, " must return a valid value, it now returns an error: ", tryCatch(eval(dots[[i]][[3]]), error = function(e) e$message))
stop_if(length(val) > 1, "element ", i, " must return a value of length 1, not ", length(val))
stop_if(qry %like% "(&&|\\|\\|)",
"element ", i, " contains `&&` or `||` which will return `TRUE`/`FALSE` with length 1 (i.e., unvectorised)")
out[[i]]$query <- parse(text = qry)
out[[i]]$value <- as.character(val)
}
names(out) <- paste0("rule", seq_len(n_dots))
set_clean_class(out, new_class = c("custom_mdro_guideline", "list"))
}
#' @method print custom_mdro_guideline
#' @export
#' @noRd
print.custom_mdro_guideline <- function(x, ...) {
cat("A set of custom MDRO rules:\n")
for (i in seq_len(length(x))) {
rule <- x[[i]]
cat(" ", i, ". ", font_blue(as.character(rule$query)), " -> ", font_red(paste0('"', rule$value, '"')), "\n", sep = "")
}
cat(" ", i + 1, ". Otherwise -> ", font_red(paste0('"Negative"')), "\n", sep = "")
cat("\nUnmatched rows will return ", font_red("NA"), ".\n", sep = "")
}
run_custom_mdro_guideline <- function(df, guideline) {
n_dots <- length(guideline)
stop_if(n_dots == 0, "no custom guidelines set", call = -2)
out <- character(length = NROW(df))
reasons <- character(length = NROW(df))
for (i in seq_len(n_dots)) {
qry <- eval(guideline[[i]]$query, envir = df, enclos = parent.frame())
stop_ifnot(is.logical(qry), "`", guideline[[i]]$query, "` must return `TRUE` or `FALSE`", call = -2)
val <- guideline[[i]]$value
out[which(qry)] <- val
reasons[which(qry)] <- paste0("matched ", names(guideline)[i], ": ", as.character(guideline[[i]]$query))
}
out[out == ""] <- "Negative"
reasons[out == "Negative"] <- "no rules matched"
rsi_cols <- vapply(FUN.VALUE = logical(1), df, function(x) is.rsi(x))
columns_nonsusceptible <- as.data.frame(t(df[, rsi_cols] == "R"))
columns_nonsusceptible <- vapply(FUN.VALUE = character(1),
columns_nonsusceptible,
function(x) paste0(rownames(columns_nonsusceptible)[which(x)], collapse = " "))
columns_nonsusceptible[is.na(out)] <- NA_character_
data.frame(row_number = seq_len(NROW(df)),
MDRO = out,
reason = reasons,
columns_nonsusceptible = columns_nonsusceptible,
stringsAsFactors = FALSE)
}
#' @rdname mdro
#' @export
brmo <- function(x, guideline = "BRMO", ...) {

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data-raw/AMR_1.5.0.9003.tar.gz → data-raw/AMR_1.5.0.9004.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>

13
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509003" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9003">
<a href="#amr-1509003" class="anchor"></a>AMR 1.5.0.9003<small> Unreleased </small>
<div id="amr-1509004" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9004">
<a href="#amr-1509004" class="anchor"></a>AMR 1.5.0.9004<small> Unreleased </small>
</h1>
<div id="last-updated-15-january-2021" class="section level2">
<div id="last-updated-17-january-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-15-january-2021" class="anchor"></a><small>Last updated: 15 January 2021</small>
<a href="#last-updated-17-january-2021" class="anchor"></a><small>Last updated: 17 January 2021</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -251,6 +251,7 @@
<li><p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p></li>
<li><p>Data set <code>dosage</code> to fuel the new <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> function and to make this data available in a structured way</p></li>
<li><p>Function <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> to get a <code>data.frame</code> with advised dosages of a certain bug-drug combination, which is based on the new <code>dosage</code> data set</p></li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p>Function <code><a href="../reference/isolate_identifier.html">isolate_identifier()</a></code>, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-01-15T21:44Z
last_built: 2021-01-16T23:26Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

4
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>
@ -508,7 +508,7 @@
</tr><tr>
<td>
<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
<p><code><a href="mdro.html">mdro()</a></code> <code><a href="mdro.html">custom_mdro_guideline()</a></code> <code><a href="mdro.html">brmo()</a></code> <code><a href="mdro.html">mrgn()</a></code> <code><a href="mdro.html">mdr_tb()</a></code> <code><a href="mdro.html">mdr_cmi2012()</a></code> <code><a href="mdro.html">eucast_exceptional_phenotypes()</a></code> </p>
</td>
<td><p>Determine multidrug-resistant organisms (MDRO)</p></td>
</tr><tr>

45
docs/reference/mdro.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -82,7 +82,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>
@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.</p>
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.</p>
</div>
<pre class="usage"><span class='fu'>mdro</span><span class='op'>(</span>
@ -253,6 +253,8 @@
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span>
<span class='fu'>brmo</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"BRMO"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mrgn</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"MRGN"</span>, <span class='va'>...</span><span class='op'>)</span>
@ -272,7 +274,7 @@
</tr>
<tr>
<th>guideline</th>
<td><p>a specific guideline to follow. When left empty, the publication by Magiorakos <em>et al.</em> (2012, Clinical Microbiology and Infection) will be followed, please see <em>Details</em>.</p></td>
<td><p>a specific guideline to follow. Can also have <code>custom_mdro_guideline()</code> as input. When left empty, the publication by Magiorakos <em>et al.</em> (2012, Clinical Microbiology and Infection) will be followed, please see <em>Details</em>.</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -313,7 +315,7 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>Negative</code> &lt; <code>Mono-resistant</code> &lt; <code>Poly-resistant</code> &lt; <code>Multi-drug-resistant</code> &lt; <code>Extensively drug-resistant</code></p></li>
<li><p>German guideline - function <code>mrgn()</code> or <code>mdro(..., guideline = "MRGN")</code>:<br />
Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>Negative</code> &lt; <code>3MRGN</code> &lt; <code>4MRGN</code></p></li>
<li><p>Everything else:<br />
<li><p>Everything else, except for custom guidelines:<br />
Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>Negative</code> &lt; <code>Positive, unconfirmed</code> &lt; <code>Positive</code>. The value <code>"Positive, unconfirmed"</code> means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests</p></li>
</ul>
@ -321,6 +323,9 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> argument can be left blank, please see <em>Examples</em>.</p>
<p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or <code>3/4</code>) and percentages (<code>75</code>).</p>
<p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named <em>order</em> Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>International / National guidelines</h3>
<p>Currently supported guidelines are (case-insensitive):</p><ul>
<li><p><code>guideline = "CMI2012"</code> (default)</p>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href='https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext'>link</a>)</p></li>
@ -337,7 +342,31 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
<p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named <em>order</em> Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom guidelines</h3>
<p>Custom guidelines can be set with the <code>custom_mdro_guideline()</code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
<p>If you are familiar with <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation':</p><pre><span class='va'>custom</span> <span class='op'>&lt;-</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='st'>"CIP == 'R' &amp; age &gt; 60"</span> <span class='op'>~</span> <span class='st'>"Elderly Type A"</span>,
<span class='st'>"ERY == 'R' &amp; age &gt; 60"</span> <span class='op'>~</span> <span class='st'>"Elderly Type B"</span><span class='op'>)</span>
</pre>
<p>If a row/an isolate matches the first rule, the value after the first <code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code> (in this case <em>'Elderly Type A'</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.</p>
<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p><pre><span class='va'>custom</span>
<span class='co'>#&gt; A set of custom MDRO rules:</span>
<span class='co'>#&gt; 1. CIP == "R" &amp; age &gt; 60 -&gt; "Elderly Type A"</span>
<span class='co'>#&gt; 2. ERY == "R" &amp; age &gt; 60 -&gt; "Elderly Type B"</span>
<span class='co'>#&gt; 3. Otherwise -&gt; "Negative"</span>
<span class='co'>#&gt; </span>
<span class='co'>#&gt; Unmatched rows will return NA.</span>
</pre>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='va'>custom</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
</pre>
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>,</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -375,6 +404,10 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
guideline <span class='op'>=</span> <span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='st'>"AMX == 'R'"</span> <span class='op'>~</span> <span class='st'>"Custom MDRO 1"</span>,
<span class='st'>"VAN == 'R'"</span> <span class='op'>~</span> <span class='st'>"Custom MDRO 2"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9004</span>
</span>
</div>

43
man/mdro.Rd
View File

@ -8,6 +8,7 @@
\alias{BRMO}
\alias{3MRGN}
\alias{4MRGN}
\alias{custom_mdro_guideline}
\alias{brmo}
\alias{mrgn}
\alias{mdr_tb}
@ -29,6 +30,8 @@ mdro(
...
)
custom_mdro_guideline(...)
brmo(x, guideline = "BRMO", ...)
mrgn(x, guideline = "MRGN", ...)
@ -42,7 +45,7 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
\item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.}
\item{guideline}{a specific guideline to follow. Can also have \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} as input. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.}
\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()}}.}
@ -64,18 +67,21 @@ Ordered \link{factor} with levels \code{Negative} < \code{Multi-drug-resistant (
Ordered \link{factor} with levels \code{Negative} < \code{Mono-resistant} < \code{Poly-resistant} < \code{Multi-drug-resistant} < \verb{Extensively drug-resistant}
\item German guideline - function \code{\link[=mrgn]{mrgn()}} or \code{\link[=mdro]{mdro(..., guideline = "MRGN")}}:\cr
Ordered \link{factor} with levels \code{Negative} < \verb{3MRGN} < \verb{4MRGN}
\item Everything else:\cr
\item Everything else, except for custom guidelines:\cr
Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed} < \code{Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests
}
}
\description{
Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
}
\details{
These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, please see \emph{Examples}.
For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named \emph{order} Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
\subsection{International / National guidelines}{
Currently supported guidelines are (case-insensitive):
\itemize{
\item \code{guideline = "CMI2012"} (default)
@ -99,8 +105,33 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
}
Please suggest your own (country-specific) guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}.
}
\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named \emph{order} Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
\subsection{Custom guidelines}{
Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
If you are familiar with \code{case_when()} of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation':\preformatted{custom <- custom_mdro_guideline("CIP == 'R' & age > 60" ~ "Elderly Type A",
"ERY == 'R' & age > 60" ~ "Elderly Type B")
}
If a row/an isolate matches the first rule, the value after the first \code{~} (in this case \emph{'Elderly Type A'}) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.
You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.\preformatted{custom
#> A set of custom MDRO rules:
#> 1. CIP == "R" & age > 60 -> "Elderly Type A"
#> 2. ERY == "R" & age > 60 -> "Elderly Type B"
#> 3. Otherwise -> "Negative"
#>
#> Unmatched rows will return NA.
}
The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:\preformatted{x <- mdro(example_isolates, guideline = custom)
table(x)
}
The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}},
}
}
\section{Stable lifecycle}{
@ -142,6 +173,10 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
\examples{
mdro(example_isolates, guideline = "EUCAST")
mdro(example_isolates,
guideline = custom_mdro_guideline("AMX == 'R'" ~ "Custom MDRO 1",
"VAN == 'R'" ~ "Custom MDRO 2"))
\donttest{
if (require("dplyr")) {
example_isolates \%>\%

11
tests/testthat/test-mdro.R
View File

@ -223,4 +223,15 @@ test_that("mdro works", {
expect_equal(as.integer(mdro(acin)), c(1:4))
expect_s3_class(mdro(acin, verbose = TRUE), "data.frame")
# custom rules
custom <- custom_mdro_guideline("CIP == 'R' & age > 60" ~ "Elderly Type A",
"ERY == 'R' & age > 60" ~ "Elderly Type B")
expect_output(print(custom))
x <- mdro(example_isolates, guideline = custom, info = TRUE)
expect_equal(as.double(table(x)), c(43, 891, 1066))
expect_error(custom_mdro_guideline())
expect_error(custom_mdro_guideline("test"))
expect_error(custom_mdro_guideline("test" ~ c(1:3)))
expect_error(custom_mdro_guideline("test" ~ A))
})