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(v0.7.1.9096) German guideline for mdro()

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dr. M.S. (Matthijs) Berends 2019-10-07 14:32:06 +02:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9095
Date: 2019-10-06
Version: 0.7.1.9096
Date: 2019-10-07
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

9
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.7.1.9095
<small>Last updated: 06-Oct-2019</small>
# AMR 0.7.1.9096
<small>Last updated: 07-Oct-2019</small>
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@ -23,6 +23,7 @@
```
This is important, because a value like `"testvalue"` could never be understood by e.g. `mo_name()`, although the class would suggest a valid microbial code.
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)), since creating frequency tables actually does not fit the scope of this package. The `freq()` function still works, since it is re-exported from the `clean` package (which will be installed automatically upon updating this `AMR` package).
* Renamed data set `septic_patients` to `example_isolates`
### New
* Function `bug_drug_combinations()` to quickly get a `data.frame` with the antimicrobial resistance of any bug-drug combination in a data set. The columns with microorganism codes is guessed automatically and its input is transformed with `mo_shortname()` at default:
@ -94,8 +95,8 @@
* Added support for unknown yeasts and fungi
* Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
**IMPORTANT:** Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format. Using functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) on old codes, will throw a warning.
* More intelligent guessing for `as.ab()` which also led to bidirectional language support
* Renamed data set `septic_patients` to `example_isolates`
* More intelligent guessing for `as.ab()`, including bidirectional language support
* Added support for the German national guideline (3MRGN/4MRGN) in the `mdro()` function, to determine multi-drug resistant organisms
* Function `eucast_rules()`:
* Fixed a bug for *Yersinia pseudotuberculosis*
* Added more informative errors and warnings

2
R/eucast_rules.R
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@ -41,7 +41,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' @section Antibiotics:
#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
#'
#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name:
#'
#' \strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
#' \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),

102
R/mdro.R
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@ -28,18 +28,20 @@
#' @inheritParams eucast_rules
#' @param verbose print additional info: missing antibiotic columns per parameter
#' @inheritSection eucast_rules Antibiotics
#' @details Currently supported guidelines are:
#' @details Currently supported guidelines are (case-insensitive):
#' \itemize{
#' \item{\code{guideline = "EUCAST"}: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
#' \item{\code{guideline = "TB"}: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
#' \item{\code{guideline = "MRGN"}: (work in progress)}
#' \item{\code{guideline = "BRMO"}: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
#' \item{\code{guideline = "EUCAST"}: The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
#' \item{\code{guideline = "TB"}: The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
#' \item{\code{guideline = "MRGN"}: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6}
#' \item{\code{guideline = "BRMO"}: The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
#' }
#'
#' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
#' @return For TB (\code{mdr_tb()}): Ordered factor with levels \code{Negative < Mono-resistance < Poly-resistance < Multidrug resistance < Extensive drug resistance}.
#'
#' For everything else: Ordered factor with levels \code{Negative < Positive, unconfirmed < 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.
#' @return \itemize{
#' \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant}}
#' \item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
#' \item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < 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}
#' }
#' @rdname mdro
#' @importFrom dplyr %>%
#' @importFrom crayon red blue bold
@ -56,7 +58,13 @@
#'
#' example_isolates %>%
#' mutate(EUCAST = mdro(.),
#' BRMO = brmo(.))
#' BRMO = brmo(.),
#' MRGN = mrgn(.))
#'
#' example_isolates %>%
#' rename(PIP = TZP) # no piperacillin, so take piperacillin/tazobactam
#' mrgn() %>% # check German guideline
#' freq() # check frequencies
mdro <- function(x,
guideline = NULL,
col_mo = NULL,
@ -120,10 +128,10 @@ mdro <- function(x,
# support per country:
} else if (guideline$code == "mrgn") {
guideline$name <- "Germany"
guideline$name <- ""
guideline$version <- ""
guideline$source <- ""
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
guideline$author <- "J. M\u00fcller, A. Voss, R. K\u00f6ck, ..., W.V. Kern, C. Wendt, A.W. Friedrich"
guideline$version <- "N/A"
guideline$source <- "M\u00fcller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6"
} else if (guideline$code == "brmo") {
guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
@ -153,6 +161,15 @@ mdro <- function(x,
"RIB",
"RFP"),
verbose = verbose, ...)
} else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("PIP",
"CTX",
"CAZ",
"IPM",
"MEM",
"CIP"),
verbose = verbose, ...)
} else {
cols_ab <- get_column_abx(x = x, verbose = verbose, ...)
}
@ -269,7 +286,9 @@ mdro <- function(x,
# join to microorganisms data set
left_join_microorganisms(by = col_mo) %>%
# add unconfirmed to where genus is available
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_))
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_)) %>%
# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
as.data.frame(stringsAsFactors = FALSE)
if (guideline$code == "eucast") {
# EUCAST ------------------------------------------------------------------
@ -302,7 +321,7 @@ mdro <- function(x,
"any")
# Table 6
trans_tbl(3,
which(x$fullname %like% "^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)"),
which(x$fullname %like% "^(Coagulase-negative|Staphylococcus (aureus|epidermidis|hominis|haemolyticus|intermedius|pseudointermedius))"),
c(VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
@ -314,7 +333,7 @@ mdro <- function(x,
c(carbapenems, VAN, TEC, DAP, LNZ, QDA, TGC, RIF),
"any")
trans_tbl(3, # Sr. groups A/B/C/G
which(x$fullname %like% "^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)"),
which(x$fullname %like% "^Streptococcus (group (A|B|C|G)|pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)"),
c(PEN, cephalosporins, VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
@ -338,7 +357,51 @@ mdro <- function(x,
if (guideline$code == "mrgn") {
# Germany -----------------------------------------------------------------
stop("We are still working on German guidelines in this beta version.", call. = FALSE)
CTX_or_CAZ <- CTX %or% CAZ
IPM_or_MEM <- IPM %or% MEM
x$missing <- NA_character_
if (is.na(PIP)) PIP <- "missing"
if (is.na(CTX_or_CAZ)) CTX_or_CAZ <- "missing"
if (is.na(IPM_or_MEM)) IPM_or_MEM <- "missing"
if (is.na(IPM)) IPM <- "missing"
if (is.na(MEM)) MEM <- "missing"
if (is.na(CIP)) CIP <- "missing"
# Table 1
x[which((x$family == "Enterobacteriaceae" |
x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
x[, IPM_or_MEM] == "S" &
x[, CIP] == "R"),
"MDRO"] <- 2 # 2 = 3MRGN
x[which((x$family == "Enterobacteriaceae" |
x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
x[, IPM_or_MEM] == "R" &
x[, CIP] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable
x[which((x$family == "Enterobacteriaceae" |
x$fullname %like% "^Acinetobacter baumannii") &
x[, IPM] == "R" | x[, MEM] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R
x[which(x$fullname %like% "^Pseudomonas aeruginosa" &
(x[, PIP] == "S") +
(x[, CTX_or_CAZ] == "S") +
(x[, IPM_or_MEM] == "S") +
(x[, CIP] == "S") == 1),
"MDRO"] <- 2 # 2 = 3MRGN, if only 1 group is S
x[which((x$fullname %like% "^Pseudomonas aeruginosa") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
x[, IPM_or_MEM] == "R" &
x[, CIP] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN
}
if (guideline$code == "brmo") {
@ -486,6 +549,11 @@ mdro <- function(x,
levels = 1:5,
labels = c("Negative", "Mono-resistant", "Poly-resistant", "Multi-drug-resistant", "Extensive drug-resistant"),
ordered = TRUE)
} else if (guideline$code == "mrgn") {
factor(x = x$MDRO,
levels = 1:3,
labels = c("Negative", "3MRGN", "4MRGN"),
ordered = TRUE)
} else {
factor(x = x$MDRO,
levels = 1:3,

2
docs/404.html
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@ -84,7 +84,7 @@
</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">0.7.1.9095</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.7.1.9095</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>

574
docs/articles/AMR.html
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@ -41,7 +41,7 @@
</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">0.7.1.9091</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 September 2019</h4>
<h4 class="date">07 October 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -196,7 +196,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 30 September 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 07 October 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -212,21 +212,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-09-30</td>
<td align="center">2019-10-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-09-30</td>
<td align="center">2019-10-07</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-09-30</td>
<td align="center">2019-10-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -321,68 +321,68 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-02-07</td>
<td align="center">I4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-09-17</td>
<td align="center">V3</td>
<td align="center">2012-10-04</td>
<td align="center">J3</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-03-12</td>
<td align="center">S8</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-05-15</td>
<td align="center">Q9</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-02-01</td>
<td align="center">K5</td>
<tr class="even">
<td align="center">2012-10-15</td>
<td align="center">G6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-03-05</td>
<td align="center">X1</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2012-01-13</td>
<td align="center">V5</td>
<td align="center">2012-04-15</td>
<td align="center">G8</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-03-26</td>
<td align="center">M3</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-11-13</td>
<td align="center">C4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
@ -407,8 +407,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,446 52.23% 10,446 52.23%
# 2 F 9,554 47.77% 20,000 100.00%</code></pre>
# 1 M 10,403 52.02% 10,403 52.02%
# 2 F 9,597 47.99% 20,000 100.00%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -438,14 +438,14 @@
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,448 values changed)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,466 values changed)</span></a>
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,335 values changed)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,304 values changed)</span></a>
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,751 values changed)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,787 values changed)</span></a>
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
@ -453,24 +453,24 @@
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,259 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (125 values changed)</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,243 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (114 values changed)</span></a>
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,609 out of 20,000 rows, making a total of 7,918 edits</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,571 out of 20,000 rows, making a total of 7,914 edits</span></a>
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,918 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 101 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,771 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,065 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 321 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,636 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 24 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,914 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 104 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,762 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,059 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 331 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,638 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 20 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -498,8 +498,8 @@
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,685 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,696 first isolates (28.5% of total)</span></a></code></pre></div>
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -509,7 +509,7 @@
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient K5, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient E8, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -525,8 +525,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-28</td>
<td align="center">K5</td>
<td align="center">2010-01-14</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -536,8 +536,8 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-06-18</td>
<td align="center">K5</td>
<td align="center">2010-03-24</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -547,10 +547,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-10-15</td>
<td align="center">K5</td>
<td align="center">2010-05-23</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -558,8 +558,8 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-12-16</td>
<td align="center">K5</td>
<td align="center">2010-08-30</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -569,30 +569,19 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-01-17</td>
<td align="center">K5</td>
<td align="center">2010-09-04</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-06-30</td>
<td align="center">K5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-08-11</td>
<td align="center">K5</td>
<td align="center">2010-09-14</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -600,42 +589,53 @@
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-10-02</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-10-18</td>
<td align="center">K5</td>
<td align="center">2011-01-01</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-04-24</td>
<td align="center">K5</td>
<td align="center">2011-02-10</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2012-10-30</td>
<td align="center">K5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-03-11</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 3 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -646,7 +646,7 @@
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,102 first weighted isolates (75.5% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,087 first weighted isolates (75.4% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -663,8 +663,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-04-28</td>
<td align="center">K5</td>
<td align="center">2010-01-14</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -675,8 +675,8 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-06-18</td>
<td align="center">K5</td>
<td align="center">2010-03-24</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -687,8 +687,44 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-10-15</td>
<td align="center">K5</td>
<td align="center">2010-05-23</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-08-30</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-04</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-14</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
@ -697,61 +733,25 @@
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-12-16</td>
<td align="center">K5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-01-17</td>
<td align="center">K5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-06-30</td>
<td align="center">K5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-08-11</td>
<td align="center">K5</td>
<td align="center">2010-10-02</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-10-18</td>
<td align="center">K5</td>
<td align="center">2011-01-01</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -759,35 +759,35 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2012-04-24</td>
<td align="center">K5</td>
<td align="center">2011-02-10</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2012-10-30</td>
<td align="center">K5</td>
<td align="center">2011-03-11</td>
<td align="center">E8</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 3, now 9 isolates are flagged. In total, 75.5% of all isolates are marked ‘first weighted’ - 47.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 7 isolates are flagged. In total, 75.4% of all isolates are marked ‘first weighted’ - 47.0% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,102 isolates for analysis.</p>
<p>So we end up with 15,087 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</a></code></pre></div>
@ -813,25 +813,89 @@
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2016-02-07</td>
<td align="center">I4</td>
<td align="center">2012-10-04</td>
<td align="center">J3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2015-09-17</td>
<td align="center">V3</td>
<td align="center">2015-03-12</td>
<td align="center">S8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2015-05-15</td>
<td align="center">Q9</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2012-04-15</td>
<td align="center">G8</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2015-03-26</td>
<td align="center">M3</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2011-08-08</td>
<td align="center">V10</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -843,70 +907,6 @@
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2015-02-01</td>
<td align="center">K5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>4</td>
<td align="center">2010-03-05</td>
<td align="center">X1</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2016-04-24</td>
<td align="center">I9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2015-09-18</td>
<td align="center">O7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -926,7 +926,7 @@
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,102 (of which NA: 0 = 0%)<br>
Length: 15,087 (of which NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -943,33 +943,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,408</td>
<td align="right">49.05%</td>
<td align="right">7,408</td>
<td align="right">49.05%</td>
<td align="right">7,412</td>
<td align="right">49.13%</td>
<td align="right">7,412</td>
<td align="right">49.13%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,747</td>
<td align="right">24.81%</td>
<td align="right">11,155</td>
<td align="right">73.86%</td>
<td align="right">3,773</td>
<td align="right">25.01%</td>
<td align="right">11,185</td>
<td align="right">74.14%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,341</td>
<td align="right">15.50%</td>
<td align="right">13,496</td>
<td align="right">89.37%</td>
<td align="right">2,331</td>
<td align="right">15.45%</td>
<td align="right">13,516</td>
<td align="right">89.59%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,606</td>
<td align="right">10.63%</td>
<td align="right">15,102</td>
<td align="right">1,571</td>
<td align="right">10.41%</td>
<td align="right">15,087</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -980,7 +980,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4662959</span></a></code></pre></div>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4716643</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -993,19 +993,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4653354</td>
<td align="center">0.4725537</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4673178</td>
<td align="center">0.4704871</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4720576</td>
<td align="center">0.4684529</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4613045</td>
<td align="center">0.4749061</td>
</tr>
</tbody>
</table>
@ -1023,23 +1023,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4653354</td>
<td align="center">4457</td>
<td align="center">0.4725537</td>
<td align="center">4609</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4673178</td>
<td align="center">5324</td>
<td align="center">0.4704871</td>
<td align="center">5235</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4720576</td>
<td align="center">2362</td>
<td align="center">0.4684529</td>
<td align="center">2314</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4613045</td>
<td align="center">2959</td>
<td align="center">0.4749061</td>
<td align="center">2929</td>
</tr>
</tbody>
</table>
@ -1059,27 +1059,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9226512</td>
<td align="center">0.8964633</td>
<td align="center">0.9943305</td>
<td align="center">0.9202644</td>
<td align="center">0.8950351</td>
<td align="center">0.9919050</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8281445</td>
<td align="center">0.8953923</td>
<td align="center">0.9856787</td>
<td align="center">0.8166773</td>
<td align="center">0.9019733</td>
<td align="center">0.9847231</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9236723</td>
<td align="center">0.9196691</td>
<td align="center">0.9954630</td>
<td align="center">0.9247283</td>
<td align="center">0.9196926</td>
<td align="center">0.9939041</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6253738</td>
<td align="center">0.6194766</td>
<td align="center">0.0000000</td>
<td align="center">0.6253738</td>
<td align="center">0.6194766</td>
</tr>
</tbody>
</table>

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</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">0.7.1.9095</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>

2
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@ -84,7 +84,7 @@
</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">0.7.1.9095</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>

2
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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">0.7.1.9095</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>

18
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9095</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
</div>
@ -231,11 +231,11 @@
</div>
<div id="amr-0-7-1-9095" class="section level1">
<div id="amr-0-7-1-9096" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9095" class="anchor"></a>AMR 0.7.1.9095<small> Unreleased </small>
<a href="#amr-0-7-1-9096" class="anchor"></a>AMR 0.7.1.9096<small> Unreleased </small>
</h1>
<p><small>Last updated: 06-Oct-2019</small></p>
<p><small>Last updated: 07-Oct-2019</small></p>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -258,7 +258,8 @@ For WHONET users, this means that all records/isolates with organism code <code>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#&gt; Warning message:</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#&gt; invalid microorganism code, NA generated</span></a></code></pre></div>
This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
<li><p>Function <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li>Function <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</li>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
<div id="new" class="section level3">
@ -336,9 +337,8 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<li>Changed most microorganism IDs to improve readability. For example, the old code <code>B_ENTRC_FAE</code> could have been both <em>E. faecalis</em> and <em>E. faecium</em>. Its new code is <code>B_ENTRC_FCLS</code> and <em>E. faecium</em> has become <code>B_ENTRC_FACM</code>. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for <em>Aerococcus urinae</em> was <code>B_ARCCC_NAE</code>. This is now <code>B_AERCC_URIN</code>. <strong>IMPORTANT:</strong> Old microorganism IDs are still supported, but support will be dropped in a future version. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> on your old codes to transform them to the new format. Using functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) on old codes, will throw a warning.</li>
</ul>
</li>
<li>More intelligent guessing for <code><a href="../reference/as.ab.html">as.ab()</a></code> which also led to bidirectional language support</li>
<li>Renamed data set <code>septic_patients</code> to <code>example_isolates</code>
</li>
<li>More intelligent guessing for <code><a href="../reference/as.ab.html">as.ab()</a></code>, including bidirectional language support</li>
<li>Added support for the German national guideline (3MRGN/4MRGN) in the <code><a href="../reference/mdro.html">mdro()</a></code> function, to determine multi-drug resistant organisms</li>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
<li>Fixed a bug for <em>Yersinia pseudotuberculosis</em>
@ -1289,7 +1289,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9095">0.7.1.9095</a></li>
<li><a href="#amr-0-7-1-9096">0.7.1.9096</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

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@ -85,7 +85,7 @@
</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">0.7.1.9092</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
</span>
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@ -15,21 +15,25 @@
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<p>Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.</p>
</div>
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>,
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>,
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@ -254,7 +257,7 @@
</tr>
<tr>
<th>rules</th>
<td><p>a character vector that specifies which rules should be applied - one or more of <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c("breakpoints", "expert", "other", "all")</a></code></p></td>
<td><p>a character vector that specifies which rules should be applied - one or more of <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert", "other", "all")</a></code></p></td>
</tr>
<tr>
<th>verbose</th>
@ -265,10 +268,11 @@
<td><p>column name of an antibiotic, see section Antibiotics</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<ul>
<ul>
<li><p>EUCAST Expert Rules. Version 2.0, 2012. <br />
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br />
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
@ -277,22 +281,21 @@
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
</ul>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The input of <code>x</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <code>data.frame</code> with all original and new values of the affected bug-drug combinations.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code>eucast_rules</code> and <code><a href='mdro.html'>mdro</a></code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)', sorted by name:</p>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code>eucast_rules</code> and <code><a href='mdro.html'>mdro</a></code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p>
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
@ -365,16 +368,14 @@
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<pre class="examples"><span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
<span class='st'>"Klebsiella pneumoniae"</span>,
@ -409,7 +410,7 @@
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># \donttest{</span>
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span>
<span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
@ -419,31 +420,27 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.</p>
</div>
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@ -244,7 +247,7 @@
<span class='fu'>mdr_tb</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"TB"</span>, <span class='no'>...</span>)
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@ -273,33 +276,37 @@
<td><p>column name of an antibiotic, see section Antibiotics</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p>
<p>World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p>
<p>Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (<a href='https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'>link</a>)</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>For TB (<code>mdr_tb()</code>): Ordered factor with levels <code>Negative &lt; Mono-resistance &lt; Poly-resistance &lt; Multidrug resistance &lt; Extensive drug resistance</code>.</p>
<p>For everything else: Ordered factor with levels <code>Negative &lt; Positive, unconfirmed &lt; 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>
<ul>
<li><p>TB guideline - function <code>mdr_tb()</code> or <code>mdro(..., guideline = "TB")</code>:<br /> Ordered factor with levels <code>Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt; Extensive drug-resistant</code></p></li>
<li><p>German guideline - function <code>mrgn()</code> or <code>mdro(..., guideline = "MRGN")</code>:<br /> Ordered factor with levels <code>Negative &lt; 3MRGN &lt; 4MRGN</code></p></li>
<li><p>Everything else:<br /> Ordered factor with levels <code>Negative &lt; Positive, unconfirmed &lt; 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>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Currently supported guidelines are:</p><ul>
<li><p><code>guideline = "EUCAST"</code>: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "TB"</code>: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code>: (work in progress)</p></li>
<li><p><code>guideline = "BRMO"</code>: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (<a href='https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'>link</a>)</p></li>
<p>Currently supported guidelines are (case-insensitive):</p><ul>
<li><p><code>guideline = "EUCAST"</code>: The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "TB"</code>: The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code>: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
<li><p><code>guideline = "BRMO"</code>: The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (<a href='https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'>link</a>)</p></li>
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules</a></code> and <code>mdro</code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)', sorted by name:</p>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules</a></code> and <code>mdro</code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p>
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
@ -372,51 +379,50 @@
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>),
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>))
<span class='co'># }</span></pre>
<span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>),
<span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>rename</a></span>(<span class='kw'>PIP</span> <span class='kw'>=</span> <span class='no'>TZP</span>) <span class='co'># no piperacillin, so take piperacillin/tazobactam</span>
<span class='fu'>mrgn</span>() <span class='kw'>%&gt;%</span> <span class='co'># check German guideline</span>
<span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>() <span class='co'># check frequencies</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
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@ -439,6 +445,8 @@
</script>
</body>
</html>

2
man/eucast_rules.Rd
View File

@ -53,7 +53,7 @@ The file containing all EUCAST rules is located here: \url{https://gitlab.com/ms
To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name:
\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),

28
man/mdro.Rd
View File

@ -40,20 +40,22 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{...}{column name of an antibiotic, see section Antibiotics}
}
\value{
For TB (\code{mdr_tb()}): Ordered factor with levels \code{Negative < Mono-resistance < Poly-resistance < Multidrug resistance < Extensive drug resistance}.
For everything else: Ordered factor with levels \code{Negative < Positive, unconfirmed < 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.
\itemize{
\item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant}}
\item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
\item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < 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 (country-specific) guidelines.
}
\details{
Currently supported guidelines are:
Currently supported guidelines are (case-insensitive):
\itemize{
\item{\code{guideline = "EUCAST"}: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
\item{\code{guideline = "TB"}: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
\item{\code{guideline = "MRGN"}: (work in progress)}
\item{\code{guideline = "BRMO"}: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
\item{\code{guideline = "EUCAST"}: The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
\item{\code{guideline = "TB"}: The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})}
\item{\code{guideline = "MRGN"}: The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6}
\item{\code{guideline = "BRMO"}: The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})}
}
Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
@ -62,7 +64,7 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name:
\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
@ -148,5 +150,11 @@ library(dplyr)
example_isolates \%>\%
mutate(EUCAST = mdro(.),
BRMO = brmo(.))
BRMO = brmo(.),
MRGN = mrgn(.))
example_isolates \%>\%
rename(PIP = TZP) # no piperacillin, so take piperacillin/tazobactam
mrgn() \%>\% # check German guideline
freq() # check frequencies
}

22
tests/testthat/test-mdro.R
View File

@ -75,7 +75,27 @@ test_that("mdro works", {
col_mo = "mo",
info = FALSE)),
"Positive")
# German 3MRGN and 4MRGN
expect_equal(as.character(mrgn(
data.frame(mo = c("E. coli", "E. coli", "K. pneumoniae", "E. coli",
"A. baumannii", "A. baumannii", "A. baumannii",
"P. aeruginosa", "P. aeruginosa", "P. aeruginosa"),
PIP = c("S", "R", "R", "S",
"S", "R", "R",
"S", "R", "R"),
CTX = c("S", "R", "R", "S",
"R", "R", "R",
"R", "R", "R"),
IPM = c("S", "R", "S", "R",
"R", "R", "S",
"S", "R", "R"),
CIP = c("S", "R", "R", "S",
"R", "R", "R",
"R", "S", "R"),
stringsAsFactors = FALSE))),
c("Negative", "4MRGN", "3MRGN", "4MRGN", "4MRGN", "4MRGN", "3MRGN", "Negative", "3MRGN", "4MRGN"))
# MDR TB
expect_equal(
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),