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(v1.2.0.9019) ab_from_text() dose and administration

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dr. M.S. (Matthijs) Berends 2020-07-01 11:07:01 +02:00
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commit 329a0eb0b6
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.2.0.9018
Date: 2020-06-26
Version: 1.2.0.9019
Date: 2020-07-01
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.2.0.9018
## <small>Last updated: 26-Jun-2020</small>
# AMR 1.2.0.9019
## <small>Last updated: 01-Jul-2020</small>
### New
* Function `ab_from_text()` to retrieve antimicrobial drugs from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally:

28
R/aa_helper_functions.R
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@ -201,8 +201,7 @@ import_fn <- function(name, pkg) {
get(name, envir = asNamespace(pkg))
}
stop_if <- function(expr, ..., call = TRUE) {
if (isTRUE(expr)) {
stop_ <- function(..., call = TRUE) {
msg <- paste0(c(...), collapse = "")
if (!isFALSE(call)) {
if (isTRUE(call)) {
@ -214,22 +213,31 @@ stop_if <- function(expr, ..., call = TRUE) {
msg <- paste0("in ", call, "(): ", msg)
}
stop(msg, call. = FALSE)
}
stop_if <- function(expr, ..., call = TRUE) {
if (isTRUE(expr)) {
if (isTRUE(call)) {
call <- -1
}
if (!isFALSE(call)) {
# since we're calling stop_(), which is another call
call <- call - 1
}
stop_(..., call = call)
}
}
stop_ifnot <- function(expr, ..., call = TRUE) {
if (!isTRUE(expr)) {
msg <- paste0(c(...), collapse = "")
if (!isFALSE(call)) {
if (isTRUE(call)) {
call <- as.character(sys.call(-1)[1])
} else {
# so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
call <- as.character(sys.call(call)[1])
call <- -1
}
msg <- paste0("in ", call, "(): ", msg)
if (!isFALSE(call)) {
# since we're calling stop_(), which is another call
call <- call - 1
}
stop(msg, call. = FALSE)
stop_(..., call = call)
}
}

122
R/ab_from_text.R
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@ -19,55 +19,90 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Retrieve antimicrobial drugs from clinical text
#' Retrieve antimicrobial drug names and doses from clinical text
#'
#' Use this function on e.g. clinical texts from health care records. It returns a [list] with all antimicrobial drugs found in the texts.
#' Use this function on e.g. clinical texts from health care records. It returns a [list] with all antimicrobial drugs, doses and forms of administration found in the texts.
#' @inheritSection lifecycle Maturing lifecycle
#' @param text text to analyse
#' @param collapse character to pass on to `paste(..., collapse = ...)` to only return one character per element of `text`, see Examples
#' @param translate_ab a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
#' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
#' @param collapse character to pass on to `paste(..., collapse = ...)` to only return one character per element of `text`, see *Examples*
#' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
#' @param ... parameters passed on to [as.ab()]
#' @details Without using `collapse`, this function will return a [list]. This can be convenient to use e.g. inside a `mutate()`):\cr
#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned.
#'
#' ## Parameter `type`
#' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling.
#'
#' With `type = "dose"` (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see *Examples*.
#'
#' With `type = "administration"` (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see *Examples*.
#'
#' ## Parameter `collapse`
#' Without using `collapse`, this function will return a [list]. This can be convenient to use e.g. inside a `mutate()`):\cr
#' `df %>% mutate(abx = ab_from_text(clinical_text))`
#'
#' The returned AB codes can be transformed to official names, groups, etc. with all [ab_property()] functions like [ab_name()] and [ab_group()], or by using the `translate_ab` parameter.
#'
#' With using `collapse`, this function will return a [character]:\cr
#' `df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))`
#'
#' This function is also internally used by [as.ab()], although it then only returns the first hit and will throw a note if more results could have been returned.
#' @export
#' @return A [list], or a [character] if `collapse` is not `NULL`
#' @inheritSection AMR Read more on our website!
#' @examples
#' # mind the bad spelling of amoxicillin in this line,
#' # straight from a true health care record:
#' ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")
#'
#' ab_from_text("administered amoxi/clav and cipro")
#' ab_from_text("administered amoxi/clav and cipro", collapse = ", ")
#' ab_from_text("500 mg amoxi po and 400mg cipro iv")
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "admin")
#'
#' # if you want to know which antibiotic groups were administered, check it:
#' abx <- ab_from_text("administered amoxi/clav and cipro")
#' ab_from_text("500 mg amoxi po and 400mg cipro iv", collapse = ", ")
#'
#' # if you want to know which antibiotic groups were administered, do e.g.:
#' abx <- ab_from_text("500 mg amoxi po and 400mg cipro iv")
#' ab_group(abx[[1]])
#'
#' if (require(dplyr)) {
#' tibble(clinical_text = c("given cipro and mero",
#' "started on doxy today")) %>%
#' mutate(abx = ab_from_text(clinical_text),
#' abx2 = ab_from_text(clinical_text,
#' collapse = "|"),
#' abx3 = ab_from_text(clinical_text,
#' tibble(clinical_text = c("given 400mg cipro and 500 mg amox",
#' "started on doxy iv today")) %>%
#' mutate(abx_codes = ab_from_text(clinical_text),
#' abx_doses = ab_from_text(clinical_text, type = "doses"),
#' abx_admin = ab_from_text(clinical_text, type = "admin"),
#' abx_coll = ab_from_text(clinical_text, collapse = "|"),
#' abx_coll_names = ab_from_text(clinical_text,
#' collapse = "|",
#' translate_ab = "name"))
#' translate_ab = "name"),
#' abx_coll_doses = ab_from_text(clinical_text,
#' type = "doses",
#' collapse = "|"),
#' abx_coll_admin = ab_from_text(clinical_text,
#' type = "admin",
#' collapse = "|"))
#'
#' }
ab_from_text <- function(text, collapse = NULL, translate_ab = FALSE, ...) {
ab_from_text <- function(text,
type = c("drug", "dose", "administration"),
collapse = NULL,
translate_ab = FALSE,
...) {
if (missing(type)) {
type <- type[1L]
}
type <- tolower(trimws(type))
stop_if(length(type) != 1, "`type` must be of length 1")
text <- tolower(as.character(text))
text_split_all <- strsplit(text, "[ ;.,:/\\|-]")
if (type %like% "(drug|ab|anti)") {
translate_ab <- get_translate_ab(translate_ab)
abbr <- unlist(antibiotics$abbreviations)
abbr <- abbr[nchar(abbr) >= 4]
names <- substr(antibiotics$name, 1, 5)
names_atc <- substr(c(antibiotics$name, antibiotics$atc), 1, 5)
synonyms <- unlist(antibiotics$synonyms)
synonyms <- synonyms[nchar(synonyms) >= 4]
to_regex <- function(x) {
@ -76,11 +111,10 @@ ab_from_text <- function(text, collapse = NULL, translate_ab = FALSE, ...) {
").*")
}
text_split_all <- strsplit(text, "[ ;.,:/\\|-]")
result <- lapply(text_split_all, function(text_split) {
suppressWarnings(
out <- as.ab(unique(c(text_split[grep(to_regex(abbr), text_split)],
text_split[grep(to_regex(names), text_split)],
text_split[grep(to_regex(names_atc), text_split)],
# regular expression must not be too long, so split synonyms in two:
text_split[grep(to_regex(synonyms[c(1:0.5 * length(synonyms))]), text_split)],
text_split[grep(to_regex(synonyms[c(0.5 * length(synonyms):length(synonyms))]), text_split)])),
@ -96,9 +130,51 @@ ab_from_text <- function(text, collapse = NULL, translate_ab = FALSE, ...) {
}
})
} else if (type %like% "dos") {
text_split_all <- strsplit(text, " ")
result <- lapply(text_split_all, function(text_split) {
text_split <- text_split[text_split %like% "^[0-9]{2,}(/[0-9]+)?[a-z]*$"]
# only left part of "/", like 500 in "500/125"
text_split <- gsub("/.*", "", text_split)
text_split <- gsub(",", ".", text_split, fixed = TRUE) # foreign system using comma as decimal sep
text_split <- as.double(gsub("[^0-9.]", "", text_split))
# minimal 100 units/mg and no years that unlikely doses
text_split <- text_split[text_split >= 100 & !text_split %in% c(1951:1999, 2001:2049)]
if (length(text_split) > 0) {
text_split
} else {
NA_real_
}
})
} else if (type %like% "adm") {
result <- lapply(text_split_all, function(text_split) {
text_split <- text_split[text_split %like% "(^iv$|intraven|^po$|per os|oral|implant|inhal|instill|nasal|paren|rectal|sublingual|buccal|trans.*dermal|vaginal)"]
if (length(text_split) > 0) {
text_split <- gsub("(^po$|.*per os.*)", "oral", text_split)
text_split <- gsub("(^iv$|.*intraven.*)", "iv", text_split)
text_split
} else {
NA_character_
}
})
} else {
stop_("`type` must be either 'drug', 'dose' or 'administration'")
}
# collapse text if needed
if (!is.null(collapse)) {
result <- sapply(result, function(x) paste0(x, collapse = collapse))
result <- sapply(result, function(x) {
if(length(x) == 1 & all(is.na(x))) {
NA_character_
} else {
paste0(x, collapse = collapse)
}
})
}
result
}

6
R/amr.R
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@ -30,6 +30,7 @@
#' This package can be used for:
#' - Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org)
#' - Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
#' - Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
#' - Determining first isolates to be used for AMR analysis
#' - Calculating antimicrobial resistance
#' - Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
@ -45,12 +46,13 @@
#' @section Read more on our website!:
#' On our website <https://msberends.gitlab.io/AMR> you can find [a comprehensive tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
#' @section Contact us:
#' @section Contact Us:
#' For suggestions, comments or questions, please contact us at:
#'
#' Matthijs S. Berends \cr
#' m.s.berends \[at\] umcg \[dot\] nl \cr
#' Department of Medical Microbiology, University of Groningen \cr
#' University of Groningen
#' Department of Medical Microbiology
#' University Medical Center Groningen \cr
#' Post Office Box 30001 \cr
#' 9700 RB Groningen \cr

2
R/lifecycle.R
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@ -35,7 +35,7 @@
#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
#' @section Maturing lifecycle:
#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://gitlab.com/msberends/AMR/-/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
#' @section Stable lifecycle:
#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

2
R/rsi_calc.R
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@ -174,6 +174,8 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
combine_SI <- FALSE
}
stop_if(isTRUE(combine_SI) & isTRUE(combine_IR), "either `combine_SI` or `combine_IR` can be TRUE, not both", call = -2)
stop_ifnot(is.numeric(minimum), "`minimum` must be numeric", call = -2)
stop_ifnot(is.logical(as_percent), "`as_percent` must be logical", call = -2)
translate_ab <- get_translate_ab(translate_ab)

BIN
R/sysdata.rda
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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.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</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">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</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">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</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">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>

3
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">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -223,6 +223,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
<li>Determining first isolates to be used for AMR analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>

12
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">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209018" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9018">
<a href="#amr-1209018" class="anchor"></a>AMR 1.2.0.9018<small> Unreleased </small>
<div id="amr-1209019" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9019">
<a href="#amr-1209019" class="anchor"></a>AMR 1.2.0.9019<small> Unreleased </small>
</h1>
<div id="last-updated-26-jun-2020" class="section level2">
<div id="last-updated-01-jul-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-26-jun-2020" class="anchor"></a><small>Last updated: 26-Jun-2020</small>
<a href="#last-updated-01-jul-2020" class="anchor"></a><small>Last updated: 01-Jul-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-06-26T11:15Z
last_built: 2020-07-01T09:03Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

8
docs/reference/AMR.html
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@ -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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -244,6 +244,7 @@
<p>This package can be used for:</p><ul>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href='http://www.catalogueoflife.org'>Catalogue of Life</a></p></li>
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
<li><p>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</p></li>
<li><p>Determining first isolates to be used for AMR analysis</p></li>
<li><p>Calculating antimicrobial resistance</p></li>
<li><p>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</p></li>
@ -263,14 +264,15 @@
<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 comprehensive 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="contact-us"><a class="anchor" href="#contact-us"></a>Contact us</h2>
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
<p>For suggestions, comments or questions, please contact us at:</p>
<p>Matthijs S. Berends <br />
m.s.berends [at] umcg [dot] nl <br />
Department of Medical Microbiology, University of Groningen <br />
University of Groningen
Department of Medical Microbiology
University Medical Center Groningen <br />
Post Office Box 30001 <br />
9700 RB Groningen <br />

85
docs/reference/ab_from_text.html
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Retrieve antimicrobial drugs from clinical text — ab_from_text • AMR (for R)</title>
<title>Retrieve antimicrobial drug names and doses from clinical text — ab_from_text • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,8 +48,8 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Retrieve antimicrobial drugs from clinical text — ab_from_text" />
<meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs found in the texts." />
<meta property="og:title" content="Retrieve antimicrobial drug names and doses from clinical text — ab_from_text" />
<meta property="og:description" content="Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs, doses and forms of administration found in the texts." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -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">1.2.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -226,16 +226,22 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Retrieve antimicrobial drugs from clinical text</h1>
<h1>Retrieve antimicrobial drug names and doses from clinical text</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
<div class="hidden name"><code>ab_from_text.Rd</code></div>
</div>
<div class="ref-description">
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href='https://rdrr.io/r/base/list.html'>list</a> with all antimicrobial drugs found in the texts.</p>
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href='https://rdrr.io/r/base/list.html'>list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
</div>
<pre class="usage"><span class='fu'>ab_from_text</span>(<span class='no'>text</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
<pre class="usage"><span class='fu'>ab_from_text</span>(
<span class='no'>text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>translate_ab</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">
@ -244,13 +250,17 @@
<th>text</th>
<td><p>text to analyse</p></td>
</tr>
<tr>
<th>type</th>
<td><p>type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></td>
</tr>
<tr>
<th>collapse</th>
<td><p>character to pass on to <code><a href='https://rdrr.io/r/base/paste.html'>paste(..., collapse = ...)</a></code> to only return one character per element of <code>text</code>, see Examples</p></td>
<td><p>character to pass on to <code><a href='https://rdrr.io/r/base/paste.html'>paste(..., collapse = ...)</a></code> to only return one character per element of <code>text</code>, see <em>Examples</em></p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></td>
<td><p>if <code>type = "drug"</code>: a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></td>
</tr>
<tr>
<th>...</th>
@ -263,34 +273,65 @@
<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.</p><h3>Parameter <code>type</code></h3>
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
<h3>Parameter <code>collapse</code></h3>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text))</code></p>
<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_property()</a></code> functions like <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> parameter.</p>
<p>With using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/character.html'>character</a>:<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only returns the first hit and will throw a note if more results could have been returned.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</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 comprehensive 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'># mind the bad spelling of amoxicillin in this line, </span>
<span class='co'># straight from a true health care record:</span>
<span class='fu'>ab_from_text</span>(<span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"administered amoxi/clav and cipro"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"administered amoxi/clav and cipro"</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>", "</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"dose"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>)
<span class='co'># if you want to know which antibiotic groups were administered, check it:</span>
<span class='no'>abx</span> <span class='kw'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"administered amoxi/clav and cipro"</span>)
<span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>", "</span>)
<span class='co'># if you want to know which antibiotic groups were administered, do e.g.:</span>
<span class='no'>abx</span> <span class='kw'>&lt;-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"500 mg amoxi po and 400mg cipro iv"</span>)
<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='no'>abx</span><span class='kw'>[[</span><span class='fl'>1</span>]])
<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>dplyr</span>)) {
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given cipro and mero"</span>,
<span class='st'>"started on doxy today"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),
<span class='kw'>abx2</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx3</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given 400mg cipro and 500 mg amox"</span>,
<span class='st'>"started on doxy iv today"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx_codes</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),
<span class='kw'>abx_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>),
<span class='kw'>abx_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>),
<span class='kw'>abx_coll</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx_coll_names</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>))
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>),
<span class='kw'>abx_coll_doses</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"doses"</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
<span class='kw'>abx_coll_admin</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"admin"</span>,
<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>))
}</pre>
</div>

4
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@ -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">1.2.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -275,7 +275,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>

4
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -398,7 +398,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</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>

4
docs/reference/ggplot_pca.html
View File

@ -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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -376,7 +376,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

4
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View File

@ -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">1.2.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -404,7 +404,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</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>

4
docs/reference/guess_ab_col.html
View File

@ -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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -265,7 +265,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</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>

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">1.2.0.9018</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -289,7 +289,7 @@
<td>
<p><code><a href="ab_from_text.html">ab_from_text()</a></code> </p>
</td>
<td><p>Retrieve antimicrobial drugs from clinical text</p></td>
<td><p>Retrieve antimicrobial drug names and doses from clinical text</p></td>
</tr><tr>
<td>

4
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View File

@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">1.2.0.9011</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -252,7 +252,7 @@ The lifecycle of this function is <strong>experimental</strong>. An experimental
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The lifecycle of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

4
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@ -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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -333,7 +333,7 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>

4
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@ -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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -309,7 +309,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

4
docs/reference/resistance_predict.html
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@ -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">1.2.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9019</span>
</span>
</div>
@ -362,7 +362,7 @@
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://gitlab.com/msberends/AMR/-/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>

1
index.md
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@ -38,6 +38,7 @@ This package can be used for:
* Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org) and [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) ([manual](./reference/mo_property.html))
* Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines ([manual](./reference/as.rsi.html))
* Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records ([manual](./reference/ab_from_text.html))
* Determining first isolates to be used for AMR analysis ([manual](./reference/first_isolate.html))
* Calculating antimicrobial resistance ([tutorial](./articles/AMR.html))
* Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) ([tutorial](./articles/MDR.html))

6
man/AMR.Rd
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@ -15,6 +15,7 @@ This package can be used for:
\itemize{
\item Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the \href{http://www.catalogueoflife.org}{Catalogue of Life}
\item Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
\item Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
\item Determining first isolates to be used for AMR analysis
\item Calculating antimicrobial resistance
\item Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
@ -34,13 +35,14 @@ This package can be used for:
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\section{Contact us}{
\section{Contact Us}{
For suggestions, comments or questions, please contact us at:
Matthijs S. Berends \cr
m.s.berends [at] umcg [dot] nl \cr
Department of Medical Microbiology, University of Groningen \cr
University of Groningen
Department of Medical Microbiology
University Medical Center Groningen \cr
Post Office Box 30001 \cr
9700 RB Groningen \cr

76
man/ab_from_text.Rd
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@ -2,16 +2,24 @@
% Please edit documentation in R/ab_from_text.R
\name{ab_from_text}
\alias{ab_from_text}
\title{Retrieve antimicrobial drugs from clinical text}
\title{Retrieve antimicrobial drug names and doses from clinical text}
\usage{
ab_from_text(text, collapse = NULL, translate_ab = FALSE, ...)
ab_from_text(
text,
type = c("drug", "dose", "administration"),
collapse = NULL,
translate_ab = FALSE,
...
)
}
\arguments{
\item{text}{text to analyse}
\item{collapse}{character to pass on to \code{paste(..., collapse = ...)} to only return one character per element of \code{text}, see Examples}
\item{type}{type of property to search for, either \code{"drug"}, \code{"dose"} or \code{"administration"}, see \emph{Examples}}
\item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Defaults to \code{FALSE}. Using \code{TRUE} is equal to using "name".}
\item{collapse}{character to pass on to \code{paste(..., collapse = ...)} to only return one character per element of \code{text}, see \emph{Examples}}
\item{translate_ab}{if \code{type = "drug"}: a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Defaults to \code{FALSE}. Using \code{TRUE} is equal to using "name".}
\item{...}{parameters passed on to \code{\link[=as.ab]{as.ab()}}}
}
@ -19,9 +27,21 @@ ab_from_text(text, collapse = NULL, translate_ab = FALSE, ...)
A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
}
\description{
Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs found in the texts.
Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs, doses and forms of administration found in the texts.
}
\details{
This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned.
\subsection{Parameter \code{type}}{
At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling.
With \code{type = "dose"} (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see \emph{Examples}.
With \code{type = "administration"} (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see \emph{Examples}.
}
\subsection{Parameter \code{collapse}}{
Without using \code{collapse}, this function will return a \link{list}. This can be convenient to use e.g. inside a \code{mutate()}):\cr
\code{df \%>\% mutate(abx = ab_from_text(clinical_text))}
@ -29,30 +49,50 @@ The returned AB codes can be transformed to official names, groups, etc. with al
With using \code{collapse}, this function will return a \link{character}:\cr
\code{df \%>\% mutate(abx = ab_from_text(clinical_text, collapse = "|"))}
This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only returns the first hit and will throw a note if more results could have been returned.
}
}
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\examples{
# mind the bad spelling of amoxicillin in this line,
# straight from a true health care record:
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")
ab_from_text("administered amoxi/clav and cipro")
ab_from_text("administered amoxi/clav and cipro", collapse = ", ")
ab_from_text("500 mg amoxi po and 400mg cipro iv")
ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "dose")
ab_from_text("500 mg amoxi po and 400mg cipro iv", type = "admin")
# if you want to know which antibiotic groups were administered, check it:
abx <- ab_from_text("administered amoxi/clav and cipro")
ab_from_text("500 mg amoxi po and 400mg cipro iv", collapse = ", ")
# if you want to know which antibiotic groups were administered, do e.g.:
abx <- ab_from_text("500 mg amoxi po and 400mg cipro iv")
ab_group(abx[[1]])
if (require(dplyr)) {
tibble(clinical_text = c("given cipro and mero",
"started on doxy today")) \%>\%
mutate(abx = ab_from_text(clinical_text),
abx2 = ab_from_text(clinical_text,
collapse = "|"),
abx3 = ab_from_text(clinical_text,
tibble(clinical_text = c("given 400mg cipro and 500 mg amox",
"started on doxy iv today")) \%>\%
mutate(abx_codes = ab_from_text(clinical_text),
abx_doses = ab_from_text(clinical_text, type = "doses"),
abx_admin = ab_from_text(clinical_text, type = "admin"),
abx_coll = ab_from_text(clinical_text, collapse = "|"),
abx_coll_names = ab_from_text(clinical_text,
collapse = "|",
translate_ab = "name"))
translate_ab = "name"),
abx_coll_doses = ab_from_text(clinical_text,
type = "doses",
collapse = "|"),
abx_coll_admin = ab_from_text(clinical_text,
type = "admin",
collapse = "|"))
}
}

2
man/as.ab.Rd
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@ -40,7 +40,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{WHOCC}{

2
man/eucast_rules.Rd
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@ -156,7 +156,7 @@ The following antibiotics are used for the functions \code{\link[=eucast_rules]{
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Read more on our website!}{

2
man/ggplot_pca.Rd
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@ -107,7 +107,7 @@ The colours for labels and points can be changed by adding another scale layer f
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\examples{

2
man/ggplot_rsi.Rd
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@ -138,7 +138,7 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Read more on our website!}{

2
man/guess_ab_col.Rd
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@ -25,7 +25,7 @@ You can look for an antibiotic (trade) name or abbreviation and it will search \
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Read more on our website!}{

2
man/lifecycle.Rd
View File

@ -18,7 +18,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{experimental}. A
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Stable lifecycle}{

2
man/mdro.Rd
View File

@ -95,7 +95,7 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Antibiotics}{

2
man/pca.Rd
View File

@ -62,7 +62,7 @@ The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object,
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\examples{

2
man/resistance_predict.Rd
View File

@ -103,7 +103,7 @@ Valid options for the statistical model (parameter \code{model}) are:
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
}
\section{Interpretation of R and S/I}{

5
tests/testthat/test-ab_from_text.R
View File

@ -29,4 +29,9 @@ test_that("ab_from_text works", {
"Amoxicillin")
expect_identical(ab_from_text("administered amoxi/clav and cipro", collapse = ", ")[[1]],
"AMX, CIP")
expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "dose")[[1]],
500)
expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "admin")[[1]],
"oral")
})