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(v0.9.0.9009) antibiotics data set update

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dr. M.S. (Matthijs) Berends 2020-01-08 11:30:33 +01:00
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commit 64f5ceef03
49 changed files with 134 additions and 59 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.9.0.9008 Version: 0.9.0.9009
Date: 2020-01-05 Date: 2020-01-08
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -63,5 +63,5 @@ BugReports: https://gitlab.com/msberends/AMR/issues
License: GPL-2 | file LICENSE License: GPL-2 | file LICENSE
Encoding: UTF-8 Encoding: UTF-8
LazyData: true LazyData: true
RoxygenNote: 7.0.1 RoxygenNote: 7.0.2
Roxygen: list(markdown = TRUE) Roxygen: list(markdown = TRUE)

9
NEWS.md
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@ -1,10 +1,15 @@
# AMR 0.9.0.9008 # AMR 0.9.0.9009
## <small>Last updated: 05-Jan-2020</small> ## <small>Last updated: 08-Jan-2020</small>
### Changes ### Changes
* Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae* * Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae*
* Input values for `as.disk()` limited to a maximum of 50 millimeters * Input values for `as.disk()` limited to a maximum of 50 millimeters
* Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle) * Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle)
* For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
* Changes to the `antibiotics` data set (thanks to Peter Dutey):
* Added more synonyms to colistin, imipenem and piperacillin/tazobactam
* Moved synonyms Rifinah and Rimactazid from rifampicin (`RIF`) to rifampicin/isoniazid (`RFI`). Please note that [the combination rifampicin/isoniazid has no DDDs defined](https://www.whocc.no/atc_ddd_index/?code=J04AM02&showdescription=no), so e.g. `ab_ddd("Rimactazid")` will now return `NA`.
* Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (`SMX`) to trimethoprim/sulfamethoxazole (`SXT`)
### Other ### Other
* Add a `CITATION` file * Add a `CITATION` file

14
R/ab.R
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@ -43,7 +43,7 @@
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @export #' @export
#' @examples #' @examples
#' # These examples all return "ERY", the ID of Erythromycin: #' # these examples all return "ERY", the ID of erythromycin:
#' as.ab("J01FA01") #' as.ab("J01FA01")
#' as.ab("J 01 FA 01") #' as.ab("J 01 FA 01")
#' as.ab("Erythromycin") #' as.ab("Erythromycin")
@ -55,7 +55,13 @@
#' as.ab("Erythrocin") # trade name #' as.ab("Erythrocin") # trade name
#' as.ab("Romycin") # trade name #' as.ab("Romycin") # trade name
#' #'
#' # Use ab_* functions to get a specific properties (see ?ab_property); #' # spelling from different languages and dyslexia are no problem
#' ab_atc("ceftriaxon")
#' ab_atc("cephtriaxone")
#' ab_atc("cephthriaxone")
#' ab_atc("seephthriaaksone")
#'
#' # use ab_* functions to get a specific properties (see ?ab_property);
#' # they use as.ab() internally: #' # they use as.ab() internally:
#' ab_name("J01FA01") # "Erythromycin" #' ab_name("J01FA01") # "Erythromycin"
#' ab_name("eryt") # "Erythromycin" #' ab_name("eryt") # "Erythromycin"
@ -87,6 +93,10 @@ as.ab <- function(x, ...) {
# spaces around non-characters must be removed: amox + clav -> amox/clav # spaces around non-characters must be removed: amox + clav -> amox/clav
x_bak_clean <- gsub("(.*[a-zA-Z0-9]) ([^a-zA-Z0-9].*)", "\\1\\2", x_bak_clean) x_bak_clean <- gsub("(.*[a-zA-Z0-9]) ([^a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
x_bak_clean <- gsub("(.*[^a-zA-Z0-9]) ([a-zA-Z0-9].*)", "\\1\\2", x_bak_clean) x_bak_clean <- gsub("(.*[^a-zA-Z0-9]) ([a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
# remove hyphen after a starting "co"
x_bak_clean <- gsub("^co-", "co", x_bak_clean, ignore.case = TRUE)
# replace text 'and' with a slash
x_bak_clean <- gsub(" and ", "/", x_bak_clean, ignore.case = TRUE)
x <- unique(x_bak_clean) x <- unique(x_bak_clean)
x_new <- rep(NA_character_, length(x)) x_new <- rep(NA_character_, length(x))

6
R/ab_property.R
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@ -72,6 +72,12 @@
#' ab_name("floxapen") # "Flucloxacillin" #' ab_name("floxapen") # "Flucloxacillin"
#' ab_name(21319) # "Flucloxacillin" (using CID) #' ab_name(21319) # "Flucloxacillin" (using CID)
#' ab_name("J01CF05") # "Flucloxacillin" (using ATC) #' ab_name("J01CF05") # "Flucloxacillin" (using ATC)
#'
#' # spelling from different languages and dyslexia are no problem
#' ab_atc("ceftriaxon")
#' ab_atc("cephtriaxone")
#' ab_atc("cephthriaxone")
#' ab_atc("seephthriaaksone")
ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) { ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language) x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
if (tolower == TRUE) { if (tolower == TRUE) {

1
_pkgdown.yml
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@ -148,6 +148,7 @@ reference:
- "`catalogue_of_life`" - "`catalogue_of_life`"
- "`catalogue_of_life_version`" - "`catalogue_of_life_version`"
- "`WHOCC`" - "`WHOCC`"
- "`lifecycle`"
- title: Other functions - title: Other functions
desc: > desc: >
These functions are mostly for internal use, but some of These functions are mostly for internal use, but some of

17
data-raw/reproduction_of_antibiotics.R
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@ -327,8 +327,23 @@ antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(anti
# High level Gentamcin and Streptomycin # High level Gentamcin and Streptomycin
antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high")) antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high")) antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
# add imi to imipenem # add imi and "imipenem/cilastatine" to imipenem
antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp")) antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp"))
antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]], "imipenem/cilastatin")))
# add synonyms of ones not found
antibiotics[which(antibiotics$ab == "TZP"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TZP"), "synonyms"][[1]], "Tazocel", "tazocillin", "Tazocin", "Zosyn")))
antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Colisticin", "Polymyxin E", "Colimycin", "Coly-Mycin", "Totazina", "Colistimethate", "Promixin", "Colistimethate Sodium"))))
# remove incorrect synonyms from rifampicin (RIF) and add them to the combination rifampicin/isoniazid (RFI)
old_sym <- antibiotics[which(antibiotics$ab == "RIF"), "synonyms"][[1]]
old_sym <- old_sym[!old_sym %in% c("Rifinah", "Rimactazid")]
antibiotics[which(antibiotics$ab == "RIF"), "synonyms"][[1]] <- list(old_sym)
antibiotics[which(antibiotics$ab == "RFI"), "synonyms"][[1]] <- list(sort(c("Rifinah", "Rimactazid")))
# remove incorrect synonyms from sulfamethoxazole (SMX) and add them to the combination trimethoprim/sulfamethoxazole (SXT)
old_sym <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]]
old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym)
antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole"))))
## new ATC codes ## new ATC codes
# ceftaroline # ceftaroline

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docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <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">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

4
docs/authors.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>
@ -238,7 +238,7 @@
</p> </p>
<pre>@Article{, <pre>@Article{,
title = {AMR - An R Package for Working with Antimicrobial Resistance Data}, title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
author = {Matthijs S Berends and Christian F Luz and Alexander W Friedrich and Bhanu N M Sinha and Casper J Albers and Corinna Glasner}, author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
journal = {bioRxiv}, journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory}, publisher = {Cold Spring Harbor Laboratory},
year = {2019}, year = {2019},

2
docs/index.html
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@ -45,7 +45,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>
@ -231,13 +231,13 @@
</div> </div>
<div id="amr-0-9-0-9008" class="section level1"> <div id="amr-0-9-0-9009" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-9-0-9008" class="anchor"></a>AMR 0.9.0.9008<small> Unreleased </small> <a href="#amr-0-9-0-9009" class="anchor"></a>AMR 0.9.0.9009<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-05-jan-2020" class="section level2"> <div id="last-updated-08-jan-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-05-jan-2020" class="anchor"></a><small>Last updated: 05-Jan-2020</small> <a href="#last-updated-08-jan-2020" class="anchor"></a><small>Last updated: 08-Jan-2020</small>
</h2> </h2>
<div id="changes" class="section level3"> <div id="changes" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -248,6 +248,14 @@
<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li> <li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
<li>Added a lifecycle state to every function, following <a href="https://www.tidyverse.org/lifecycle">the lifecycle circle of the <code>tidyverse</code></a> <li>Added a lifecycle state to every function, following <a href="https://www.tidyverse.org/lifecycle">the lifecycle circle of the <code>tidyverse</code></a>
</li> </li>
<li>For in <code><a href="../reference/as.ab.html">as.ab()</a></code>: support for drugs starting with “co-” like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)</li>
<li>Changes to the <code>antibiotics</code> data set (thanks to Peter Dutey):
<ul>
<li>Added more synonyms to colistin, imipenem and piperacillin/tazobactam</li>
<li>Moved synonyms Rifinah and Rimactazid from rifampicin (<code>RIF</code>) to rifampicin/isoniazid (<code>RFI</code>). Please note that <a href="https://www.whocc.no/atc_ddd_index/?code=J04AM02&amp;showdescription=no">the combination rifampicin/isoniazid has no DDDs defined</a>, so e.g. <code><a href="../reference/ab_property.html">ab_ddd("Rimactazid")</a></code> will now return <code>NA</code>.</li>
<li>Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (<code>SMX</code>) to trimethoprim/sulfamethoxazole (<code>SXT</code>)</li>
</ul>
</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">
@ -1418,7 +1426,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-9-0-9008">0.9.0.9008</a></li> <li><a href="#amr-0-9-0-9009">0.9.0.9009</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li> <li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li> <li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>

2
docs/reference/AMR-deprecated.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

10
docs/reference/ab_property.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>
@ -356,7 +356,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'>ab_name</span>(<span class='st'>"fluklox"</span>) <span class='co'># "Flucloxacillin"</span> <span class='fu'>ab_name</span>(<span class='st'>"fluklox"</span>) <span class='co'># "Flucloxacillin"</span>
<span class='fu'>ab_name</span>(<span class='st'>"floxapen"</span>) <span class='co'># "Flucloxacillin"</span> <span class='fu'>ab_name</span>(<span class='st'>"floxapen"</span>) <span class='co'># "Flucloxacillin"</span>
<span class='fu'>ab_name</span>(<span class='fl'>21319</span>) <span class='co'># "Flucloxacillin" (using CID)</span> <span class='fu'>ab_name</span>(<span class='fl'>21319</span>) <span class='co'># "Flucloxacillin" (using CID)</span>
<span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (using ATC)</span></pre> <span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (using ATC)</span>
<span class='co'># spelling from different languages and dyslexia are no problem</span>
<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2> <h2>Contents</h2>

2
docs/reference/age.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

12
docs/reference/as.ab.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>
@ -293,7 +293,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs.</p></div> <div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># These examples all return "ERY", the ID of Erythromycin:</span> <pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>) <span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>) <span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>) <span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
@ -305,7 +305,13 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span> <span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
<span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span> <span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span>
<span class='co'># Use ab_* functions to get a specific properties (see ?ab_property);</span> <span class='co'># spelling from different languages and dyslexia are no problem</span>
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>)
<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
<span class='co'># they use as.ab() internally:</span> <span class='co'># they use as.ab() internally:</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span> <span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre> <span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>

2
docs/reference/as.disk.html
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@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/as.mic.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/as.mo.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/as.rsi.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/atc_online.html
View File

@ -86,7 +86,7 @@ This function requires an internet connection." />
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/availability.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/bug_drug_combinations.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/count.html
View File

@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/eucast_rules.html
View File

@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/extended-functions.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/filter_ab_class.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/g.test.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/ggplot_rsi.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/guess_ab_col.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

8
docs/reference/index.html
View File

@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>
@ -517,6 +517,12 @@
<p><code><a href="WHOCC.html">WHOCC</a></code> </p> <p><code><a href="WHOCC.html">WHOCC</a></code> </p>
</td> </td>
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td> <td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
</tr><tr>
<td>
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
</td>
<td><p>Lifecycles of functions in the <code>AMR</code> package</p></td>
</tr> </tr>
</tbody><tbody> </tbody><tbody>
<tr> <tr>

2
docs/reference/join.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/key_antibiotics.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/kurtosis.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/lifecycle.html
View File

@ -87,7 +87,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/like.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/mdro.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/mo_source.html
View File

@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/p_symbol.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/proportion.html
View File

@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/read.4D.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/resistance_predict.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/skewness.html
View File

@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
docs/reference/translate.html
View File

@ -85,7 +85,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span> </span>
</div> </div>

2
inst/CITATION
View File

@ -3,7 +3,7 @@ citHeader("To cite our AMR package in publications, please use (for now):")
citEntry( citEntry(
entry = "Article", entry = "Article",
title = "AMR - An R Package for Working with Antimicrobial Resistance Data", title = "AMR - An R Package for Working with Antimicrobial Resistance Data",
author = "Matthijs S Berends and Christian F Luz and Alexander W Friedrich and Bhanu N M Sinha and Casper J Albers and Corinna Glasner", author = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner",
journal = "bioRxiv", journal = "bioRxiv",
publisher = "Cold Spring Harbor Laboratory", publisher = "Cold Spring Harbor Laboratory",
year = 2019, year = 2019,

6
man/ab_property.Rd
View File

@ -116,6 +116,12 @@ ab_name("fluklox") # "Flucloxacillin"
ab_name("floxapen") # "Flucloxacillin" ab_name("floxapen") # "Flucloxacillin"
ab_name(21319) # "Flucloxacillin" (using CID) ab_name(21319) # "Flucloxacillin" (using CID)
ab_name("J01CF05") # "Flucloxacillin" (using ATC) ab_name("J01CF05") # "Flucloxacillin" (using ATC)
# spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon")
ab_atc("cephtriaxone")
ab_atc("cephthriaxone")
ab_atc("seephthriaaksone")
} }
\seealso{ \seealso{
\link{antibiotics} \link{antibiotics}

10
man/as.ab.Rd
View File

@ -59,7 +59,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
# These examples all return "ERY", the ID of Erythromycin: # these examples all return "ERY", the ID of erythromycin:
as.ab("J01FA01") as.ab("J01FA01")
as.ab("J 01 FA 01") as.ab("J 01 FA 01")
as.ab("Erythromycin") as.ab("Erythromycin")
@ -71,7 +71,13 @@ as.ab("eritromicine") # spelled wrong, yet works
as.ab("Erythrocin") # trade name as.ab("Erythrocin") # trade name
as.ab("Romycin") # trade name as.ab("Romycin") # trade name
# Use ab_* functions to get a specific properties (see ?ab_property); # spelling from different languages and dyslexia are no problem
ab_atc("ceftriaxon")
ab_atc("cephtriaxone")
ab_atc("cephthriaxone")
ab_atc("seephthriaaksone")
# use ab_* functions to get a specific properties (see ?ab_property);
# they use as.ab() internally: # they use as.ab() internally:
ab_name("J01FA01") # "Erythromycin" ab_name("J01FA01") # "Erythromycin"
ab_name("eryt") # "Erythromycin" ab_name("eryt") # "Erythromycin"