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(v0.9.0.9009) antibiotics data set update
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.9.0.9008
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Date: 2020-01-05
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Version: 0.9.0.9009
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Date: 2020-01-08
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -63,5 +63,5 @@ BugReports: https://gitlab.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.0.1
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RoxygenNote: 7.0.2
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Roxygen: list(markdown = TRUE)
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9
NEWS.md
9
NEWS.md
@ -1,10 +1,15 @@
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# AMR 0.9.0.9008
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## <small>Last updated: 05-Jan-2020</small>
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# AMR 0.9.0.9009
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## <small>Last updated: 08-Jan-2020</small>
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### Changes
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* 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*
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* Input values for `as.disk()` limited to a maximum of 50 millimeters
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* Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle)
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* For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
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* Changes to the `antibiotics` data set (thanks to Peter Dutey):
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* Added more synonyms to colistin, imipenem and piperacillin/tazobactam
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* 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`.
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* Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (`SMX`) to trimethoprim/sulfamethoxazole (`SXT`)
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### Other
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* Add a `CITATION` file
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14
R/ab.R
14
R/ab.R
@ -43,7 +43,7 @@
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#' @inheritSection AMR Read more on our website!
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#' @export
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#' @examples
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#' # These examples all return "ERY", the ID of Erythromycin:
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#' # these examples all return "ERY", the ID of erythromycin:
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#' as.ab("J01FA01")
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#' as.ab("J 01 FA 01")
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#' as.ab("Erythromycin")
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@ -54,8 +54,14 @@
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#' as.ab("eritromicine") # spelled wrong, yet works
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#' as.ab("Erythrocin") # trade name
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#' as.ab("Romycin") # trade name
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#'
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#' # spelling from different languages and dyslexia are no problem
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#' ab_atc("ceftriaxon")
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#' ab_atc("cephtriaxone")
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#' ab_atc("cephthriaxone")
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#' ab_atc("seephthriaaksone")
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#'
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#' # Use ab_* functions to get a specific properties (see ?ab_property);
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#' # use ab_* functions to get a specific properties (see ?ab_property);
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#' # they use as.ab() internally:
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#' ab_name("J01FA01") # "Erythromycin"
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#' ab_name("eryt") # "Erythromycin"
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@ -87,6 +93,10 @@ as.ab <- function(x, ...) {
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# spaces around non-characters must be removed: amox + clav -> amox/clav
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x_bak_clean <- gsub("(.*[a-zA-Z0-9]) ([^a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
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x_bak_clean <- gsub("(.*[^a-zA-Z0-9]) ([a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
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# remove hyphen after a starting "co"
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x_bak_clean <- gsub("^co-", "co", x_bak_clean, ignore.case = TRUE)
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# replace text 'and' with a slash
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x_bak_clean <- gsub(" and ", "/", x_bak_clean, ignore.case = TRUE)
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x <- unique(x_bak_clean)
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x_new <- rep(NA_character_, length(x))
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@ -72,6 +72,12 @@
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#' ab_name("floxapen") # "Flucloxacillin"
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#' ab_name(21319) # "Flucloxacillin" (using CID)
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#' ab_name("J01CF05") # "Flucloxacillin" (using ATC)
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#'
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#' # spelling from different languages and dyslexia are no problem
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#' ab_atc("ceftriaxon")
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#' ab_atc("cephtriaxone")
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#' ab_atc("cephthriaxone")
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#' ab_atc("seephthriaaksone")
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ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
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x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
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if (tolower == TRUE) {
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@ -148,6 +148,7 @@ reference:
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- "`catalogue_of_life`"
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- "`catalogue_of_life_version`"
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- "`WHOCC`"
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- "`lifecycle`"
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- title: Other functions
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desc: >
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These functions are mostly for internal use, but some of
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@ -327,8 +327,23 @@ antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(anti
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# High level Gentamcin and Streptomycin
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antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
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antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
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# add imi to imipenem
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# add imi and "imipenem/cilastatine" to imipenem
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antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp"))
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antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]], "imipenem/cilastatin")))
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# add synonyms of ones not found
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antibiotics[which(antibiotics$ab == "TZP"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TZP"), "synonyms"][[1]], "Tazocel", "tazocillin", "Tazocin", "Zosyn")))
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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"))))
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# remove incorrect synonyms from rifampicin (RIF) and add them to the combination rifampicin/isoniazid (RFI)
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old_sym <- antibiotics[which(antibiotics$ab == "RIF"), "synonyms"][[1]]
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old_sym <- old_sym[!old_sym %in% c("Rifinah", "Rimactazid")]
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antibiotics[which(antibiotics$ab == "RIF"), "synonyms"][[1]] <- list(old_sym)
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antibiotics[which(antibiotics$ab == "RFI"), "synonyms"][[1]] <- list(sort(c("Rifinah", "Rimactazid")))
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# remove incorrect synonyms from sulfamethoxazole (SMX) and add them to the combination trimethoprim/sulfamethoxazole (SXT)
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old_sym <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]]
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old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")]
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antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym)
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antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole"))))
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## new ATC codes
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# ceftaroline
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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||||
<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>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<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>
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</span>
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</div>
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@ -238,7 +238,7 @@
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</p>
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<pre>@Article{,
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title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
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author = {Matthijs S Berends and Christian F Luz and Alexander W Friedrich and Bhanu N M Sinha and Casper J Albers and Corinna Glasner},
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author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
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journal = {bioRxiv},
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publisher = {Cold Spring Harbor Laboratory},
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year = {2019},
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@ -45,7 +45,7 @@
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</button>
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<span class="navbar-brand">
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||||
<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>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<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>
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</span>
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||||
</div>
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@ -231,13 +231,13 @@
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</div>
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<div id="amr-0-9-0-9008" class="section level1">
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<div id="amr-0-9-0-9009" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-9-0-9008" class="anchor"></a>AMR 0.9.0.9008<small> Unreleased </small>
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<a href="#amr-0-9-0-9009" class="anchor"></a>AMR 0.9.0.9009<small> Unreleased </small>
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</h1>
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<div id="last-updated-05-jan-2020" class="section level2">
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<div id="last-updated-08-jan-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-05-jan-2020" class="anchor"></a><small>Last updated: 05-Jan-2020</small>
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<a href="#last-updated-08-jan-2020" class="anchor"></a><small>Last updated: 08-Jan-2020</small>
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</h2>
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<div id="changes" class="section level3">
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<h3 class="hasAnchor">
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@ -248,6 +248,14 @@
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<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
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<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>
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</li>
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<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>
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<li>Changes to the <code>antibiotics</code> data set (thanks to Peter Dutey):
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<ul>
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<li>Added more synonyms to colistin, imipenem and piperacillin/tazobactam</li>
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<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&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>
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<li>Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (<code>SMX</code>) to trimethoprim/sulfamethoxazole (<code>SXT</code>)</li>
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</ul>
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</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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@ -1418,7 +1426,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-9-0-9008">0.9.0.9008</a></li>
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<li><a href="#amr-0-9-0-9009">0.9.0.9009</a></li>
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<li><a href="#amr-0-9-0">0.9.0</a></li>
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<li><a href="#amr-0-8-0">0.8.0</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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@ -85,7 +85,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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@ -85,7 +85,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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@ -356,7 +356,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<span class='fu'>ab_name</span>(<span class='st'>"fluklox"</span>) <span class='co'># "Flucloxacillin"</span>
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<span class='fu'>ab_name</span>(<span class='st'>"floxapen"</span>) <span class='co'># "Flucloxacillin"</span>
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<span class='fu'>ab_name</span>(<span class='fl'>21319</span>) <span class='co'># "Flucloxacillin" (using CID)</span>
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<span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (using ATC)</span></pre>
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<span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (using ATC)</span>
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<span class='co'># spelling from different languages and dyslexia are no problem</span>
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<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
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<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
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<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
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<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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@ -85,7 +85,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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@ -85,7 +85,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
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</span>
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</div>
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@ -293,7 +293,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs.</p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># These examples all return "ERY", the ID of Erythromycin:</span>
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<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
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<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
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@ -305,7 +305,13 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
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<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='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>
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -86,7 +86,7 @@ This function requires an internet connection." />
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -86,7 +86,7 @@ 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">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>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -84,7 +84,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -517,6 +517,12 @@
|
||||
<p><code><a href="WHOCC.html">WHOCC</a></code> </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>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -87,7 +87,7 @@ 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">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>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -85,7 +85,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -3,7 +3,7 @@ citHeader("To cite our AMR package in publications, please use (for now):")
|
||||
citEntry(
|
||||
entry = "Article",
|
||||
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",
|
||||
publisher = "Cold Spring Harbor Laboratory",
|
||||
year = 2019,
|
||||
|
@ -116,6 +116,12 @@ ab_name("fluklox") # "Flucloxacillin"
|
||||
ab_name("floxapen") # "Flucloxacillin"
|
||||
ab_name(21319) # "Flucloxacillin" (using CID)
|
||||
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{
|
||||
\link{antibiotics}
|
||||
|
10
man/as.ab.Rd
10
man/as.ab.Rd
@ -59,7 +59,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
|
||||
}
|
||||
|
||||
\examples{
|
||||
# These examples all return "ERY", the ID of Erythromycin:
|
||||
# these examples all return "ERY", the ID of erythromycin:
|
||||
as.ab("J01FA01")
|
||||
as.ab("J 01 FA 01")
|
||||
as.ab("Erythromycin")
|
||||
@ -71,7 +71,13 @@ as.ab("eritromicine") # spelled wrong, yet works
|
||||
as.ab("Erythrocin") # 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:
|
||||
ab_name("J01FA01") # "Erythromycin"
|
||||
ab_name("eryt") # "Erythromycin"
|
||||
|
Loading…
Reference in New Issue
Block a user