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Conduct AMR Analysis
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Get Taxonomy of a Microorganism
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Get Properties of an Antibiotic Drug
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Get Properties of an Antiviral Drug
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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Get Properties of an Antibiotic< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/ab_property.R" class = "external-link" > < code > R/ab_property.R< / code > < / a > < / small >
< div class = "d-none name" > < code > ab_property.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
< p > Use these functions to return a specific property of an antibiotic from the < a href = "antibiotics.html" > antibiotics< / a > data set. All input values will be evaluated internally with < code > < a href = "as.ab.html" > as.ab()< / a > < / code > .< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , tolower < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_cid< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_synonyms< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_tradenames< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_group< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , only_first < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_atc_group1< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_atc_group2< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_loinc< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_ddd< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , administration < span class = "op" > =< / span > < span class = "st" > "oral"< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_ddd_units< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , administration < span class = "op" > =< / span > < span class = "st" > "oral"< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_info< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_url< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , open < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > ab_property< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , property < span class = "op" > =< / span > < span class = "st" > "name"< / span > , language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < / span >
< span > < span class = "va" > data< / span > ,< / span >
< span > < span class = "va" > ...< / span > ,< / span >
< span > property < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "fu" > < a href = "translate.html" > get_AMR_locale< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > snake_case < span class = "op" > =< / span > < span class = "cn" > NULL< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
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< dd > < p > any (vector of) text that can be coerced to a valid antibiotic drug code with < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < / p > < / dd >
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< dt > language< / dt >
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< dd > < p > language of the returned text - the default is the current system language (see < code > < a href = "translate.html" > get_AMR_locale()< / a > < / code > ) and can also be set with the < a href = "AMR-options.html" > package option< / a > < code > < a href = "AMR-options.html" > AMR_locale< / a > < / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / dd >
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< dt > tolower< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether the first < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > of every output should be transformed to a lower case < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > . This will lead to e.g. "polymyxin B" and not "polymyxin b".< / p > < / dd >
< dt > ...< / dt >
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< dd > < p > in case of < code > set_ab_names()< / code > and < code > data< / code > is a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > : columns to select (supports tidy selection such as < code > column1:column4< / code > ), otherwise other arguments passed on to < code > < a href = "as.ab.html" > as.ab()< / a > < / code > < / p > < / dd >
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< dt > only_first< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)< / p > < / dd >
< dt > administration< / dt >
< dd > < p > way of administration, either < code > "oral"< / code > or < code > "iv"< / code > < / p > < / dd >
< dt > open< / dt >
< dd > < p > browse the URL using < code > < a href = "https://rdrr.io/r/utils/browseURL.html" class = "external-link" > utils::browseURL()< / a > < / code > < / p > < / dd >
< dt > property< / dt >
< dd > < p > one of the column names of one of the < a href = "antibiotics.html" > antibiotics< / a > data set: < code > vector_or(colnames(antibiotics), sort = FALSE)< / code > .< / p > < / dd >
< dt > data< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > of which the columns need to be renamed, or a < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > vector of column names< / p > < / dd >
< dt > snake_case< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether the names should be in so-called < a href = "https://en.wikipedia.org/wiki/Snake_case" class = "external-link" > snake case< / a > : in lower case and all spaces/slashes replaced with an underscore (< code > _< / code > )< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
< ul > < li > < p > An < a href = "https://rdrr.io/r/base/integer.html" class = "external-link" > integer< / a > in case of < code > ab_cid()< / code > < / p > < / li >
< li > < p > A named < a href = "https://rdrr.io/r/base/list.html" class = "external-link" > list< / a > in case of < code > ab_info()< / code > and multiple < code > ab_atc()< / code > /< code > ab_synonyms()< / code > /< code > ab_tradenames()< / code > < / p > < / li >
< li > < p > A < a href = "https://rdrr.io/r/base/double.html" class = "external-link" > double< / a > in case of < code > ab_ddd()< / code > < / p > < / li >
< li > < p > A < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > in case of < code > set_ab_names()< / code > < / p > < / li >
< li > < p > A < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > in all other cases< / p > < / li >
< / ul > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > All output < a href = "translate.html" > will be translated< / a > where possible.< / p >
< p > The function < code > ab_url()< / code > will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.< / p >
< p > The function < code > set_ab_names()< / code > is a special column renaming function for < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If < code > property = "atc"< / code > is set, preference is given to ATC codes from the J-group.< / p >
< / div >
< div class = "section level2" >
< h2 id = "source" > Source< a class = "anchor" aria-label = "anchor" href = "#source" > < / a > < / h2 >
2024-03-03 23:31:52 +01:00
< p > World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: < a href = "https://atcddd.fhi.no/atc_ddd_index/" class = "external-link" > https://atcddd.fhi.no/atc_ddd_index/< / a > < / p >
2022-08-21 16:59:35 +02:00
< p > European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: < a href = "https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class = "external-link" > https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm< / a > < / p >
< / div >
< div class = "section level2" >
< h2 id = "reference-data-publicly-available" > Reference Data Publicly Available< a class = "anchor" aria-label = "anchor" href = "#reference-data-publicly-available" > < / a > < / h2 >
2023-01-21 23:53:21 +01:00
< p > All data sets in this < code > AMR< / code > package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit < a href = "https://msberends.github.io/AMR/articles/datasets.html" > our website for the download links< / a > . The actual files are of course available on < a href = "https://github.com/msberends/AMR/tree/main/data-raw" class = "external-link" > our GitHub repository< / a > .< / p >
2022-08-21 16:59:35 +02:00
< / div >
< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
< div class = "dont-index" > < p > < a href = "antibiotics.html" > antibiotics< / a > < / p > < / div >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # all properties:< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Amoxicillin"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CA04"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_cid< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 33613< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_synonyms< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "actimoxi" "amoclen" "amolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [4] "amopen" "amopenixin" "amoxibiotic" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "amoxicaps" "amoxicilina" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "amoxiden" "amoxil" "amoxivet" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [16] "amoxy" "amoxycillin" "amoxyke" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "anemolin" "aspenil" "atoksilin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "biomox" "bristamox" "cemoxin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "clamoxyl" "damoxy" "delacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [28] "demoksil" "dispermox" "efpenix" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "flemoxin" "hiconcil" "histocillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [34] "hydroxyampicillin" "ibiamox" "imacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "lamoxy" "largopen" "metafarma capsules" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [40] "metifarma capsules" "moksilin" "moxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "moxatag" "ospamox" "pamoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [46] "piramox" "promoxil" "remoxil" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] "robamox" "sawamox pm" "tolodina" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [52] "topramoxin" "unicillin" "utimox" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [55] "vetramox" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_tradenames< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-30 14:40:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "actimoxi" "amoclen" "amolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [4] "amopen" "amopenixin" "amoxibiotic" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "amoxicaps" "amoxicilina" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "amoxiden" "amoxil" "amoxivet" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [16] "amoxy" "amoxycillin" "amoxyke" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "anemolin" "aspenil" "atoksilin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "biomox" "bristamox" "cemoxin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "clamoxyl" "damoxy" "delacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [28] "demoksil" "dispermox" "efpenix" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "flemoxin" "hiconcil" "histocillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [34] "hydroxyampicillin" "ibiamox" "imacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "lamoxy" "largopen" "metafarma capsules" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [40] "metifarma capsules" "moksilin" "moxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "moxatag" "ospamox" "pamoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [46] "piramox" "promoxil" "remoxil" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] "robamox" "sawamox pm" "tolodina" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [52] "topramoxin" "unicillin" "utimox" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [55] "vetramox" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_group< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactams/penicillins"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc_group1< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactam antibacterials, penicillins"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc_group2< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Penicillins with extended spectrum"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_url< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < / span > < / span >
2024-03-03 23:31:52 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Amoxicillin < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > "https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04& showdescription=no" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < / span > < / span >
2023-05-24 16:03:18 +02:00
< span class = "r-in" > < span > < span class = "co" > # smart lowercase transformation< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > x < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "PLB"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Amoxicillin/clavulanic acid" "Polymyxin B" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > x < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "PLB"< / span > < span class = "op" > )< / span > , tolower < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "amoxicillin/clavulanic acid" "polymyxin B" < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # defined daily doses (DDD)< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "oral"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 1.5< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd_units< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "oral"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "iv"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 3< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_ddd_units< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > , < span class = "st" > "iv"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
< span class = "r-in" > < span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < span class = "fu" > ab_info< / span > < span class = "op" > (< / span > < span class = "st" > "AMX"< / span > < span class = "op" > )< / span > < span class = "co" > # all properties as a list< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ab< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "AMX"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $cid< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 33613< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $name< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Amoxicillin"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $group< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactams/penicillins"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CA04"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactam antibacterials, penicillins"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Penicillins with extended spectrum"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $tradenames< / span >
2022-10-30 14:40:31 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "actimoxi" "amoclen" "amolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [4] "amopen" "amopenixin" "amoxibiotic" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "amoxicaps" "amoxicilina" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "amoxiden" "amoxil" "amoxivet" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [16] "amoxy" "amoxycillin" "amoxyke" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "anemolin" "aspenil" "atoksilin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "biomox" "bristamox" "cemoxin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "clamoxyl" "damoxy" "delacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [28] "demoksil" "dispermox" "efpenix" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "flemoxin" "hiconcil" "histocillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [34] "hydroxyampicillin" "ibiamox" "imacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "lamoxy" "largopen" "metafarma capsules" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [40] "metifarma capsules" "moksilin" "moxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "moxatag" "ospamox" "pamoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [46] "piramox" "promoxil" "remoxil" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [49] "robamox" "sawamox pm" "tolodina" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [52] "topramoxin" "unicillin" "utimox" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [55] "vetramox" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $loinc< / span >
2023-10-20 15:01:19 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "101498-4" "15-8" "16-6" "16365-9" "17-4" "18-2" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "18861-5" "18862-3" "19-0" "20-8" "21-6" "22-4" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "25274-2" "25310-4" "3344-9" "55614-2" "55615-9" "55616-7" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "6976-5" "6977-3" "80133-2" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 1.5< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] 3< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "g"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':< / span > < / span > < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "AMP"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CA01" "S01AA19"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_group< / span > < span class = "op" > (< / span > < span class = "st" > "J01CA01"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Beta-lactams/penicillins"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_loinc< / span > < span class = "op" > (< / span > < span class = "st" > "ampicillin"< / span > < span class = "op" > )< / span > < / span > < / span >
2023-10-20 15:01:19 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "101477-8" "101478-6" "18864-9" "18865-6" "20374-5" "21066-6" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "23618-2" "27-3" "28-1" "29-9" "30-7" "31-5" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "32-3" "33-1" "3355-5" "33562-0" "33919-2" "34-9" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "43883-8" "43884-6" "6979-9" "6980-7" "87604-5" < / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "st" > "21066-6"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Ampicillin"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "fl" > 6249< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Ampicillin"< / span >
2022-11-13 08:54:32 +01:00
< span class = "r-in" > < span > < span class = "fu" > ab_name< / span > < span class = "op" > (< / span > < span class = "st" > "J01CA01"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Ampicillin"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # spelling from different languages and dyslexia are no problem< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "ceftriaxon"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "cephtriaxone"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "cephthriaxone"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < span class = "fu" > ab_atc< / span > < span class = "op" > (< / span > < span class = "st" > "seephthriaaksone"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01DD04"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # use set_ab_names() for renaming columns< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" "age" "gender" "ward" "mo" "PEN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [8] "OXA" "FLC" "AMX" "AMC" "AMP" "TZP" "CZO" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [15] "FEP" "CXM" "FOX" "CTX" "CAZ" "CRO" "GEN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [22] "TOB" "AMK" "KAN" "TMP" "SXT" "NIT" "FOS" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "LNZ" "CIP" "MFX" "VAN" "TEC" "TCY" "TGC" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [36] "DOX" "ERY" "CLI" "AZM" "IPM" "MEM" "MTR" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "CHL" "COL" "MUP" "RIF" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [3] "age" "gender" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "ward" "mo" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [7] "benzylpenicillin" "oxacillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "flucloxacillin" "amoxicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [11] "amoxicillin_clavulanic_acid" "ampicillin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "piperacillin_tazobactam" "cefazolin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [15] "cefepime" "cefuroxime" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "cefoxitin" "cefotaxime" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [19] "ceftazidime" "ceftriaxone" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "gentamicin" "tobramycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [23] "amikacin" "kanamycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "trimethoprim" "trimethoprim_sulfamethoxazole"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [27] "nitrofurantoin" "fosfomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "linezolid" "ciprofloxacin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [31] "moxifloxacin" "vancomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [33] "teicoplanin" "tetracycline" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [35] "tigecycline" "doxycycline" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "erythromycin" "clindamycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [39] "azithromycin" "imipenem" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [41] "meropenem" "metronidazole" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [43] "chloramphenicol" "colistin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [45] "mupirocin" "rifampicin" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > , < span class = "va" > NIT< / span > < span class = "op" > :< / span > < span class = "va" > VAN< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" "age" "gender" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "ward" "mo" "PEN" "OXA" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "FLC" "AMX" "AMC" "AMP" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "TZP" "CZO" "FEP" "CXM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "FOX" "CTX" "CAZ" "CRO" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "GEN" "TOB" "AMK" "KAN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [33] "TEC" "TCY" "TGC" "DOX" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "ERY" "CLI" "AZM" "IPM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [41] "MEM" "MTR" "CHL" "COL" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [45] "MUP" "RIF" < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # this does the same:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/rename.html" class = "external-link" > rename_with< / a > < / span > < span class = "op" > (< / span > < span class = "va" > set_ab_names< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "co" > # set_ab_names() works with any AB property:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-08 17:01:47 +01:00
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > property < span class = "op" > =< / span > < span class = "st" > "atc"< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
2023-02-10 16:26:36 +01:00
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > set_ab_names< / span > < span class = "op" > (< / span > < span class = "va" > NIT< / span > < span class = "op" > :< / span > < span class = "va" > VAN< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/colnames.html" class = "external-link" > colnames< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
2022-08-21 16:59:35 +02:00
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
2022-08-28 22:45:38 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "date" "patient" "age" "gender" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "ward" "mo" "PEN" "OXA" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "FLC" "AMX" "AMC" "AMP" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "TZP" "CZO" "FEP" "CXM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "FOX" "CTX" "CAZ" "CRO" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "GEN" "TOB" "AMK" "KAN" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [33] "TEC" "TCY" "TGC" "DOX" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [37] "ERY" "CLI" "AZM" "IPM" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [41] "MEM" "MTR" "CHL" "COL" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [45] "MUP" "RIF" < / span >
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< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
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