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< h1 > Get ATC properties from WHOCC website< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/atc_online.R' > < code > R/atc_online.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > atc_online.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > atc_online_property< / span > (
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< span class = 'kw' > atc_code< / span > ,
< span class = 'kw' > property< / span > ,
administration = < span class = 'st' > "O"< / span > ,
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url = < span class = 'st' > "https://www.whocc.no/atc_ddd_index/?code=%s& showdescription=no"< / span > ,
url_vet = < span class = 'st' > "https://www.whocc.no/atcvet/atcvet_index/?code=%s& showdescription=no"< / span >
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)
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< span class = 'fu' > atc_online_groups< / span > (< span class = 'kw' > atc_code< / span > , < span class = 'kw' > ...< / span > )
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< span class = 'fu' > atc_online_ddd< / span > (< span class = 'kw' > atc_code< / span > , < span class = 'kw' > ...< / span > )< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > atc_code< / th >
< td > < p > a character or character vector with ATC code(s) of antibiotic(s)< / p > < / td >
< / tr >
< tr >
< th > property< / th >
< td > < p > property of an ATC code. Valid values are < code > "ATC"< / code > , < code > "Name"< / code > , < code > "DDD"< / code > , < code > "U"< / code > (< code > "unit"< / code > ), < code > "Adm.R"< / code > , < code > "Note"< / code > and < code > groups< / code > . For this last option, all hierarchical groups of an ATC code will be returned, see Examples.< / p > < / td >
< / tr >
< tr >
< th > administration< / th >
< td > < p > type of administration when using < code > property = "Adm.R"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > url< / th >
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< td > < p > url of website of the WHOCC. The sign < code > %s< / code > can be used as a placeholder for ATC codes.< / p > < / td >
< / tr >
< tr >
< th > url_vet< / th >
< td > < p > url of website of the WHOCC for veterinary medicine. The sign < code > %s< / code > can be used as a placeholder for ATC_vet codes (that all start with "Q").< / p > < / td >
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< / tr >
< tr >
< th > ...< / th >
< td > < p > parameters to pass on to < code > atc_property< / code > < / p > < / td >
< / tr >
< / table >
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< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< p > < a href = 'https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/' > https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/< / a > < / p >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > Options for parameter < code > administration< / code > :< / p > < ul >
< li > < p > < code > "Implant"< / code > = Implant< / p > < / li >
< li > < p > < code > "Inhal"< / code > = Inhalation< / p > < / li >
< li > < p > < code > "Instill"< / code > = Instillation< / p > < / li >
< li > < p > < code > "N"< / code > = nasal< / p > < / li >
< li > < p > < code > "O"< / code > = oral< / p > < / li >
< li > < p > < code > "P"< / code > = parenteral< / p > < / li >
< li > < p > < code > "R"< / code > = rectal< / p > < / li >
< li > < p > < code > "SL"< / code > = sublingual/buccal< / p > < / li >
< li > < p > < code > "TD"< / code > = transdermal< / p > < / li >
< li > < p > < code > "V"< / code > = vaginal< / p > < / li >
< / ul >
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< p > Abbreviations of return values when using < code > property = "U"< / code > (unit):< / p > < ul >
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< li > < p > < code > "g"< / code > = gram< / p > < / li >
< li > < p > < code > "mg"< / code > = milligram< / p > < / li >
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< li > < p > `"mcg"`` = microgram< / p > < / li >
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< li > < p > < code > "U"< / code > = unit< / p > < / li >
< li > < p > < code > "TU"< / code > = thousand units< / p > < / li >
< li > < p > < code > "MU"< / code > = million units< / p > < / li >
< li > < p > < code > "mmol"< / code > = millimole< / p > < / li >
< li > < p > < code > "ml"< / code > = milliliter (e.g. eyedrops)< / p > < / li >
< / ul >
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< p > < strong > N.B. This function requires an internet connection and only works if the following packages are installed: < code > curl< / code > , < code > rvest< / code > , < code > xml2< / code > .< / strong > < / p >
< h2 class = "hasAnchor" id = "stable-lifecycle" > < a class = "anchor" href = "#stable-lifecycle" > < / a > Stable lifecycle< / h2 >
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< p > < img src = 'figures/lifecycle_stable.svg' style = margin-bottom:5px / > < br / >
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > stable< / strong > . In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.< / p >
< p > If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.< / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
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< p > On our website < a href = 'https://msberends.github.io/AMR' > https://msberends.github.io/AMR< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.github.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / a > !< / p >
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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' > if< / span > (< span class = 'fl' > FALSE< / span > ) {
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< span class = 'co' > # oral DDD (Defined Daily Dose) of amoxicillin< / span >
< span class = 'fu' > atc_online_property< / span > (< span class = 'st' > "J01CA04"< / span > , < span class = 'st' > "DDD"< / span > , < span class = 'st' > "O"< / span > )
< span class = 'co' > # parenteral DDD (Defined Daily Dose) of amoxicillin< / span >
< span class = 'fu' > atc_online_property< / span > (< span class = 'st' > "J01CA04"< / span > , < span class = 'st' > "DDD"< / span > , < span class = 'st' > "P"< / span > )
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< span class = 'fu' > atc_online_property< / span > (< span class = 'st' > "J01CA04"< / span > , property = < span class = 'st' > "groups"< / span > ) < span class = 'co' > # search hierarchical groups of amoxicillin< / span >
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< span class = 'co' > # [1] "ANTIINFECTIVES FOR SYSTEMIC USE"< / span >
< span class = 'co' > # [2] "ANTIBACTERIALS FOR SYSTEMIC USE"< / span >
< span class = 'co' > # [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"< / span >
< span class = 'co' > # [4] "Penicillins with extended spectrum"< / span >
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}
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