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reference/as.av.md

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+# Transform Input to an Antiviral Drug ID
+
+Use this function to determine the antiviral drug code of one or more
+antiviral drugs. The data set
+[antivirals](https://amr-for-r.org/reference/antimicrobials.md) will be
+searched for abbreviations, official names and synonyms (brand names).
+
+## Usage
+
+``` r
+as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)
+
+is.av(x)
+```
+
+## Arguments
+
+- x:
+
+  A [character](https://rdrr.io/r/base/character.html) vector to
+  determine to antiviral drug ID.
+
+- flag_multiple_results:
+
+  A [logical](https://rdrr.io/r/base/logical.html) to indicate whether a
+  note should be printed to the console that probably more than one
+  antiviral drug code or name can be retrieved from a single input
+  value.
+
+- info:
+
+  A [logical](https://rdrr.io/r/base/logical.html) to indicate whether a
+  progress bar should be printed - the default is `TRUE` only in
+  interactive mode.
+
+- ...:
+
+  Arguments passed on to internal functions.
+
+## Value
+
+A [character](https://rdrr.io/r/base/character.html)
+[vector](https://rdrr.io/r/base/vector.html) with additional class
+[`ab`](https://amr-for-r.org/reference/as.ab.md)
+
+## Details
+
+All entries in the
+[antivirals](https://amr-for-r.org/reference/antimicrobials.md) data set
+have three different identifiers: a human readable EARS-Net code (column
+`ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO),
+and a CID code (column `cid`, Compound ID, used by PubChem). The data
+set contains more than 5,000 official brand names from many different
+countries, as found in PubChem. Not that some drugs contain multiple ATC
+codes.
+
+All these properties will be searched for the user input. The `as.av()`
+can correct for different forms of misspelling:
+
+- Wrong spelling of drug names (such as "acyclovir"), which corrects for
+  most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
+
+- Too few or too many vowels or consonants
+
+- Switching two characters (such as "aycclovir", often the case in
+  clinical data, when doctors typed too fast)
+
+- Digitalised paper records, leaving artefacts like 0/o/O (zero and
+  O's), B/8, n/r, etc.
+
+Use the [`av_*`](https://amr-for-r.org/reference/av_property.md)
+functions to get properties based on the returned antiviral drug ID, see
+*Examples*.
+
+Note: the `as.av()` and
+[`av_*`](https://amr-for-r.org/reference/av_property.md) functions may
+use very long regular expression to match brand names of antimicrobial
+drugs. This may fail on some systems.
+
+## Source
+
+World Health Organization (WHO) Collaborating Centre for Drug Statistics
+Methodology: <https://atcddd.fhi.no/atc_ddd_index/>
+
+European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER:
+<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
+
+## WHOCC
+
+This package contains **all ~550 antibiotic, antimycotic and antiviral
+drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC
+groups and Defined Daily Dose (DDD) from the World Health Organization
+Collaborating Centre for Drug Statistics Methodology (WHOCC,
+<https://atcddd.fhi.no>) and the Pharmaceuticals Community Register of
+the European Commission
+(<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
+
+These have become the gold standard for international drug utilisation
+monitoring and research.
+
+The WHOCC is located in Oslo at the Norwegian Institute of Public Health
+and funded by the Norwegian government. The European Commission is the
+executive of the European Union and promotes its general interest.
+
+**NOTE: The WHOCC copyright does not allow use for commercial purposes,
+unlike any other info from this package.** See
+<https://atcddd.fhi.no/copyright_disclaimer/.>
+
+## Download Our Reference Data
+
+All reference data sets in the AMR package - including information on
+microorganisms, antimicrobials, and clinical breakpoints - are freely
+available for download in multiple formats: R, MS Excel, Apache Feather,
+Apache Parquet, SPSS, and Stata.
+
+For maximum compatibility, we also provide machine-readable,
+tab-separated plain text files suitable for use in any software,
+including laboratory information systems.
+
+Visit [our website for direct download
+links](https://amr-for-r.org/articles/datasets.html), or explore the
+actual files in [our GitHub
+repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
+
+## See also
+
+- [antivirals](https://amr-for-r.org/reference/antimicrobials.md) for
+  the [data.frame](https://rdrr.io/r/base/data.frame.html) that is being
+  used to determine ATCs
+
+- [`av_from_text()`](https://amr-for-r.org/reference/av_from_text.md)
+  for a function to retrieve antimicrobial drugs from clinical text
+  (from health care records)
+
+## Examples
+
+``` r
+# these examples all return "ACI", the ID of aciclovir:
+as.av("J05AB01")
+#> Class 'av'
+#> [1] ACI
+as.av("J 05 AB 01")
+#> Class 'av'
+#> [1] ACI
+as.av("Aciclovir")
+#> Class 'av'
+#> [1] ACI
+as.av("aciclo")
+#> Class 'av'
+#> [1] ACI
+as.av("   aciclo 123")
+#> Class 'av'
+#> [1] ACI
+as.av("ACICL")
+#> Class 'av'
+#> [1] ACI
+as.av("ACI")
+#> Class 'av'
+#> [1] ACI
+as.av("Virorax") # trade name
+#> Class 'av'
+#> [1] ACI
+as.av("Zovirax") # trade name
+#> Class 'av'
+#> [1] ACI
+
+as.av("acyklofir") # severe spelling error, yet works
+#> Class 'av'
+#> [1] ACI
+
+# use av_* functions to get a specific properties (see ?av_property);
+# they use as.av() internally:
+av_name("J05AB01")
+#> [1] "Aciclovir"
+av_name("acicl")
+#> [1] "Aciclovir"
+```