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# Package index
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## Introduction to the package
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Please find the introduction to (and some general information about) our
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package here.
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- [`AMR-package`](https://amr-for-r.org/reference/AMR.md)
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[`AMR`](https://amr-for-r.org/reference/AMR.md) :
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The `AMR` Package
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## Preparing data: microorganisms
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These functions are meant to get taxonomically valid properties of
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microorganisms from any input, but also properties derived from
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taxonomy, such as the Gram stain
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([`mo_gramstain()`](https://amr-for-r.org/reference/mo_property.md)) ,
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or [`mo_is_yeast()`](https://amr-for-r.org/reference/mo_property.md).
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Use [`mo_source()`](https://amr-for-r.org/reference/mo_source.md) to
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teach this package how to translate your own codes to valid
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microorganisms, and use
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[`add_custom_microorganisms()`](https://amr-for-r.org/reference/add_custom_microorganisms.md)
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to add your own custom microorganisms to this package.
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- [`as.mo()`](https://amr-for-r.org/reference/as.mo.md)
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[`is.mo()`](https://amr-for-r.org/reference/as.mo.md)
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[`mo_uncertainties()`](https://amr-for-r.org/reference/as.mo.md)
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[`mo_renamed()`](https://amr-for-r.org/reference/as.mo.md)
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[`mo_failures()`](https://amr-for-r.org/reference/as.mo.md)
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[`mo_reset_session()`](https://amr-for-r.org/reference/as.mo.md)
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[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md) :
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Transform Arbitrary Input to Valid Microbial Taxonomy
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- [`mo_name()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_fullname()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_shortname()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_subspecies()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_species()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_genus()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_family()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_order()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_class()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_phylum()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_domain()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_type()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_status()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_pathogenicity()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_gramstain()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_is_gram_negative()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_is_gram_positive()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_is_yeast()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_is_intrinsic_resistant()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_oxygen_tolerance()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_is_anaerobic()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_snomed()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_ref()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_authors()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_year()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_lpsn()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_mycobank()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_gbif()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_rank()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_taxonomy()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_synonyms()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_current()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_group_members()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_info()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_url()`](https://amr-for-r.org/reference/mo_property.md)
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[`mo_property()`](https://amr-for-r.org/reference/mo_property.md) :
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Get Properties of a Microorganism
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- [`add_custom_microorganisms()`](https://amr-for-r.org/reference/add_custom_microorganisms.md)
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[`clear_custom_microorganisms()`](https://amr-for-r.org/reference/add_custom_microorganisms.md)
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: Add Custom Microorganisms
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- [`set_mo_source()`](https://amr-for-r.org/reference/mo_source.md)
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[`get_mo_source()`](https://amr-for-r.org/reference/mo_source.md) :
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User-Defined Reference Data Set for Microorganisms
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## Preparing data: antimicrobials
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Use these functions to get valid properties of antimicrobials from any
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input or to clean your input. You can even retrieve drug names and doses
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from clinical text records, using
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[`ab_from_text()`](https://amr-for-r.org/reference/ab_from_text.md).
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- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
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[`is.ab()`](https://amr-for-r.org/reference/as.ab.md)
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[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md) :
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Transform Input to an Antibiotic ID
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- [`ab_name()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_cid()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_synonyms()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_tradenames()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_group()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_atc()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_atc_group1()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_atc_group2()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_loinc()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_ddd()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_ddd_units()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_info()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_url()`](https://amr-for-r.org/reference/ab_property.md)
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[`ab_property()`](https://amr-for-r.org/reference/ab_property.md)
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[`set_ab_names()`](https://amr-for-r.org/reference/ab_property.md) :
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Get Properties of an Antibiotic
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- [`ab_from_text()`](https://amr-for-r.org/reference/ab_from_text.md) :
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Retrieve Antimicrobial Drug Names and Doses from Clinical Text
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- [`atc_online_property()`](https://amr-for-r.org/reference/atc_online.md)
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[`atc_online_groups()`](https://amr-for-r.org/reference/atc_online.md)
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[`atc_online_ddd()`](https://amr-for-r.org/reference/atc_online.md)
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[`atc_online_ddd_units()`](https://amr-for-r.org/reference/atc_online.md)
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: Get ATC Properties from WHOCC Website
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- [`add_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md)
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[`clear_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md)
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: Add Custom Antimicrobials
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## Preparing data: antimicrobial results
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With [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
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[`as.disk()`](https://amr-for-r.org/reference/as.disk.md) you can
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transform your raw input to valid MIC or disk diffusion values. Use
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[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for cleaning raw
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data to let it only contain “R”, “I” and “S”, or to interpret MIC or
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disk diffusion values as SIR based on the lastest EUCAST and CLSI
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guidelines. Afterwards, you can extend antibiotic interpretations by
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applying [EUCAST
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rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
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with
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[`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md).
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- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
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[`NA_sir_`](https://amr-for-r.org/reference/as.sir.md)
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[`is.sir()`](https://amr-for-r.org/reference/as.sir.md)
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[`is_sir_eligible()`](https://amr-for-r.org/reference/as.sir.md)
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[`sir_interpretation_history()`](https://amr-for-r.org/reference/as.sir.md)
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: Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
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- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md)
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[`is.mic()`](https://amr-for-r.org/reference/as.mic.md)
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[`NA_mic_`](https://amr-for-r.org/reference/as.mic.md)
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[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md)
|
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[`mic_p50()`](https://amr-for-r.org/reference/as.mic.md)
|
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[`mic_p90()`](https://amr-for-r.org/reference/as.mic.md)
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[`droplevels(`*`<mic>`*`)`](https://amr-for-r.org/reference/as.mic.md)
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: Transform Input to Minimum Inhibitory Concentrations (MIC)
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- [`as.disk()`](https://amr-for-r.org/reference/as.disk.md)
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[`NA_disk_`](https://amr-for-r.org/reference/as.disk.md)
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[`is.disk()`](https://amr-for-r.org/reference/as.disk.md) : Transform
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Input to Disk Diffusion Diameters
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- [`eucast_rules()`](https://amr-for-r.org/reference/eucast_rules.md)
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[`eucast_dosage()`](https://amr-for-r.org/reference/eucast_rules.md) :
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Apply EUCAST Rules
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- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md)
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: Define Custom EUCAST Rules
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## Analysing data
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Use these function for the analysis part. You can use
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[`susceptibility()`](https://amr-for-r.org/reference/proportion.md) or
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[`resistance()`](https://amr-for-r.org/reference/proportion.md) on any
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antibiotic column. With
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[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md), you
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can generate a traditional, combined, syndromic, or weighted-incidence
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syndromic combination antibiogram (WISCA). This function also comes with
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support for R Markdown and Quarto. Be sure to first select the isolates
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that are appropiate for analysis, by using
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[`first_isolate()`](https://amr-for-r.org/reference/first_isolate.md) or
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[`is_new_episode()`](https://amr-for-r.org/reference/get_episode.md).
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You can also filter your data on certain resistance in certain
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antibiotic classes
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([`carbapenems()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
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[`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)),
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or determine multi-drug resistant microorganisms (MDRO,
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[`mdro()`](https://amr-for-r.org/reference/mdro.md)).
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- [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
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[`wisca()`](https://amr-for-r.org/reference/antibiogram.md)
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[`retrieve_wisca_parameters()`](https://amr-for-r.org/reference/antibiogram.md)
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[`plot(`*`<antibiogram>`*`)`](https://amr-for-r.org/reference/antibiogram.md)
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[`autoplot(`*`<antibiogram>`*`)`](https://amr-for-r.org/reference/antibiogram.md)
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[`knit_print(`*`<antibiogram>`*`)`](https://amr-for-r.org/reference/antibiogram.md)
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: Generate Traditional, Combination, Syndromic, or WISCA Antibiograms
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- [`resistance()`](https://amr-for-r.org/reference/proportion.md)
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[`susceptibility()`](https://amr-for-r.org/reference/proportion.md)
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[`sir_confidence_interval()`](https://amr-for-r.org/reference/proportion.md)
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[`proportion_R()`](https://amr-for-r.org/reference/proportion.md)
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[`proportion_IR()`](https://amr-for-r.org/reference/proportion.md)
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[`proportion_I()`](https://amr-for-r.org/reference/proportion.md)
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[`proportion_SI()`](https://amr-for-r.org/reference/proportion.md)
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[`proportion_S()`](https://amr-for-r.org/reference/proportion.md)
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[`proportion_df()`](https://amr-for-r.org/reference/proportion.md)
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[`sir_df()`](https://amr-for-r.org/reference/proportion.md) :
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Calculate Antimicrobial Resistance
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- [`count_resistant()`](https://amr-for-r.org/reference/count.md)
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[`count_susceptible()`](https://amr-for-r.org/reference/count.md)
|
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[`count_S()`](https://amr-for-r.org/reference/count.md)
|
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[`count_SI()`](https://amr-for-r.org/reference/count.md)
|
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[`count_I()`](https://amr-for-r.org/reference/count.md)
|
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[`count_IR()`](https://amr-for-r.org/reference/count.md)
|
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[`count_R()`](https://amr-for-r.org/reference/count.md)
|
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[`count_all()`](https://amr-for-r.org/reference/count.md)
|
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[`n_sir()`](https://amr-for-r.org/reference/count.md)
|
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[`count_df()`](https://amr-for-r.org/reference/count.md) : Count
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Available Isolates
|
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|
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- [`get_episode()`](https://amr-for-r.org/reference/get_episode.md)
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[`is_new_episode()`](https://amr-for-r.org/reference/get_episode.md) :
|
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Determine Clinical or Epidemic Episodes
|
||||
|
||||
- [`first_isolate()`](https://amr-for-r.org/reference/first_isolate.md)
|
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[`filter_first_isolate()`](https://amr-for-r.org/reference/first_isolate.md)
|
||||
: Determine First Isolates
|
||||
|
||||
- [`key_antimicrobials()`](https://amr-for-r.org/reference/key_antimicrobials.md)
|
||||
[`all_antimicrobials()`](https://amr-for-r.org/reference/key_antimicrobials.md)
|
||||
[`antimicrobials_equal()`](https://amr-for-r.org/reference/key_antimicrobials.md)
|
||||
: (Key) Antimicrobials for First Weighted Isolates
|
||||
|
||||
- [`mdro()`](https://amr-for-r.org/reference/mdro.md)
|
||||
[`brmo()`](https://amr-for-r.org/reference/mdro.md)
|
||||
[`mrgn()`](https://amr-for-r.org/reference/mdro.md)
|
||||
[`mdr_tb()`](https://amr-for-r.org/reference/mdro.md)
|
||||
[`mdr_cmi2012()`](https://amr-for-r.org/reference/mdro.md)
|
||||
[`eucast_exceptional_phenotypes()`](https://amr-for-r.org/reference/mdro.md)
|
||||
: Determine Multidrug-Resistant Organisms (MDRO)
|
||||
|
||||
- [`custom_mdro_guideline()`](https://amr-for-r.org/reference/custom_mdro_guideline.md)
|
||||
[`c(`*`<custom_mdro_guideline>`*`)`](https://amr-for-r.org/reference/custom_mdro_guideline.md)
|
||||
: Define Custom MDRO Guideline
|
||||
|
||||
- [`bug_drug_combinations()`](https://amr-for-r.org/reference/bug_drug_combinations.md)
|
||||
[`format(`*`<bug_drug_combinations>`*`)`](https://amr-for-r.org/reference/bug_drug_combinations.md)
|
||||
: Determine Bug-Drug Combinations
|
||||
|
||||
- [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`aminopenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`antifungals()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`antimycobacterials()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`betalactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`betalactams_with_inhibitor()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`carbapenems()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`cephalosporins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`cephalosporins_1st()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`cephalosporins_2nd()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`cephalosporins_3rd()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`cephalosporins_4th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`macrolides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`monobactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`nitrofurans()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`oxazolidinones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`penicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`phenicols()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`polymyxins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`quinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`rifamycins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`streptogramins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`sulfonamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`tetracyclines()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`trimethoprims()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`ureidopenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`amr_class()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`amr_selector()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`administrable_per_os()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`administrable_iv()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
[`not_intrinsic_resistant()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
: Antimicrobial Selectors
|
||||
|
||||
- [`top_n_microorganisms()`](https://amr-for-r.org/reference/top_n_microorganisms.md)
|
||||
:
|
||||
|
||||
Filter Top *n* Microorganisms
|
||||
|
||||
- [`mean_amr_distance()`](https://amr-for-r.org/reference/mean_amr_distance.md)
|
||||
[`amr_distance_from_row()`](https://amr-for-r.org/reference/mean_amr_distance.md)
|
||||
: Calculate the Mean AMR Distance
|
||||
|
||||
- [`resistance_predict()`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
[`sir_predict()`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
[`plot(`*`<resistance_predict>`*`)`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
[`ggplot_sir_predict()`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
[`autoplot(`*`<resistance_predict>`*`)`](https://amr-for-r.org/reference/resistance_predict.md)
|
||||
: Predict Antimicrobial Resistance
|
||||
|
||||
- [`guess_ab_col()`](https://amr-for-r.org/reference/guess_ab_col.md) :
|
||||
Guess Antibiotic Column
|
||||
|
||||
## Plotting data
|
||||
|
||||
Use these functions for the plotting part. The `scale_*_mic()` functions
|
||||
extend the ggplot2 package to allow plotting of MIC values, even within
|
||||
a manually set range. If using
|
||||
[`plot()`](https://amr-for-r.org/reference/plot.md) (base R) or
|
||||
[`autoplot()`](https://ggplot2.tidyverse.org/reference/autoplot.html)
|
||||
(ggplot2) on MIC values or disk diffusion values, the user can set the
|
||||
interpretation guideline to give the bars the right SIR colours. The
|
||||
[`ggplot_sir()`](https://amr-for-r.org/reference/ggplot_sir.md) function
|
||||
is a short wrapper for users not much accustomed to ggplot2 yet. The
|
||||
[`ggplot_pca()`](https://amr-for-r.org/reference/ggplot_pca.md) function
|
||||
is a specific function to plot so-called biplots for PCA (principal
|
||||
component analysis).
|
||||
|
||||
- [`scale_x_mic()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_y_mic()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_colour_mic()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_fill_mic()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_x_sir()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_colour_sir()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_fill_sir()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`plot(`*`<mic>`*`)`](https://amr-for-r.org/reference/plot.md)
|
||||
[`autoplot(`*`<mic>`*`)`](https://amr-for-r.org/reference/plot.md)
|
||||
[`plot(`*`<disk>`*`)`](https://amr-for-r.org/reference/plot.md)
|
||||
[`autoplot(`*`<disk>`*`)`](https://amr-for-r.org/reference/plot.md)
|
||||
[`plot(`*`<sir>`*`)`](https://amr-for-r.org/reference/plot.md)
|
||||
[`autoplot(`*`<sir>`*`)`](https://amr-for-r.org/reference/plot.md)
|
||||
[`facet_sir()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_y_percent()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`scale_sir_colours()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`theme_sir()`](https://amr-for-r.org/reference/plot.md)
|
||||
[`labels_sir_count()`](https://amr-for-r.org/reference/plot.md) :
|
||||
Plotting Helpers for AMR Data Analysis
|
||||
|
||||
- [`ggplot_sir()`](https://amr-for-r.org/reference/ggplot_sir.md)
|
||||
[`geom_sir()`](https://amr-for-r.org/reference/ggplot_sir.md) :
|
||||
|
||||
AMR Plots with `ggplot2`
|
||||
|
||||
- [`ggplot_pca()`](https://amr-for-r.org/reference/ggplot_pca.md) :
|
||||
|
||||
PCA Biplot with `ggplot2`
|
||||
|
||||
## AMR-specific options
|
||||
|
||||
The AMR package is customisable, by providing settings that can be set
|
||||
per user or per team. For example, the default interpretation guideline
|
||||
can be changed from EUCAST to CLSI, or a supported language can be set
|
||||
for the whole team (system-language independent) for antibiotic names in
|
||||
a foreign language.
|
||||
|
||||
- [`AMR-options`](https://amr-for-r.org/reference/AMR-options.md) :
|
||||
Options for the AMR package
|
||||
|
||||
## Other: antiviral drugs
|
||||
|
||||
This package also provides extensive support for antiviral agents, even
|
||||
though it is not the primary scope of this package. Working with data
|
||||
containing information about antiviral drugs was never easier. Use these
|
||||
functions to get valid properties of antiviral drugs from any input or
|
||||
to clean your input. You can even retrieve drug names and doses from
|
||||
clinical text records, using
|
||||
[`av_from_text()`](https://amr-for-r.org/reference/av_from_text.md).
|
||||
|
||||
- [`as.av()`](https://amr-for-r.org/reference/as.av.md)
|
||||
[`is.av()`](https://amr-for-r.org/reference/as.av.md) : Transform
|
||||
Input to an Antiviral Drug ID
|
||||
- [`av_name()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_cid()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_synonyms()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_tradenames()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_group()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_atc()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_loinc()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_ddd()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_ddd_units()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_info()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_url()`](https://amr-for-r.org/reference/av_property.md)
|
||||
[`av_property()`](https://amr-for-r.org/reference/av_property.md) :
|
||||
Get Properties of an Antiviral Drug
|
||||
- [`av_from_text()`](https://amr-for-r.org/reference/av_from_text.md) :
|
||||
Retrieve Antiviral Drug Names and Doses from Clinical Text
|
||||
|
||||
## Other: background information on included data
|
||||
|
||||
Some pages about our package and its external sources. Be sure to read
|
||||
our [How To’s](https://amr-for-r.org/articles/index.md) for more
|
||||
information about how to work with functions in this package.
|
||||
|
||||
- [`microorganisms`](https://amr-for-r.org/reference/microorganisms.md)
|
||||
: Data Set with 78 679 Taxonomic Records of Microorganisms
|
||||
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
|
||||
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
|
||||
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
|
||||
Data Sets with 618 Antimicrobial Drugs
|
||||
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
|
||||
: Data Set with Clinical Breakpoints for SIR Interpretation
|
||||
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)
|
||||
: Data Set with 2 000 Example Isolates
|
||||
- [`microorganisms.codes`](https://amr-for-r.org/reference/microorganisms.codes.md)
|
||||
: Data Set with 6 036 Common Microorganism Codes
|
||||
- [`microorganisms.groups`](https://amr-for-r.org/reference/microorganisms.groups.md)
|
||||
: Data Set with 534 Microorganisms In Species Groups
|
||||
- [`intrinsic_resistant`](https://amr-for-r.org/reference/intrinsic_resistant.md)
|
||||
: Data Set Denoting Bacterial Intrinsic Resistance
|
||||
- [`dosage`](https://amr-for-r.org/reference/dosage.md) : Data Set with
|
||||
Treatment Dosages as Defined by EUCAST
|
||||
- [`WHOCC`](https://amr-for-r.org/reference/WHOCC.md) : WHOCC: WHO
|
||||
Collaborating Centre for Drug Statistics Methodology
|
||||
- [`example_isolates_unclean`](https://amr-for-r.org/reference/example_isolates_unclean.md)
|
||||
: Data Set with Unclean Data
|
||||
- [`WHONET`](https://amr-for-r.org/reference/WHONET.md) : Data Set with
|
||||
500 Isolates - WHONET Example
|
||||
|
||||
## Other: miscellaneous functions
|
||||
|
||||
These functions are mostly for internal use, but some of them may also
|
||||
be suitable for your analysis. Especially the ‘like’ function can be
|
||||
useful: `if (x %like% y) {...}`.
|
||||
|
||||
- [`age_groups()`](https://amr-for-r.org/reference/age_groups.md) :
|
||||
Split Ages into Age Groups
|
||||
- [`age()`](https://amr-for-r.org/reference/age.md) : Age in Years of
|
||||
Individuals
|
||||
- [`export_ncbi_biosample()`](https://amr-for-r.org/reference/export_ncbi_biosample.md)
|
||||
: Export Data Set as NCBI BioSample Antibiogram
|
||||
- [`availability()`](https://amr-for-r.org/reference/availability.md) :
|
||||
Check Availability of Columns
|
||||
- [`get_AMR_locale()`](https://amr-for-r.org/reference/translate.md)
|
||||
[`set_AMR_locale()`](https://amr-for-r.org/reference/translate.md)
|
||||
[`reset_AMR_locale()`](https://amr-for-r.org/reference/translate.md)
|
||||
[`translate_AMR()`](https://amr-for-r.org/reference/translate.md) :
|
||||
Translate Strings from the AMR Package
|
||||
- [`italicise_taxonomy()`](https://amr-for-r.org/reference/italicise_taxonomy.md)
|
||||
[`italicize_taxonomy()`](https://amr-for-r.org/reference/italicise_taxonomy.md)
|
||||
: Italicise Taxonomic Families, Genera, Species, Subspecies
|
||||
- [`inner_join_microorganisms()`](https://amr-for-r.org/reference/join.md)
|
||||
[`left_join_microorganisms()`](https://amr-for-r.org/reference/join.md)
|
||||
[`right_join_microorganisms()`](https://amr-for-r.org/reference/join.md)
|
||||
[`full_join_microorganisms()`](https://amr-for-r.org/reference/join.md)
|
||||
[`semi_join_microorganisms()`](https://amr-for-r.org/reference/join.md)
|
||||
[`anti_join_microorganisms()`](https://amr-for-r.org/reference/join.md)
|
||||
: Join microorganisms to a Data Set
|
||||
- [`like()`](https://amr-for-r.org/reference/like.md)
|
||||
[`` `%like%` ``](https://amr-for-r.org/reference/like.md)
|
||||
[`` `%unlike%` ``](https://amr-for-r.org/reference/like.md)
|
||||
[`` `%like_case%` ``](https://amr-for-r.org/reference/like.md)
|
||||
[`` `%unlike_case%` ``](https://amr-for-r.org/reference/like.md) :
|
||||
Vectorised Pattern Matching with Keyboard Shortcut
|
||||
- [`mo_matching_score()`](https://amr-for-r.org/reference/mo_matching_score.md)
|
||||
: Calculate the Matching Score for Microorganisms
|
||||
- [`pca()`](https://amr-for-r.org/reference/pca.md) : Principal
|
||||
Component Analysis (for AMR)
|
||||
- [`random_mic()`](https://amr-for-r.org/reference/random.md)
|
||||
[`random_disk()`](https://amr-for-r.org/reference/random.md)
|
||||
[`random_sir()`](https://amr-for-r.org/reference/random.md) : Random
|
||||
MIC Values/Disk Zones/SIR Generation
|
||||
|
||||
## Other: statistical tests
|
||||
|
||||
Some statistical tests or methods are not part of base R and were added
|
||||
to this package for convenience.
|
||||
|
||||
- [`g.test()`](https://amr-for-r.org/reference/g.test.md) :
|
||||
|
||||
*G*-test for Count Data
|
||||
|
||||
- [`kurtosis()`](https://amr-for-r.org/reference/kurtosis.md) : Kurtosis
|
||||
of the Sample
|
||||
|
||||
- [`skewness()`](https://amr-for-r.org/reference/skewness.md) : Skewness
|
||||
of the Sample
|
||||
|
||||
## Other: deprecated functions/arguments/datasets
|
||||
|
||||
These objects are deprecated, meaning that they will still work but show
|
||||
a warning that they will be removed in a future version.
|
||||
|
||||
- [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
|
||||
[`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md) :
|
||||
Deprecated Functions, Arguments, or Datasets
|
||||
Reference in New Issue
Block a user