Function reference • AMR (for R)

Preparing data: microorganisms

These functions are meant to get taxonomically valid properties of microorganisms from any input. Use mo_source() to teach this package how to translate your own codes to valid microorganism codes.

as.mo() is.mo() mo_failures() mo_uncertainties() mo_renamed(): Transform Input to a Microorganism Code

mo_name() mo_fullname() mo_shortname() mo_subspecies() mo_species() mo_genus() mo_family() mo_order() mo_class() mo_phylum() mo_kingdom() mo_domain() mo_type() mo_gramstain() mo_is_gram_negative() mo_is_gram_positive() mo_is_yeast() mo_is_intrinsic_resistant() mo_snomed() mo_ref() mo_authors() mo_year() mo_lpsn() mo_rank() mo_taxonomy() mo_synonyms() mo_info() mo_url() mo_property(): Get Properties of a Microorganism

set_mo_source() get_mo_source(): User-Defined Reference Data Set for Microorganisms

Preparing data: antibiotics

Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using ab_from_text().

as.ab() is.ab(): Transform Input to an Antibiotic ID

ab_name() ab_cid() ab_synonyms() ab_tradenames() ab_group() ab_atc() ab_atc_group1() ab_atc_group2() ab_loinc() ab_ddd() ab_ddd_units() ab_info() ab_url() ab_property() set_ab_names(): Get Properties of an Antibiotic

ab_from_text(): Retrieve Antimicrobial Drug Names and Doses from Clinical Text

atc_online_property() atc_online_groups() atc_online_ddd() atc_online_ddd_units(): Get ATC Properties from WHOCC Website

Preparing data: antimicrobial resistance

With as.mic() and as.disk() you can transform your raw input to valid MIC or disk diffusion values. Use as.rsi() for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying EUCAST rules with eucast_rules().

as.rsi() NA_rsi_ is.rsi() is.rsi.eligible() rsi_interpretation_history(): Interpret MIC and Disk Values, or Clean Raw R/SI Data

as.mic() NA_mic_ is.mic() droplevels(<mic>): Transform Input to Minimum Inhibitory Concentrations (MIC)

as.disk() NA_disk_ is.disk(): Transform Input to Disk Diffusion Diameters

eucast_rules() eucast_dosage(): Apply EUCAST Rules

custom_eucast_rules(): Define Custom EUCAST Rules

Analysing data: antimicrobial resistance

Use these function for the analysis part. You can use susceptibility() or resistance() on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using first_isolate() or is_new_episode(). You can also filter your data on certain resistance in certain antibiotic classes (carbapenems(), aminoglycosides()), or determine multi-drug resistant microorganisms (MDRO, mdro()).

resistance() susceptibility() proportion_R() proportion_IR() proportion_I() proportion_SI() proportion_S() proportion_df() rsi_df(): Calculate Microbial Resistance

count_resistant() count_susceptible() count_R() count_IR() count_I() count_SI() count_S() count_all() n_rsi() count_df(): Count Available Isolates

get_episode() is_new_episode(): Determine (New) Episodes for Patients

first_isolate() filter_first_isolate(): Determine First Isolates

key_antimicrobials() all_antimicrobials() antimicrobials_equal(): (Key) Antimicrobials for First Weighted Isolates

mdro() custom_mdro_guideline() brmo() mrgn() mdr_tb() mdr_cmi2012() eucast_exceptional_phenotypes(): Determine Multidrug-Resistant Organisms (MDRO)

plot(<mic>) autoplot(<mic>) fortify(<mic>) plot(<disk>) autoplot(<disk>) fortify(<disk>) plot(<rsi>) autoplot(<rsi>) fortify(<rsi>): Plotting for Classes rsi, mic and disk

ggplot_rsi() geom_rsi() facet_rsi() scale_y_percent() scale_rsi_colours() theme_rsi() labels_rsi_count(): AMR Plots with ggplot2

bug_drug_combinations() format(<bug_drug_combinations>): Determine Bug-Drug Combinations

ab_class() ab_selector() aminoglycosides() aminopenicillins() antifungals() antimycobacterials() betalactams() carbapenems() cephalosporins() cephalosporins_1st() cephalosporins_2nd() cephalosporins_3rd() cephalosporins_4th() cephalosporins_5th() fluoroquinolones() glycopeptides() lincosamides() lipoglycopeptides() macrolides() oxazolidinones() penicillins() polymyxins() streptogramins() quinolones() tetracyclines() trimethoprims() ureidopenicillins() administrable_per_os() administrable_iv() not_intrinsic_resistant(): Antibiotic Selectors

mean_amr_distance() distance_from_row(): Mean AMR Distance

resistance_predict() rsi_predict() plot(<resistance_predict>) ggplot_rsi_predict() autoplot(<resistance_predict>): Predict Antimicrobial Resistance

guess_ab_col(): Guess Antibiotic Column

Background information on included data

Some pages about our package and its external sources. Be sure to read our How To’s for more information about how to work with functions in this package.

AMR: The AMR Package

example_isolates: Data Set with 2,000 Example Isolates

microorganisms: Data Set with 70,764 Microorganisms

microorganisms.codes: Data Set with 5,604 Common Microorganism Codes

microorganisms.old: Data Set with Previously Accepted Taxonomic Names

antibiotics antivirals: Data Sets with 566 Antimicrobial Drugs

intrinsic_resistant: Data Set with Bacterial Intrinsic Resistance

dosage: Data Set with Treatment Dosages as Defined by EUCAST

catalogue_of_life: The Catalogue of Life

catalogue_of_life_version(): Version info of included Catalogue of Life

WHOCC: WHOCC: WHO Collaborating Centre for Drug Statistics Methodology

example_isolates_unclean: Data Set with Unclean Data

rsi_translation: Data Set for R/SI Interpretation

WHONET: 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(): Split Ages into Age Groups

age(): Age in Years of Individuals

availability(): Check Availability of Columns

get_AMR_locale() set_AMR_locale() reset_AMR_locale() translate_AMR(): Translate Strings from the AMR Package

ggplot_pca(): PCA Biplot with ggplot2

italicise_taxonomy() italicize_taxonomy(): Italicise Taxonomic Families, Genera, Species, Subspecies

inner_join_microorganisms() left_join_microorganisms() right_join_microorganisms() full_join_microorganisms() semi_join_microorganisms() anti_join_microorganisms(): Join microorganisms to a Data Set

like() `%like%` `%unlike%` `%like_case%` `%unlike_case%`: Vectorised Pattern Matching with Keyboard Shortcut

mo_matching_score(): Calculate the Matching Score for Microorganisms

pca(): Principal Component Analysis (for AMR)

random_mic() random_disk() random_rsi(): Random MIC Values/Disk Zones/RSI 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(): G-test for Count Data

kurtosis(): Kurtosis of the Sample

skewness(): Skewness of the Sample

Other: deprecated functions

These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.

AMR-deprecated: Deprecated Functions