Cleaning your data

Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying EUCAST rules.

as.ab() is.ab()

Transform to antibiotic ID

as.disk() is.disk()

Class 'disk'

as.mic() is.mic()

Class 'mic' mo_failures() mo_uncertainties() mo_renamed()

Transform to microorganism ID

as.rsi() is.rsi() is.rsi.eligible()

Class 'rsi'


Apply EUCAST rules


Retrieve antimicrobial drug names and doses from clinical text


Guess antibiotic column

set_mo_source() get_mo_source()

User-defined reference data set for microorganisms

Enhancing your data

Functions to add new data to your existing data, such as the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.

ab_name() ab_atc() ab_cid() ab_synonyms() ab_tradenames() ab_group() ab_atc_group1() ab_atc_group2() ab_loinc() ab_ddd() ab_info() ab_url() ab_property()

Property of an antibiotic


Split ages into age groups


Age in years of individuals

atc_online_property() atc_online_groups() atc_online_ddd()

Get ATC properties from WHOCC website

first_isolate() filter_first_isolate() filter_first_weighted_isolate()

Determine first (weighted) isolates

inner_join_microorganisms() left_join_microorganisms() right_join_microorganisms() full_join_microorganisms() semi_join_microorganisms() anti_join_microorganisms()

Join microorganisms to a data set

key_antibiotics() key_antibiotics_equal()

Key antibiotics for first weighted isolates

mdro() brmo() mrgn() mdr_tb() mdr_cmi2012() eucast_exceptional_phenotypes()

Determine multidrug-resistant organisms (MDRO)

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_snomed() mo_ref() mo_authors() mo_year() mo_rank() mo_taxonomy() mo_synonyms() mo_info() mo_url() mo_property()

Property of a microorganism


Symbol of a p-value

Analysing your data

Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, or make plots.

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


Check availability of columns

bug_drug_combinations() format(<bug_drug_combinations>)

Determine bug-drug combinations

resistance_predict() rsi_predict() plot(<resistance_predict>) ggplot_rsi_predict()

Predict antimicrobial resistance


Principal Component Analysis (for AMR)

ab_class() aminoglycosides() carbapenems() cephalosporins() cephalosporins_1st() cephalosporins_2nd() cephalosporins_3rd() cephalosporins_4th() cephalosporins_5th() fluoroquinolones() glycopeptides() macrolides() penicillins() tetracyclines()

Antibiotic class selectors

filter_ab_class() filter_aminoglycosides() filter_carbapenems() filter_cephalosporins() filter_1st_cephalosporins() filter_2nd_cephalosporins() filter_3rd_cephalosporins() filter_4th_cephalosporins() filter_5th_cephalosporins() filter_fluoroquinolones() filter_glycopeptides() filter_macrolides() filter_penicillins() filter_tetracyclines()

Filter isolates on result in antimicrobial class


G-test for Count Data

ggplot_rsi() geom_rsi() facet_rsi() scale_y_percent() scale_rsi_colours() theme_rsi() labels_rsi_count()

AMR plots with ggplot2


PCA biplot with ggplot2


Kurtosis of the sample


Skewness of the sample

Included data sets

Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.


Data set with 67,150 microorganisms

antibiotics antivirals

Data sets with 558 antimicrobials


Data set with 2,000 example isolates


Data set with unclean data


Data set for R/SI interpretation

Translation table with 5,582 common microorganism codes


Data set with previously accepted taxonomic names


Data set with 500 isolates - WHONET example

Background information

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.


The AMR Package


The Catalogue of Life


Version info of included Catalogue of Life


WHOCC: WHO Collaborating Centre for Drug Statistics Methodology


Lifecycles of functions in the AMR package

Other 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) {...}.


Translate strings from AMR package

like() `%like%` `%like_case%`

Pattern Matching

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.

portion_R() portion_IR() portion_I() portion_SI() portion_S() portion_df()

Deprecated functions