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.

AMR

The AMR Package

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

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'

as.mo() is.mo() mo_failures() mo_uncertainties() mo_renamed() clear_mo_history()

Transform to microorganism ID

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

Class 'rsi'

set_mo_source() get_mo_source()

Use predefined reference data set

eucast_rules()

EUCAST rules

rsi_translation

Data set for RSI interpretation

guess_ab_col()

Guess antibiotic column

read.4D()

Read data from 4D database

Adding variables to your data

Functions to add new data to existing data, like 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.

first_isolate() filter_first_isolate() filter_first_weighted_isolate()

Determine first (weighted) isolates

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

Determine multidrug-resistant organisms (MDRO)

key_antibiotics() key_antibiotics_equal()

Key antibiotics for first weighted isolates

mo_name() mo_fullname() mo_shortname() mo_subspecies() mo_species() mo_genus() mo_family() mo_order() mo_class() mo_phylum() mo_kingdom() mo_type() mo_gramstain() mo_ref() mo_authors() mo_year() mo_rank() mo_taxonomy() mo_synonyms() mo_info() mo_url() mo_property()

Property of a microorganism

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

Property of an antibiotic

age()

Age in years of individuals

age_groups()

Split ages into age groups

p_symbol()

Symbol of a p value

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

Join a table with microorganisms

atc_online_property() atc_online_groups() atc_online_ddd()

Get ATC properties from WHOCC website

Analysing your data

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

availability()

Check availability of columns

bug_drug_combinations() format(<bug_drug_combinations>)

Determine bug-drug combinations

count_R() count_IR() count_I() count_SI() count_S() count_all() n_rsi() count_df()

Count isolates

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

Calculate resistance of isolates

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_tetracyclines()

Filter isolates on result in antibiotic class

g.test()

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

kurtosis()

Kurtosis of the sample

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

Predict antimicrobial resistance

skewness()

Skewness of the sample

Included data sets

References for microorganisms and antibiotics, and even a genuine data set with isolates from septic patients.

antibiotics

Data set with ~450 antibiotics

microorganisms

Data set with ~70,000 microorganisms

example_isolates

Data set with 2,000 blood culture isolates

WHONET

Data set with 500 isolates - WHONET example

microorganisms.codes

Translation table for common microorganism codes

microorganisms.old

Data set with previously accepted taxonomic names

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) {...}.

get_locale()

Translate strings from AMR package

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

Pattern Matching

Extended functions

These functions are extensions of functions in other packages.

scale_type.mo() scale_type.ab()

Extended functions

functions

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

as.atc() p.symbol()

Deprecated functions