Function reference • AMR (for R)

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
`ITIS`	ITIS: Integrated Taxonomic Information System
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.atc()` `guess_atc()` `is.atc()`	Transform to ATC code
`as.mic()` `is.mic()`	Class 'mic'
`as.mo()` `is.mo()`	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()` `interpretive_reading()`	EUCAST rules
`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()` `eucast_exceptional_phenotypes()`	Determine multidrug-resistant organisms (MDRO)
`key_antibiotics()` `key_antibiotics_equal()`	Key antibiotics for first weighted isolates
`mo_fullname()` `mo_shortname()` `mo_subspecies()` `mo_species()` `mo_genus()` `mo_family()` `mo_order()` `mo_class()` `mo_phylum()` `mo_subkingdom()` `mo_kingdom()` `mo_type()` `mo_gramstain()` `mo_TSN()` `mo_ref()` `mo_authors()` `mo_year()` `mo_taxonomy()` `mo_property()`	Property of a microorganism
`ab_property()` `ab_atc()` `ab_official()` `ab_name()` `ab_trivial_nl()` `ab_certe()` `ab_umcg()` `ab_tradenames()`	Property of an antibiotic
`atc_property()` `atc_groups()` `atc_ddd()`	Properties of an ATC code
`abname()`	Name 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`
Analysing your data Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.
`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()`	Calculate resistance of isolates
`frequency_tbl()` `freq()` `top_freq()` `header()` `print(<frequency_tbl>)`	Frequency table
`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 bar plots with `ggplot`
`kurtosis()`	Kurtosis of the sample
`resistance_predict()` `rsi_predict()` `plot(<resistance_predict>)` `ggplot_rsi_predict()`	Predict antimicrobial resistance
`rsi()`	Calculate resistance of isolates
`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 423 antibiotics
`microorganisms`	Data set with taxonomic data from ITIS
`septic_patients`	Data set with 2000 blood culture isolates of septic patients
`microorganisms.codes`	Translation table for microorganism codes
`microorganisms.old`	Data set with old taxonomic data from ITIS
`microorganismsDT` `microorganisms.prevDT` `microorganisms.unprevDT` `microorganisms.oldDT`	Supplementary Data
Other 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()`	Get language for AMR
`like()` `%like%`	Pattern Matching
`mo_failures()`	Vector of failed coercion attempts
`mo_renamed()`	Vector of taxonomic renamed items

Reference

Background information

Cleaning your data

Adding variables to your data

Analysing your data

Included data sets

Other

Contents