Function reference • AMR

All functions
`AMR`	The `AMR` Package
`ab_property()` `ab_atc()` `ab_official()` `ab_name()` `ab_trivial_nl()` `ab_certe()` `ab_umcg()` `ab_tradenames()`	Property of an antibiotic
`abname()`	Name of an antibiotic
`age()`	Age in years of individuals
`age_groups()`	Split ages into age groups
`antibiotics`	Data set with 423 antibiotics
`as.atc()` `guess_atc()` `is.atc()`	Transform to ATC code
`as.mic()` `is.mic()`	Class 'mic'
`as.mo()` `is.mo()` `guess_mo()`	Transform to microorganism ID
`as.rsi()` `is.rsi()` `is.rsi.eligible()`	Class 'rsi'
`atc_property()` `atc_groups()` `atc_ddd()`	Properties of an ATC code
`count_R()` `count_IR()` `count_I()` `count_SI()` `count_S()` `count_all()` `n_rsi()` `count_df()`	Count isolates
`eucast_rules()` `EUCAST_rules()` `interpretive_reading()`	EUCAST rules
`first_isolate()` `filter_first_isolate()` `filter_first_weighted_isolate()`	Determine first (weighted) isolates
`frequency_tbl()` `freq()` `top_freq()` `print(<frequency_tbl>)`	Frequency table
`g.test()`	G-test for Count Data
`get_locale()`	Get language for AMR
`ggplot_rsi()` `geom_rsi()` `facet_rsi()` `scale_y_percent()` `scale_rsi_colours()` `theme_rsi()` `labels_rsi_count()`	AMR bar plots with `ggplot`
`inner_join_microorganisms()` `left_join_microorganisms()` `right_join_microorganisms()` `full_join_microorganisms()` `semi_join_microorganisms()` `anti_join_microorganisms()`	Join a table with `microorganisms`
`key_antibiotics()` `key_antibiotics_equal()`	Key antibiotics for first weighted isolates
`kurtosis()`	Kurtosis of the sample
`like()` `%like%`	Pattern Matching
`mdro()` `brmo()` `mrgn()` `eucast_exceptional_phenotypes()`	Determine multidrug-resistant organisms (MDRO)
`microorganisms`	Data set with taxonomic data from ITIS
`microorganisms.certe`	Translation table for Certe
`microorganisms.old`	Data set with old taxonomic data from ITIS
`microorganisms.umcg`	Translation table for UMCG
`mo_failures()`	Vector of failed coercion attempts
`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
`mo_renamed()`	Vector of taxonomic renamed items
`p.symbol()`	Symbol of a p value
`portion_R()` `portion_IR()` `portion_I()` `portion_SI()` `portion_S()` `portion_df()`	Calculate resistance of isolates
`read.4D()`	Read data from 4D database
`resistance_predict()` `rsi_predict()`	Predict antimicrobial resistance
`rsi()`	Calculate resistance of isolates
`septic_patients`	Data set with 2000 blood culture isolates of septic patients
`skewness()`	Skewness of the sample
`microorganismsDT` `microorganisms.prevDT` `microorganisms.unprevDT` `microorganisms.oldDT`	Supplementary Data

Reference

All functions

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