# Function reference • AMR (for R)

# Reference

## 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()` `guess_mo()` | Transform to microorganism ID
`as.rsi()` `is.rsi()` `is.rsi.eligible()` | Class 'rsi'
`eucast_rules()` `EUCAST_rules()` `interpretive_reading()` | EUCAST rules
`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,

`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 the data

Functions for conducting AMR analysis

`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()` | 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.certe` | Translation table for Certe
`microorganisms.old` | Data set with old taxonomic data from ITIS
`microorganisms.umcg` | Translation table for UMCG
`microorganismsDT` `microorganisms.prevDT` `microorganisms.unprevDT` `microorganisms.oldDT` | Supplementary Data

## Other

`get_locale()` | Get language for AMR
`like()` ``%like%`` | Pattern Matching
`mo_failures()` | Vector of failed coercion attempts
`mo_renamed()` | Vector of taxonomic renamed items