Antimicrobial Resistance Analysis


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Documentation for package ‘AMR’ version 0.1.1

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ablist Dataset with 420 antibiotics
abname Name of an antibiotic
anti_join_bactlist Join a table with 'bactlist'
as.mic Class 'mic'
as.rsi Class 'rsi'
atc_property Properties of an ATC code
bactlist Dataset with ~2500 microorganisms
bactlist.umcg Translation table for UMCG with ~1100 microorganisms
EUCAST_rules EUCAST expert rules
first_isolate Determine first (weighted) isolates
full_join_bactlist Join a table with 'bactlist'
inner_join Join a table with 'bactlist'
inner_join_bactlist Join a table with 'bactlist'
interpretive_reading EUCAST expert rules
is.mic Class 'mic'
is.rsi Class 'rsi'
join Join a table with 'bactlist'
key_antibiotics Key antibiotics based on bacteria ID
left_join_bactlist Join a table with 'bactlist'
mo_property Poperties of a microorganism
right_join_bactlist Join a table with 'bactlist'
rsi Resistance of isolates
rsi_df Resistance of isolates in data.frame
rsi_predict Predict antimicrobial resistance
semi_join_bactlist Join a table with 'bactlist'
septic_patients Dataset with 2000 blood culture isolates of septic patients