Man pages for AMR
Antimicrobial Resistance Analysis

ab_propertyProperty of an antibiotic
ageAge in years of individuals
age_groupsSplit ages into age groups
AMRThe 'AMR' Package
AMR-deprecatedDeprecated functions
antibioticsData sets with 557 antimicrobials
as.abTransform to antibiotic ID
as.diskClass 'disk'
as.micClass 'mic'
as.moTransform to microorganism ID
as.rsiClass 'rsi'
atc_onlineGet ATC properties from WHOCC website
availabilityCheck availability of columns
bug_drug_combinationsDetermine bug-drug combinations
catalogue_of_lifeThe Catalogue of Life
catalogue_of_life_versionVersion info of included Catalogue of Life
countCount available isolates
eucast_rulesApply EUCAST rules
example_isolatesData set with 2,000 example isolates
example_isolates_uncleanData set with unclean data
filter_ab_classFilter isolates on result in antimicrobial class
first_isolateDetermine first (weighted) isolates
ggplot_pcaPCA biplot with 'ggplot2'
ggplot_rsiAMR plots with 'ggplot2'
g.test_G_-test for Count Data
guess_ab_colGuess antibiotic column
joinJoin microorganisms to a data set
key_antibioticsKey antibiotics for first _weighted_ isolates
kurtosisKurtosis of the sample
lifecycleLifecycles of functions in the 'AMR' package
likePattern Matching
mdroDetermine multidrug-resistant organisms (MDRO)
microorganismsData set with 67,108 microorganisms
microorganisms.codesTranslation table with 5,582 common microorganism codes
microorganisms.oldData set with previously accepted taxonomic names
mo_propertyProperty of a microorganism
mo_sourceUser-defined reference data set for microorganisms
pcaPrincipal Component Analysis (for AMR)
proportionCalculate microbial resistance
p_symbolSymbol of a p-value
resistance_predictPredict antimicrobial resistance
rsi_translationData set for R/SI interpretation
skewnessSkewness of the sample
translateTranslate strings from AMR package
WHOCCWHOCC: WHO Collaborating Centre for Drug Statistics...
WHONETData set with 500 isolates - WHONET example
AMR documentation built on July 8, 2020, 6:05 p.m.