Man pages for msberends/AMR
Antimicrobial Resistance Analysis

abnameName of an antibiotic
ageAge in years of individuals
age_groupsSplit ages into age groups
AMRThe 'AMR' Package
AMR-deprecatedDeprecated functions
antibioticsData set with ~500 antibiotics
as.atcTransform to ATC code
as.micClass 'mic'
as.moTransform to microorganism ID
as.rsiClass 'rsi'
atc_onlineGet ATC properties from WHOCC website
atc_propertyProperty of an antibiotic
availabilityCheck availability of columns
countCount isolates
eucast_rulesEUCAST rules
first_isolateDetermine first (weighted) isolates
freqFrequency table
get_localeGet language for AMR
ggplot_rsiAMR plots with 'ggplot2'
g.test_G_-test for Count Data
guess_ab_colGuess antibiotic column
ITISITIS: Integrated Taxonomic Information System
joinJoin a table with 'microorganisms'
key_antibioticsKey antibiotics for first _weighted_ isolates
kurtosisKurtosis of the sample
likePattern Matching
mdroDetermine multidrug-resistant organisms (MDRO)
microorganismsData set with ~20,000 microorganisms
microorganisms.codesTranslation table for microorganism codes
microorganisms.oldData set with previously accepted taxonomic names
mo_propertyProperty of a microorganism
mo_sourceUse predefined reference data set
portionCalculate resistance of isolates
p.symbolSymbol of a p value
read.4DRead data from 4D database
resistance_predictPredict antimicrobial resistance
rsiCalculate resistance of isolates
septic_patientsData set with 2,000 blood culture isolates from septic...
skewnessSkewness of the sample
supplementary_dataSupplementary Data
WHOCCWHOCC: WHO Collaborating Centre for Drug Statistics...
WHONETData set with 500 isolates - WHONET example
msberends/AMR documentation built on Feb. 15, 2019, 3:43 a.m.