getExampleAntibiogramDAI: An example antibiogram.

In josie-hughes/EmpiricTherapyIndices: Calculate empiric therapy indices for device-associated infections.

Description

An example antibiogram.

Usage

getExampleAntibiogramDAI()

Value

An example antibiogram. Numbers are percent resistant (or non-susceptible).

Examples

#Revise the antibiogram and recalculate. PDR Acinetobacter example
pdrAcinetoAbg = getExampleAntibiogramDAI()
pdrAcinetoAbg$A.baumannii[!is.na(pdrAcinetoAbg$A.baumannii)]=100
EmpiricTherapyIndicesDAI(pdrAcinetoAbg)

#Save the example antibiogram as a delimited text file that can be edited in Excel
write.table(getExampleAntibiogramDAI(),file="myAntibiogram.txt",sep = "\t",row.names=F)

myRevisedAbg = read.table(file="myAntibiogram.txt",header=T)
EmpiricTherapyIndicesDAI(myRevisedAbg)

#Calculate the indices without reserve drugs:
ReserveDrugs = c("amika","cefta","dapto","eryth","genta","linez","merop","tobra")
abgWithoutReserves = subset(getExampleAntibiogramDAI(),!is.element(drug_d,ReserveDrugs))
EmpiricTherapyIndicesDAI(abgWithoutReserves)

josie-hughes/EmpiricTherapyIndices documentation built on May 19, 2019, 9:40 p.m.