EmpiricTherapyIndicesDAI: Calculate empiric therapy indices for device-associated...

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

Description

Calculate empiric therapy indices for device-associated infections.

Usage

EmpiricTherapyIndicesDAI(Antibiograms, Basket = getBasketDAI(),
  Drugs = getDrugsDAI(), mixingPars = list(alpha = 0), wide = T)

Arguments

Antibiograms	An antibiogram. getExampleAntibiograms() for example. Numbers are percent resistance (or non-susceptibility). One site is included in the example, but the algorithm can handle multiple sites.
Basket	The basket of infections. getBasketDAI() for example.
Drugs	The set of available drugs. getDrugsDAI() for example.
mixingPars	A list of parameters for mixingFunction(), determining the impact of drug heterogeneity on the evolution of resistance. In the default case list(alpha=0) using multiple drugs does not slow the development of resistance. list(alpha=0.1) means that using 2 drugs instead of 1 slows the developement of resistance by 10%.

Value

Empiric options index (EOI) and empiric coverage index (ECI) for each site.

Examples

#Example calculation:
EmpiricTherapyIndicesDAI(getExampleAntibiogramDAI())

#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.