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R does not subset

Maybe it didn't work because you still didn't have a space at the end of the value you were comparing (apparently the factor was defined with a space). with).  Try the following (and notice the space at the end of "Infected ". 

RECinf<-subset(REC2,  INFECTION=="Infected ")

David's suggestion worked because you did include a space there.


Dan

Daniel Nordlund
Bothell, WA USA