par(mfrow=c(2,2)) plot(prtr[,3],prtr[,2],xlab="Cancer volume", ylab="PSA") plot(prtr[,4],prtr[,2],xlab="Prostate weight", ylab="PSA") plot(prtr[,5],prtr[,2],xlab="Age", ylab="PSA") plot(prtr[,6],prtr[,2],xlab="BPH", ylab="PSA") p<-locator() plot(prtr[,7],prtr[,2],xlab="Seminal vesicle invasion", ylab="PSA") plot(prtr[,8],prtr[,2],xlab="Capsular penetration", ylab="PSA") plot(prtr[,9],prtr[,2],xlab="Gleason score", ylab="PSA") p<-locator() print("Take logs!") # par(mfrow=c(2,2)) plot(prtr[,3],log(prtr[,2]),xlab="Cancer volume", ylab="PSA") plot(prtr[,4],log(prtr[,2]),xlab="Prostate weight", ylab="PSA") plot(prtr[,5],log(prtr[,2]),xlab="Age", ylab="PSA") plot(prtr[,6],log(prtr[,2]),xlab="BPH", ylab="PSA") p<-locator() plot(prtr[,7],log(prtr[,2]),xlab="Seminal vesicle invasion", ylab="PSA") plot(prtr[,8],log(prtr[,2]),xlab="Capsular penetration", ylab="PSA") plot(prtr[,9],log(prtr[,2]),xlab="Gleason score", ylab="PSA") p<-locator() print("Non-linear on volume and weight") # par(mfrow=c(2,2)) plot(log(prtr[,3]),log(prtr[,2]),xlab="Cancer volume", ylab="PSA") plot(log(prtr[,4]),log(prtr[,2]),xlab="Prostate weight", ylab="PSA") plot(prtr[,5],log(prtr[,2]),xlab="Age", ylab="PSA") plot(prtr[,6],log(prtr[,2]),xlab="BPH", ylab="PSA") p<-locator() plot(prtr[,7],log(prtr[,2]),xlab="Seminal vesicle invasion", ylab="PSA") plot(prtr[,8],log(prtr[,2]),xlab="Capsular penetration", ylab="PSA") plot(prtr[,9],log(prtr[,2]),xlab="Gleason score", ylab="PSA") p<-locator() # # Additive model prtr2<-cbind(prtr,log(prtr[,2]),log(prtr[,3]),log(prtr[,4])) mm1<-lm(prtr2[,10]~prtr2[,11]+prtr2[,12]+prtr2[,5]+prtr2[,6]+prtr2[,7]+prtr2[,8]+prtr2[,9]) print(summary(mm1)) par(mfrow=c(2,2)) plot(mm1) p<-locator() # looks like 3 outliers maybe - unusually large/small PSA levels # perhaps interactions will help... # Look for interactions par(mfrow=c(1,1)) plot(prtr2[,12],prtr2[,10],xlab="Prostate weight", ylab="PSA",main="Interaction weight with seminal vesicle invasion?") points(prtr2[prtr2[,7]==1,12],prtr2[prtr2[,7]==1,10],col=2,pch=2) p<-locator() plot(prtr2[,11],prtr2[,10],xlab="Cancer volume", ylab="PSA",main="Interaction volume with seminal vesicle invasion?") points(prtr2[prtr2[,7]==1,11],prtr2[prtr2[,7]==1,10],col=2,pch=2) p<-locator() plot(prtr2[,8],prtr2[,10],xlab="Capsular penetration", ylab="PSA",main="Interaction Capsular penetration with seminal vesicle invasion?") points(prtr2[prtr2[,7]==1,8],prtr2[prtr2[,7]==1,10],col=2,pch=2) p<-locator()