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Feb 10th, 2016
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  1. set.seed(1)
  2. data <- data.frame(Used = rep(c(1,0,0,0),1250),
  3. Open = round(runif(5000,0,50),0),
  4. Activity = rep(sample(runif(24,.5,1.75),1250, replace=T), each=4),
  5. Strata = rep(1:1250,each=4))
  6.  
  7. mod <- clogit(Used ~ Open + I(Open*Activity) + strata(Strata),data=data)
  8.  
  9. newdata <- data.frame(Open = seq(0,50,1),
  10. Activity = rep(max(data$Activity),51))
  11.  
  12. fit<-predict(mod,newdata=newdata,type = "expected")
  13.  
  14. coef<-data.frame(coef = summary(mod)$coefficients[,1],
  15. se= summary(mod)$coefficients[,3])
  16. coef$se <-summary(mod)$coefficients[,4]
  17. coef$UpCI <- coef[,1] + (coef[,2]*2) ### this could be *1.96 but using 2 for simplicity
  18. coef$LowCI <-coef[,1] - (coef[,2]*2) ### this could be *1.96 but using 2 for simplicity
  19.  
  20. fitted<-data.frame(Open= seq(0,50,2),
  21. Activity=rep(max(data$Activity),26))
  22.  
  23. fitted$Marginal <- exp(coef[1,1]*fitted$Open +
  24. coef[2,1]*fitted$Open*fitted$Activity)/
  25. (1+exp(coef[1,1]*fitted$Open +
  26. coef[2,1]*fitted$Open*fitted$Activity))
  27.  
  28. fitted$UpCI <- exp(coef[1,3]*fitted$Open +
  29. coef[2,3]*fitted$Open*fitted$Activity)/
  30. (1+exp(coef[1,3]*fitted$Open +
  31. coef[2,3]*fitted$Open*fitted$Activity))
  32.  
  33. fitted$LowCI <- exp(coef[1,4]*fitted$Open +
  34. coef[2,4]*fitted$Open*fitted$Activity)/
  35. (1+exp(coef[1,4]*fitted$Open +
  36. coef[2,4]*fitted$Open*fitted$Activity))
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