[R] Variance-covariance matrix

[Peter Dalgaard]

Laura Bonnett wrote:
> Here is the exact code I have written which does the standard vs nt1
> and standard vs nt2 and also gives me the hazard ratio for nt1 vs nt2.
>
> with <- read.table("allwiths.txt",
> header=TRUE)
> fix(arm)
>     function (data)
>     {
>     dummy <- rep(0,2437)
>     for(i in 1:2437){
>     if(data$Arm[i]=="CBZ")
>     dummy[i] <- i
>     }
>     return(data[-dummy,])
>     }
> fix(x1)
>     function (data)
>     {
>     x1 <- rep(0,716)
>     for(i in 1:716){
>     if(data$Treat[i]=="TPM")
>     x1[i] <- 0
>     if(data$Treat[i]=="VPS")
>     x1[i] <- 0
>     if(data$Treat[i]=="LTG")
>     x1[i] <- 1
>     }
>     return(x1)
>     }
> fix(x2)
>     function (data)
>     {
>     x2 <- rep(0,716)
>     for(i in 1:716){
>     if(data$Treat[i]=="TPM")
>     x2[i] <- 1
>     if(data$Treat[i]=="VPS")
>     x2[i] <- 0
>     if(data$Treat[i]=="LTG")
>     x2[i] <- 0
>     }
>     return(x2)
>     }
> fit1 = coxph(Surv(Withtime,Wcens)~x1(armb),data=armb,method="breslow")
> exp(fit1$coefficients)
> exp(confint(fit1))
> fit2 = coxph(Surv(Withtime,Wcens)~x2(armb),data=armb,method="breslow")
> exp(fit2$coefficients)
> exp(confint(fit2))
> exp(fit2$coefficients)/exp(fit1$coefficients)
>
> From that, how do I get the necessary variance-covaraince matrix.
>
> Sorry if I appear dense.  It really isn't my intention.
>
You need to read up on vectorized arithmetic, (and don't use fix() to
define functions, x1 <- function(....) {....} will do, and what's with
the unused arm() function??).

However, if I get your data structure correctly, what I meant was that
you could just look at

fit3 <- coxph(Surv(Withtime,Wcens)~Treat, data=armb,method="breslow")

(possibly factor(Treat) instead). If VPS is your control, I think you'll
even get the desired coefficient directly from the output because the
group comparisons will be against LTG.

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907