Cox regression output in xtable - choosing rows/columns and adding a confidence interval

Question

I wan't to export the output from a cox regression to a table that I then can put into my article. I guess the best way to go about it is with xtable:

library(survival)
data(pbc)
fit.pbc <- coxph(Surv(time, status==2) ~ age + edema + log(bili) + 
    log(protime) + log(albumin), data=pbc)

summary(fit.pbc)
library(xtable)
xtable(fit.pbc)

Now I want to do the following to the output:

• Add confidence interval (CI) of 95 %
• Select certain rows, say age and log(protime)
• Round the exp(B) & CI to three decimals
• Remove the column with z & regular coef

Thanks in advance!

Answer 1

I'd approach this by first taking a look at how the survival package constructs the table it prints by default.

To find the function that does that printing, examine the class of your fit object, and then look for a print method for that class:

class(fit.pbc)
# [1] "coxph"
grep("coxph", methods("print"), value=TRUE)
# [1] "print.coxph"         "print.coxph.null"   
# [3] "print.coxph.penal"   "print.summary.coxph"

After taking a look at print.coxph, here's what I came up with:

cox  <- fit.pbc

# Prepare the columns
beta <- coef(cox)
se   <- sqrt(diag(cox$var))
p    <- 1 - pchisq((beta/se)^2, 1)
CI   <- round(confint(cox), 3)

# Bind columns together, and select desired rows
res <- cbind(beta, se = exp(beta), CI, p)
res <- res[c("age", "log(protime)"),]

# Print results in a LaTeX-ready form
xtable(res)

Answer 2

xtable(round(summary(fit.pbc)$conf.int[c(1,3),],3))
#-----------------------------#
% latex table generated in R 2.13.1 by xtable 1.5-6 package
% Sat Oct 15 18:36:04 2011
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrrr}
  \hline
 & exp(coef) & exp(-coef) & lower .95 & upper .95 \\ 
  \hline
age & 1.04 & 0.96 & 1.02 & 1.06 \\ 
  log(bili) & 2.37 & 0.42 & 2.02 & 2.79 \\ 
   \hline
\end{tabular}
\end{center}
\end{table}

This shows what you see with str on the summary-object

str(summary(fit.pbc))
# snipped
 $ conf.int    : num [1:5, 1:4] 1.0404 2.4505 2.3716 10.8791 0.0815 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:5] "age" "edema" "log(bili)" "log(protime)" ...
  .. ..$ : chr [1:4] "exp(coef)" "exp(-coef)" "lower .95" "upper .95"