xtable中的Cox回归输出-选择行/列并添加置信区间 [英] Cox regression output in xtable - choosing rows/columns and adding a confidence interval

问题描述

我不希望将cox回归的输出导出到表格中，然后可以将其放入文章中。我想最好的方法是使用xtable：

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)

现在我要对输出执行以下操作：

Now I want to do the following to the output:

• 添加置信区间（CI）为95 ％


• 选择某些行，例如age和log（protime）


• 将exp（B）& CI到小数点后三位


• 用z&删除列常规系数

• 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

谢谢！

推荐答案

我将通过首先查看 survival 包如何构造其默认打印的表的方式来实现此目的。

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

要找到执行该打印的功能，请检查fit对象的类，然后寻找该类的打印方法：

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"

看看 print.coxph 之后，这是我想出的：

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)

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