[英]What is the difference between the coxph and cph functions for calculating Cox's proportional hazards model?
I am trying to analyse a dataset ( veteran
, in package survival
in R) with survival analysis. 我试图通过生存分析来分析数据集( veteran
,R中的包survival
)。 I found the function cph
in package rms
, which seems like different to coxph
. 我在包rms
找到了函数cph
,它看起来和coxph
不同。 What is the difference between these two functions? 这两个功能有什么区别?
Also, in this example, 此外,在此示例中,
model1<-cph(with(data=veteran,Surv(time,status)~rcs(age,4)+trt),x=TRUE,y=TRUE)
what's does rcs(age,4)
mean? rcs(age,4)
是什么意思?
Thanks for your help. 谢谢你的帮助。
RCS = restricted cubic spline. RCS =受限三次样条。 You can find the function's help file by looking at help(package="rms")
你可以通过查看help(package="rms")
找到函数的帮助文件help(package="rms")
Here's an excerpt of the source code, so you can see where the cph
function calls the coxph.fit
function (the guts of coxph
in the survival
package) 这里是源代码的摘录,所以你可以看到cph
函数调用coxph.fit
函数的位置( survival
包中coxph
的内容)
>cph
[...]
if (nullmod)
f = NULL
else {
ytype = attr(Y, "type")
fitter = if (method == "breslow" || method == "efron") {
if (ytype == "right")
coxph.fit
else if (ytype == "counting")
survival:::agreg.fit
else stop(paste("Cox model doesn't support \"", ytype,
"\" survival data", sep = ""))
}
else if (method == "exact")
survival:::agexact.fit
[...]
class(f) = c("cph", "rms", "coxph")
f
}
Both cph
and coxph
give the same results as far as coefficients: 就系数而言, cph
和coxph
给出相同的结果:
>library("survival")
>library("rms")
>
>x = rbinom(100, 1,.5)
>t = rweibull(100, 1, 1)
>
>m1 = coxph(Surv(t)~x)
>m2 = cph(Surv(t)~x)
>m1$coefficients
x
0.2226732
>m2$coefficients
x
0.2226732
But you can see that the authors of the cph
function have added some extra components to the results to fit their needs. 但是你可以看到cph
函数的作者在结果中添加了一些额外的组件以满足他们的需求。 Thus cph
will be useful if you need one of those extra features, but otherwise, coxph
will do just fine. 因此,如果您需要其中一个额外功能, cph
将非常有用,否则, coxph
会做得很好。
>attributes(m1)
$names
[1] "coefficients" "var" "loglik" "score"
[5] "iter" "linear.predictors" "residuals" "means"
[9] "concordance" "method" "n" "nevent"
[13] "terms" "assign" "wald.test" "y"
[17] "formula" "call"
$class
[1] "coxph"
>attributes(m2)
$names
[1] "coefficients" "var" "loglik" "score"
[5] "iter" "linear.predictors" "residuals" "means"
[9] "concordance" "terms" "n" "call"
[13] "Design" "assign" "na.action" "fail"
[17] "non.slopes" "stats" "method" "maxtime"
[21] "time.inc" "units" "center" "scale.pred"
$class
[1] "cph" "rms" "coxph"
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