如何获得 survdiff 返回的 p 值

Question

我正在使用 R 生存包，survdiff 函数。我想知道如何从 return 值中获取 p 值。

> diff = survdiff(Surv(Time, Censored) ~ Treatment+Gender, data = dat)
&gt; diff
Call:
survdiff(formula = Surv(Time, Censored) ~ Treatment + Gender, 
    data = dat)

                            N Observed Expected (O-E)^2/E (O-E)^2/V
Treatment=Control, Gender=M 2        1     1.65  0.255876  0.360905
Treatment=Control, Gender=F 7        3     2.72  0.027970  0.046119
Treatment=IND, Gender=M     5        2     2.03  0.000365  0.000519
Treatment=IND, Gender=F     6        2     1.60  0.100494  0.139041

 Chisq= 0.5  on 3 degrees of freedom, p= 0.924

我想使用一些函数获得 p 值 0.924。谢谢

Answer 1

p 值未存储在 survdiff class 中，因此必须在输出时即时计算。要重现 p 值，可以使用 chisq 分布函数："pchisq"

diff = survdiff(Surv(Time, Censored) ~ Treatment+Gender, data = dat)
pchisq(diff$chisq, length(diff$n)-1, lower.tail = FALSE)

Answer 2

函数 print.survdiff 中显示该值的代码是：

cat("\n Chisq=", format(round(x$chisq, 1)), " on", df, 
            "degrees of freedom, p=", format(signif(1 - pchisq(x$chisq, 
                df), digits)), "\n")

导致它的代码：

if (is.matrix(x$obs)) {
            otmp <- apply(x$obs, 1, sum)
            etmp <- apply(x$exp, 1, sum)
        }         else {
            otmp <- x$obs
            etmp <- x$exp
        }
        df <- (sum(1 * (etmp > 0))) - 1

并且 'digits' 在参数列表中设置为 3，因此使用 surv.diff 帮助页面上的示例：

x <- survdiff(Surv(time, status) ~ pat.karno + strata(inst), data=lung) 
cat( "p=", format(signif(1 - pchisq(x$chisq, 
                 df), digits)) )
#p= 0.00326

解决评论：在示例中，第二个代码块减少为：

 df <- with(x,    (sum(1 * (apply(x$exp, 1, sum) > 0))) - 1 )
> df
[1] 7

Answer 3

利用broom包中的glance()函数，很容易得到p.value。

diff = survdiff(Surv(Time, Censored) ~ Treatment+Gender, data = dat)

broom::glance(diff)$p.value

如何获得 survdiff 返回的 p 值

How to get survdiff returned p value

r

survival-analysis

p-value