html - cox回归输出表或R中的图
问题描述
我有一个 Cox 回归,它使用strata()
和一个tt()
.
是否有任何软件包可以帮助以表格格式生成美观、信息丰富的结果输出?虽然ggforest()
处理tt()
它不处理strata()
我正在寻找任何方式来产生一个合适的输出,而不是 print summary(coxph)
。无论是 Latex 还是 HTML。
到目前为止,唯一的解决方案是自己构建表格,但这看起来并不吸引人,无法放入论文中......
这是虚拟数据集:
set.seed(132456)
'dummy survival data'
df<-data.frame(id=seq(1,1000,1), event=rep(0,1000),time=floor(runif(1000,7,10)),group=floor(runif(1000,0,2)),
var1 = rnorm(1000, 1, 3), var2 = seq(1,1000))
'set events for a few random subjects'
id_list<-c(as.numeric(floor(runif(500,1,1000))))
df$event[df$id %in% id_list]<-1
'set survival times for events'
t_list<-c(as.numeric(floor(runif(394,1,5))))
df2<-df[df$event==1,]
df2$time<-t_list
'combine data'
df<-rbind(df,df2)
summary(df)
'Set up surfit '
require(survminer)
KM_fit<-coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df)
ggforest()
返回以下错误:
> ggforest(KM_fit)
Error in `[.data.frame`(data, , var) : undefined columns selected
additional warning:
In .get_data(model, data = data) :
The `data` argument is not provided. Data will be extracted from model fit.
如果省略,该ggforest()
功能将起作用。strata
但是我处理的模型使用它....所以没有解决方案。
下面返回一个非常基本的表格,如果我对布局有更多了解,可以使用它,但它真的不漂亮!
# Prepare the columns
beta <- coef(KM_fit)
se <- sqrt(diag(KM_fit$var))
p <- 1 - pchisq((beta/se)^2, 1)
CI <- round(exp(confint(KM_fit)), 2)
# Bind columns together, and select desired rows
res <- cbind(beta, se = exp(beta), CI, p)
# Print results in a LaTeX-ready form
knitr::kable(
xtable(res)
)
感谢任何提示和技巧!
非常感谢!
也试过finalfit()
没有成功....
解决方案
以下是一些选项,具体取决于您希望在决赛桌中包含的内容。
coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df) %>%
finalfit::fit2df() %>%
knitr::kable()
coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df) %>%
finalfit::fit2df(condense = FALSE) %>%
knitr::kable()
coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df) %>%
broom::tidy(exp = TRUE)
编辑
该digits
参数用于压缩输出。如果您将值输出为数字,则在打印之前它们不会被四舍五入。所以这里有两个选项。
> coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df) %>%
+ finalfit::fit2df(digits = c(3,3,3)) %>%
+ knitr::kable()
|explanatory |HR |
|:-----------|:----------------------------|
|tt(var2) |0.998 (0.995-1.001, p=0.211) |
|var1 |1.006 (0.983-1.029, p=0.616) |
>
> coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df) %>%
+ finalfit::fit2df(condense = FALSE) %>%
+ knitr::kable(digits = c(0, 2, 3, 4, 5))
|explanatory | HR| L95| U95| p|
|:-----------|----:|-----:|------:|-------:|
|tt(var2) | 1.00| 0.995| 1.0010| 0.21097|
|var1 | 1.01| 0.983| 1.0294| 0.61612|
>
在 Finalfit 中编辑 2标签变量很容易。tt()
目前不支持故障。
df %>%
mutate(
var1 = ff_label(var1, "Pretty var1"),
var2 = ff_label(var2, "Also very pretty var2"),
group = factor(group) %>%
ff_label("Group (strata)")
) %>%
finalfit("Surv(time, event)", c("var1", "var2", "strata(group)"), column = TRUE)
Dependent: Surv(time, event) all HR (univariable) HR (multivariable)
Pretty var1 Mean (SD) 0.9 (3.1) 1.01 (0.98-1.03, p=0.636) 1.01 (0.98-1.03, p=0.646)
Also very pretty var2 Mean (SD) 504.5 (288.3) 1.00 (1.00-1.00, p=0.479) 1.00 (1.00-1.00, p=0.484)
Group (strata) 0 714 (51.2) - -
1 680 (48.8) - -
正如你所说,你可以手动编辑简单的表格
coxph(Surv(time , event) ~ tt(var2) + strata(group)+ var1 ,data= df) %>%
finalfit::fit2df(condense = FALSE) %>%
mutate(
explanatory = c("Pretty var2 (time dependent)", "Also pretty var1")
) %>%
knitr::kable(digits = c(3,3,3,3,3))
|explanatory | HR| L95| U95| p|
|:----------------------------|-----:|-----:|-----:|-----:|
|Pretty var2 (time dependent) | 0.998| 0.995| 1.001| 0.211|
|Also pretty var1 | 1.006| 0.983| 1.029| 0.616|
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