R语言进行多分类变量生存分析,cox模型,GBM模型,随机生存森林模型,coxboost模型,survivalsvm模型Brier Score的代码
时间: 2023-08-11 22:06:22 浏览: 399
以下是R语言进行多分类变量生存分析的代码,包括cox模型、GBM模型、随机生存森林模型、coxboost模型和survivalsvm模型的Brier Score计算:
```R
# 加载所需要的包
library(survival)
library(randomForestSRC)
library(gbm)
library(coxboost)
library(survivalsvm)
# 读取数据
data <- read.csv("data.csv", header = TRUE)
# 将分类变量转为因子变量
data$var1 <- as.factor(data$var1)
data$var2 <- as.factor(data$var2)
data$var3 <- as.factor(data$var3)
# 构建生存对象
survobj <- Surv(data$time, data$status)
# Cox模型
coxph.fit <- coxph(survobj ~ var1 + var2 + var3, data = data)
coxph.pred <- predict(coxph.fit, newdata = data, type = "lp")
coxph.bs <- BrierScore(survobj, coxph.pred)
# GBM模型
gbm.fit <- gbm(survobj ~ var1 + var2 + var3, distribution = "coxph", data = data, n.trees = 1000, interaction.depth = 4, shrinkage = 0.01, bag.fraction = 0.5, cv.folds = 5, verbose = TRUE)
gbm.pred <- predict.gbm(gbm.fit, newdata = data, n.trees = 1000, type = "response")
gbm.bs <- BrierScore(survobj, gbm.pred)
# 随机生存森林模型
rfsrc.fit <- rfsrc(survobj ~ var1 + var2 + var3, data = data, ntree = 1000, importance = TRUE)
rfsrc.pred <- predict.rfsrc(rfsrc.fit, newdata = data, proximity = FALSE, type = "response")
rfsrc.bs <- BrierScore(survobj, rfsrc.pred)
# CoxBoost模型
coxboost.fit <- coxboost(survobj ~ var1 + var2 + var3, data = data, family = "breslow", stepno = 5, nboost = 500)
coxboost.pred <- predict.coxboost(coxboost.fit, newdata = data, type = "lp")
coxboost.bs <- BrierScore(survobj, coxboost.pred)
# SurvivalSVM模型
survivalsvm.fit <- svm.survival(survobj ~ var1 + var2 + var3, data = data, kernel = "rbf", gamma = 0.1, cost = 1)
survivalsvm.pred <- predict(survivalsvm.fit, newdata = data)
survivalsvm.bs <- BrierScore(survobj, survivalsvm.pred$y)
# 输出每个模型的Brier Score
cat("Cox模型的Brier Score:", coxph.bs, "\n")
cat("GBM模型的Brier Score:", gbm.bs, "\n")
cat("随机生存森林模型的Brier Score:", rfsrc.bs, "\n")
cat("CoxBoost模型的Brier Score:", coxboost.bs, "\n")
cat("SurvivalSVM模型的Brier Score:", survivalsvm.bs, "\n")
```
需要注意的是,代码中的`data.csv`文件是需要自行准备的数据集,其中`time`表示生存时间,`status`表示存活状态(1表示死亡,0表示存活),`var1`、`var2`和`var3`是多个分类变量。
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