我有随机森林变量选择的示例代码。我们希望选择最重要的变量组合,并建立具有最低 OOB 的随机森林模型。任何人都可以为我解释函数中的 for 循环部分吗?
clinical_variables <- c("Age","location", "smoke", "perianal_disease","upper_tract", "LnASCA
IgA","LnASCA IgG", "LnANCA", "LnCbir", "LnOMPC", "CRP", "Albumin", "African American Race")
variable_selected_progress_biomarkers <- vector("list", 50)
error_rate_min_progress_biomarkers <- rep(NA, 50)
for (j in 1:50){
risk_progress_biomarker_variables <- risk_full %>%
select(names(risk), clinical_variables) %>%
select(-c("STRICTURE", "TIM2STRICTURE", "PENETRATING", "TIM2PENETRATING","BDNF","LASTFOLLOWUPDAYSPROGRESS", "PROGRESSED")) %>% names
risk_progress_biomarker_variables_total <- vector("list",104)
names(risk_progress_biomarker_variables_total) <- 104:1
error_rate_tail_progress_biomarker <- rep(NA, 104)
for (i in 1:104){
set.seed(4182019)
risk_progress_biomarker_variables_total[[i]] <- risk_progress_biomarker_variables
rf_risk_progress_biomarker <- rfsrc(
Surv(LASTFOLLOWUPDAYSPROGRESS, PROGRESSED) ~ .,
data = risk_full %>% select(risk_progress_biomarker_variables, LASTFOLLOWUPDAYSPROGRESS, PROGRESSED)%>%
mutate_if(is.factor, as.numeric),
ntree=1000,
importance = TRUE
)
error_rate_tail_progress_biomarker[i] <- tail(rf_risk_progress_biomarker$err.rate,n =1)
rf_risk_progress_biomarker_importance <- rf_risk_progress_biomarker$importance %>%
as.data.frame() %>%
rownames_to_column() %>%
as.tibble() %>%
dplyr::rename(VIMP = ".") %>%
arrange(desc(VIMP))
risk_progress_biomarker_variables <- rf_risk_progress_biomarker_importance %>%
head((dim(rf_risk_progress_biomarker_importance)[1]-1)) %>%
# top_n((dim(rf_risk_progress_biomarker_importance)[1]-1)) %>%
pull(rowname)
print(i)
}
tibble_error_rate_tail_progress_biomarker <- tibble(n = 104:1, error_rate = error_rate_tail_progress_biomarker)
suppressMessages(n_min_progress_biomarker <- tibble_error_rate_tail_progress_biomarker %>% top_n(-1) %>% pull(n))
suppressMessages(error_rate_min_progress_biomarker <- tibble_error_rate_tail_progress_biomarker %>% top_n(-1) %>% pull(error_rate))
variable_selected_progress_biomarkers[[j]] <- str_replace_all(risk_progress_biomarker_variables_total[[105-n_min_progress_biomarker]], "_", "")
error_rate_min_progress_biomarkers[j] <- error_rate_min_progress_biomarker
print(paste("Finish", j))
}