Xsurv: This function can fit the survival data with different model...

In topycyao/Xsurv: A package used to model survival data from advanced machine learning algorithms

This function can fit the survival data with different model including xgboost,lightgbm,random forests, and gbm.

Description

This function can fit the survival data with different model including xgboost,lightgbm,random forests, and gbm.

Usage

Xsurv(
  datax,
  datay,
  top_n = NULL,
  option = c("defaut", "xgb", "lgb", "gbm", "rf"),
  method = c("defaut", "pl", "C"),
  nfolds = 5,
  nround = NULL,
  lambda = NULL,
  alpha = NULL,
  eta = NULL,
  early_stopping_rounds = NULL,
  gtree = NULL,
  ncores = NULL,
  gfrac = NULL,
  gsh = NULL,
  rfnsp = NULL,
  cp = NULL,
  maxdpth = NULL
)

Arguments

datax	X data set
datay	Y data set including time and event status
top_n	number of top features for survival tree fitting(avaliable for xgb and lgb)
option	model fitting option,defaut is xgb
method	fitting metohd,defaut is 'pl' means using loss function:coxph likelihood
nfolds	number of folds for crossvalidation
lambda	l1 penalty parameter
alpha	l2 penalty parameter
eta	learning rate
early_stopping_rounds	force a stopping round
gtree	number of trees using in gbm model
ncores	number of cores using in gbm
gfrac	bag fraction in gbm with defaut 0.5
gsh	shrinkage paramter in gbm with defaut 0.001
rfnsp	number of splits in random forests
number	of rounds

Value

a list object containing:model,cindex,tree,SHAP and risk

Examples

#example
library(survival)
library(Xsurv)
data(lung)

mydata<-(lung[,-1])
mydata[,2]<-mydata[,2]-1
length(mydata[,1])
names(mydata)<-colnames(mydata)
datay_train<-mydata[1:180,c(1,2)]
datax_train<-mydata[1:180,-c(1,2)]
datay_test<-mydata[181:228,c(1,2)]
datax_test<-mydata[181:228,-c(1,2)]
xs<-Xsurv(datax_train,datay_train,top_n = 5,cp=0.01)

#xs<-Xsurv.cv(datax_train,datay_train,top_n=5)
xm<-xs$model
xtree<-xs$tree
x_ctree<-xtree$tree2
#plot(x_ctree)
shap=xs$SHAP

shap

risk=xs$risk
fit=risk$fit

#plot(fit)
#prediction

pre_time<-pre<-Xsurv_predict(xm,datax_train,datay_train,datax_test)

#predict survival probabilty

pre_x<-Xsurv_predict_sv(xm,datax_train,datay_train,datax_test[1,])

plot(pre_x)

topycyao/Xsurv documentation built on Aug. 6, 2022, 9:06 p.m.