tests/testthat/test-plotRisk.R

In riskRegression: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

### test-plotRisk.R --- 
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## Author: Thomas Alexander Gerds
## Created: Sep 15 2022 (16:04) 
## Version: 
## Last-Updated: Sep 16 2022 (12:56) 
##           By: Thomas Alexander Gerds
##     Update #: 4
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## 
### Commentary: 
## 
### Change Log:
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## 
### Code:
library(riskRegression)
library(testthat)
library(rms)
library(prodlim)
library(cmprsk)
library(survival)
library(data.table)
library(lava)
test_that("More than one competing risk",{
 set.seed(8)
 learndat = sampleData(80,outcome="competing.risk")
 testdat = sampleData(140,outcome="competing.risk")
 setkey(learndat,time)
 setkey(testdat,time)
 learndat[,event := as.character(event)]
 testdat[,event := as.character(event)]
 learndat[9:17,event := "cr2"]
 testdat[9:17,event := "cr2"]
 m1 = FGR(Hist(time,event)~X2+X7+X9,data=learndat,cause=1)
 m2 = CSC(Hist(time,event)~X2+X7+X9,data=learndat,cause=1)
 xcr=Score(list("FGR"=m1,"CSC"=m2),formula=Hist(time,event)~1,
          data=testdat,summary="risks",null.model=0L,times=c(3,5))
 plotRisk(xcr,times=3)
 # check when no censored before time horizon
 testdat[time <= 3 & event == 0, event := 1]
 xcr=Score(list("FGR"=m1,"CSC"=m2),formula=Hist(time,event)~1,
          data=testdat,summary="risks",null.model=0L,times=c(3,5))
 plotRisk(xcr,times=3)
 # check when no censored in all data
 testdat[event == 0, event := 1]
 xcr=Score(list("FGR"=m1,"CSC"=m2),formula=Hist(time,event)~1,
          data=testdat,summary="risks",null.model=0L,times=c(3,5))
 plotRisk(xcr,times=3)
 # check when no event-free at horizon
 testdat[event == 0, event := 1]
 Score(list("FGR"=m1,"CSC"=m2),formula=Hist(time,event)~1,
       data=testdat,summary="risks",null.model=0L,times=c(3,8))
 # all predicted risks of model m2 are NA
 expect_error(xcr=Score(list("FGR"=m1,"CSC"=m2),formula=Hist(time,event)~1,
          data=testdat,summary="risks",null.model=0L,times=c(3,8)))
})


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### test-plotRisk.R ends here