tests/testthat/test-idm.R

In tagteam/SmoothHazard: Estimation of Smooth Hazard Models for Interval-Censored Data with Applications to Survival and Illness-Death Models

### test-idm.R --- 
#----------------------------------------------------------------------
## author: Thomas Alexander Gerds
## created: Oct 22 2015 (13:57) 
## Version: 
## last-updated: Feb 25 2016 (08:43) 
##           By: Thomas Alexander Gerds
##     Update #: 9
#----------------------------------------------------------------------
## 
### Commentary: 
## 
### Change Log:
#----------------------------------------------------------------------
## 
### Code:
library(SmoothHazard)
library(testthat)

testthat::test_that("idm weibull paquid data with covariates",{
    data(Paq1000)
    set.seed(17)
    paq <- Paq1000[sample(1:NROW(Paq1000),size=200),]
    fit.weib <- idm(formula02=Hist(time=t,event=death,entry=e)~certif,
                    formula01=Hist(time=list(l,r),event=dementia)~certif,
                    data=paq)
    fit.weib2 <- idm(formula02=Hist(time=t,event=death,entry=e)~certif,
                    formula01=Hist(time=list(l,r),event=dementia)~certif,
                    formula12 = ~ 1,
                    data=paq)
    pred <- predict(fit.weib,70,t=80,newdata=data.frame(certif=1), conf.int = TRUE, nsim=4)
    pred2 <- predict(fit.weib2,70,t=80,newdata=data.frame(certif=1), conf.int = TRUE, nsim=4,lifeExpect=TRUE)
    expect_output(print(pred))
    expect_output(print(pred2))
})

testthat::test_that("idm splines paquid data without covariates",{
  data(Paq1000)
  set.seed(17)
  paq <- Paq1000[sample(1:NROW(Paq1000),size=200),]
  model2 <- idm(formula02=Hist(time=t,event=death, entry=e)~1,
                formula01=Hist(time=list(l,r),event=dementia)~1,
                data=paq,  method="Splines")
  s=66
  tseq <- 66:69
  p01_sp=matrix(0,length(tseq),4)
  p02_sp=matrix(0,length(tseq),4)
  p00_sp=matrix(0,length(tseq),4)
  for (t in tseq){
    # print(t)
    p_spo <- predict(model2,s,t) 
    p01_sp[(t-s)+1,]<- c(0,p_spo$transprob[2,2],p_spo$transprob[2,3],p_spo$transprob[2,4])
    p02_sp[(t-s)+1,]<- c(0,p_spo$transprob[7,2],p_spo$transprob[7,3],p_spo$transprob[7,4])
    p00_sp[(t-s)+1,]<- c(0,p_spo$transprob[1,2],p_spo$transprob[1,3],p_spo$transprob[1,4])
  }
  expect_output(print(p01_sp))
})
#----------------------------------------------------------------------
### test-idm.R ends here