Running 'asthma.R' [171s]
  Running 'culling.R' [5s]
  Running 'insem.R' [5s]
  Running 'mastitis.R' [14s]
  Running 'select.parfm.R' [26s]
Running the tests in 'tests/asthma.R' failed.
Complete output:
  > library(parfm)
  Loading required package: survival
  Loading required package: optimx
  > data(asthma)
  > head(asthma)
    Patid Begin End Status Drug Fevent
  1     1     0  15      1    0      1
  2     1    22  90      1    0      0
  3     1    96 325      1    0      0
  4     1   329 332      1    0      0
  5     1   338 369      1    0      0
  6     1   370 412      1    0      0
  > asthma <- asthma[asthma$Fevent==0,]
  > 
  > set.seed(1)
  > data <- asthma[sample(1:nrow(asthma), 200),]
  > 
  > parfm(Surv(Begin, End, Status)~Drug, cluster="Patid", 
  +       data=data, dist="weibull", frailty="gamma")
  
  Frailty distribution: gamma 
  Baseline hazard distribution: Weibull 
  Loglikelihood: -906.338 
  
         ESTIMATE SE    p-val 
  theta   0.000               
  rho     0.754               
  lambda  0.079               
  Drug   -0.004   0.104 0.969 
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  Kendall's Tau: 0 
  Warning messages:
  1: In parfm(Surv(Begin, End, Status) ~ Drug, cluster = "Patid", data = data,  :
    optimisation procedure did not converge,
                conv = : see ?optimx for details
  2: In parfm(Surv(Begin, End, Status) ~ Drug, cluster = "Patid", data = data,  :
    negative variances have been replaced by NAs
   Please, try other initial values or another optimisation method
  > 
  > data$time <- data$End - data$Begin
  > 
  > parfm(Surv(time, Status)~Drug, cluster="Patid", data=data,
  +       dist="weibull", frailty="gamma")
  
  Frailty distribution: gamma 
  Baseline hazard distribution: Weibull 
  Loglikelihood: -897.482 
  
         ESTIMATE SE    p-val 
  theta   0.289   0.157       
  rho     0.901   0.073       
  lambda  0.028   0.008       
  Drug   -0.024   0.194 0.901 
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  Kendall's Tau: 0.126 
  > 
  > proc.time()
     user  system elapsed 
    15.20    0.51   15.65