R Under development (unstable) (2024-08-21 r87038 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(coxme)
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: 'bdsmatrix'

The following object is masked from 'package:base':

    backsolve

> aeq <- function(x, y) all.equal(as.vector(x), as.vector(y))
> options(na.action=na.exclude)
> 
> #
> # trivial test of strata
> #
> tdata0 <- data.frame(time  =c(5,4,1,1,2,2,2,2,3), 
+                      status=c(0,1,1,0,1,1,1,0,0),
+                      x1    =c(0,1,2,0,1,1,0,1,0),
+                      wt    =c(1,2,1,2,3,4,3,2,1),
+                      x2    =c(1,3,5,2,3,6,4,3,1),
+                      grp   =c(1,1,2,2,1,1,2,2,1))
> 
> rcnt <- c(3,2,1,1,1,2,2,1,3)  # rep count
> tdata0b <- data.frame(time2  = c(3,4,5, 2,4, 1,1,2, 1,2, .5,2, 2, 1,2,3), 
+ 		      time1  = c(0,3,4, 0,2, 0,0,0, 0,1, 0,.5, 0, 0,1,2),
+ 		      status = c(0,0,0, 0,1, 1,0,1, 0,1, 0, 1, 0, 0,0,0),
+                       x1     = rep(tdata0$x1, rcnt),
+                       wt     = rep(tdata0$wt, rcnt),
+                       x2     = rep(tdata0$x2, rcnt),
+                       grp    = rep(tdata0$grp, rcnt))
> 
> # Undo a gchol: given gchol(x), returns x
> igchol <- function(x) {
+     dd <- diag(x)
+     ll <- as.matrix(x)
+     ll %*% diag(dd) %*% t(ll)
+     }
> 
> tfit <- coxme(Surv(time, status) ~ x1 + x2 + (1|grp), data=tdata0,
+               vfixed=.5, weight=wt, iter=0,
+               ties='breslow', init=c(pi,0), sparse.calc=0)
> 
> sdata0 <- rbind(tdata0, tdata0)
> sdata0$strat <- rep(1:2, each=nrow(tdata0))
> 
> sfit0 <- coxme(Surv(time,status) ~ x1 + x2 + strata(strat) + (1|grp), 
+                data=sdata0, ties='breslow', iter=0, sparse.calc=0,
+ 	       vfixed=0.5, weight=wt, init=c(pi,0))
> 
> sfit1 <- coxme(Surv(time,status) ~ x1 + x2 + strata(strat) + (1|grp), 
+                data=sdata0, ties='breslow', iter=0, sparse.calc=1,
+ 	       vfixed=0.5, weight=wt, init=c(pi,0))
> 
> aeq(sfit0$u, sfit1$u)
[1] TRUE
> all.equal(sfit0$hmat, sfit1$hmat)
[1] TRUE
> aeq(sfit0$u/2, tfit$u)
[1] TRUE
> tpen <- diag(c(2,2,0,0))
> aeq(igchol(sfit0$hmat)-tpen, 2*(igchol(tfit$hmat)-tpen))
[1] TRUE
> 
> #
> # Repeat for start/stop data
> #   The subset makes the test more rigorous (someone exits a risk
> #   set without entering it immediatly again).
> tfit <- coxme(Surv(time1, time2, status) ~ x1 + x2 + (1|grp), data=tdata0b,
+               vfixed=0.6, weight=wt, iter=0,
+               ties='efron', init=c(pi,0), subset=(-1))
> 
> sdata0b <- rbind(tdata0b[-1,], tdata0b[-1,])
> sdata0b$strat <- rep(1:2, each=nrow(tdata0b)-1)
> 
> sfit0 <- coxme(Surv(time1,time2,status) ~ x1 + x2 + strata(strat) +(1|grp),
+ 	       data=sdata0b, iter=0, sparse.calc=0,
+ 	       vfixed=0.6, weight=wt, init=c(pi,0))
> sfit1 <- coxme(Surv(time1,time2,status) ~ x1 + x2 + strata(strat) + (1|grp),
+ 	       data=sdata0b, iter=0, sparse.calc=1,
+ 	       vfixed=0.6, weight=wt, init=c(pi,0))
> aeq(tfit$u, sfit0$u/2)
[1] TRUE
> aeq(sfit0$u, sfit1$u)
[1] TRUE
> tpen <- diag(c(1/.6, 1/.6, 0,0))
> aeq(sfit0$imat, sfit1$imat)
[1] TRUE
> aeq(igchol(sfit0$hmat)-tpen, 2*(igchol(tfit$hmat)-tpen))
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   1.62    0.28    1.87