R Under development (unstable) (2024-08-21 r87038 ucrt) -- "Unsuffered Consequences"
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> library(coxme)
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: 'bdsmatrix'

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

    backsolve

> options(na.action='na.exclude')
> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
> 
> #
> # Similar to test1.s, but with the rats data.  This has enough groups to
> #  force sparse matrix computations.
> #
> femrat <- rats[rats$sex=='f',] 
> contr.none <- function(n,contrasts=T) {
+         if(is.numeric(n) && length(n) == 1.)
+                 levs <- 1.:n
+         else {
+                 levs <- n
+                 n <- length(n)
+         }
+         contr <- array(0., c(n, n), list(levs, levs))
+         contr[seq(1., n^2., n + 1.)] <- 1.
+ 	contr
+ 	}
> options(contrasts=c('contr.none', 'contr.poly'))
> 
> theta <- pi/2
> 
> # First with no sparse
> fit0 <- coxme(Surv(time, status) ~ rx + (1|litter), data=femrat,
+ 	      vfixed=theta, iter=0, sparse=c(100, .001))
> tfit <- coxph(Surv(time, status) ~ factor(litter) + rx,
+               data=femrat, x=T, iter=0)
> dt0 <- coxph.detail(tfit)
> 
> aeq(apply(dt0$score,2,sum), fit0$u)
[1] TRUE
> h0 <- apply(dt0$imat,1:2,sum) + diag(c(rep(1/theta, 50),0))
> aeq(as.matrix(gchol(h0)), as.matrix(fit0$hmat))
[1] TRUE
> aeq(diag(gchol(h0)), diag(fit0$hmat))
[1] TRUE
> aeq(diag(fit0$var), diag(solve(h0)))
[1] TRUE
> 
> 
> # then sparse
> fit0 <- coxme(Surv(time, status) ~ rx + (1|litter), data=femrat,
+ 	      vfixed=theta, iter=0, sparse=c(20, .1))
> 
> h0[1:50,1:50] <- diag(diag(h0)[1:50])
> aeq(as.matrix(gchol(h0)), as.matrix(fit0$hmat))
[1] TRUE
> aeq(diag(gchol(h0)), diag(fit0$hmat))
[1] TRUE
> aeq(diag(fit0$var), diag(solve(h0)))
[1] TRUE
> 
> # Now iteration 1
> fit1 <- coxme(Surv(time, status) ~ rx + (1|litter), data=femrat,
+               vfixed=theta, iter=1, sparse=c(10, .1))
> update0 <- solve(fit0$hmat, fit0$u)
> update0[1:50] <- update0[1:50] - mean(update0[1:50])
> aeq(update0, c(unlist(ranef(fit1)), fixef(fit1)))
[1] TRUE
> tfit <- coxph(Surv(time, status) ~ factor(litter) + rx,
+               data=femrat, x=T, iter=0,
+               init=c(unlist(ranef(fit1)), fixef(fit1)))
> dt1 <- coxph.detail(tfit)
> 
> aeq(apply(dt1$score,2,sum)- c(unlist(ranef(fit1)), 0)/theta, fit1$u)
[1] TRUE
> h1 <- apply(dt1$imat,1:2,sum) + diag(c(rep(1/theta, 50),0))
> h1[1:50,1:50] <- diag(diag(h1)[1:50])
> aeq(as.matrix(gchol(h1)), as.matrix(fit1$hmat))
[1] TRUE
> aeq(diag(gchol(h1)), diag(fit1$hmat))
[1] TRUE
> aeq(diag(fit1$var), diag(solve(h1)))
[1] TRUE
> 
> 
> # And iteration 2
> fit2 <- coxme(Surv(time, status) ~ rx + (1|litter), data=femrat,
+               vfixed=theta, iter=2)
> 
> update1 <- solve(fit1$hmat, fit1$u)
> update1[1:50] <- update1[1:50] - mean(update1[1:50])
> aeq(update1, c(unlist(ranef(fit2)), fixef(fit2)) -
+     c(unlist(ranef(fit1)), fixef(fit1)))
[1] TRUE
> 
> #
> # Same computation, using a specified matrix
> #
> fit2b <- coxme(Surv(time, status) ~ rx + (1|litter), data=femrat,
+               vfixed=theta, iter=2, varlist=bdsI(seq(1, 99, 2)))
> all.equal(fit2b$u, fit2$u)
[1] TRUE
> all.equal(fit2b$variance, fit2$variance)
[1] TRUE
> all.equal(fit2b$loglik, fit2$loglik)
[1] TRUE
> 
> 
> 
> proc.time()
   user  system elapsed 
   1.82    0.21    1.98