R Under development (unstable) (2024-03-03 r86036 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', contrasts=c('contr.treatment', 'contr.poly'))
> aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
> 
> #
> # Test of fitting random slopes
> #
> # Same data set as slope1, refit using variance matrices
> #
> set.seed(56)
> n.subject <- seq(180, by=21, length=9) # number of subjects
> slope <- sort(-.5 + rnorm(9, sd=.5))         # true treament effects
> 
> inst <- rep(1:9, n.subject)
> n <- length(inst)
> simdata <- data.frame(id=1:n, inst=inst,
+                       trt= rep(0:1, length=n),
+                       age= runif(n, 40, 70))
> #risk goes up 30%/decade of age
> simdata$hazard <- .8* exp(simdata$trt * rep(slope, n.subject) +
+                           (simdata$age-55) * .03)
> 
> rtime <- function(hazard, censor=c(1,2)) {
+     stime <- rexp(length(hazard), rate=hazard)
+     ctime <- runif(length(hazard), censor[1], censor[2])
+     list(time= pmin(stime, ctime), status=1*(stime <=ctime))
+     }
> temp <- rtime(simdata$hazard)
> simdata$time <- temp$time
> simdata$status <- temp$status
> 
> #Check fit1
> fit1 <- coxme(Surv(time, status) ~ age + trt + (1|inst), simdata)
> fit1b <- coxme(Surv(time, status) ~ age + trt + (1|inst), simdata,
+                varlist=diag(9))
> aeq(fit1$log, fit1b$log)
[1] TRUE
> aeq(as.matrix(fit1$var), as.matrix(fit1b$var))
[1] TRUE
> aeq(fixef(fit1), fixef(fit1b))
[1] TRUE
> 
> # Check fit2
> #  To get the same iteration path you need to force the same
> #  starting estimates
> idlist <- sort(outer(1:9, 0:1, paste, sep='/'))
> fit2 <- coxme(Surv(time, status) ~ age + trt + (1|inst/trt), simdata,
+                varlist=coxmeFull(collapse=TRUE), vinit=c(.1, .1))
> 
> mat1 <- matrix(diag(18), 18, dimnames=list(idlist, idlist))
> mat2 <-  bdsBlock(idlist, rep(1:9, each=2))
> fit2b <- coxme(Surv(time, status) ~ age + trt + (1|inst/trt), simdata,
+                varlist=list(mat1, mat2), vinit=c(.1, .1))
> aeq(fit2$log, fit2b$log)
[1] TRUE
> aeq(as.matrix(fit2$var), as.matrix(fit2b$var), tol=1e-7)
[1] TRUE
> aeq(fixef(fit2), fixef(fit2b))
[1] TRUE
> 
> # Check fit3
> # This takes two different paths to the solution, due to use of a
> #  slope coefficient rather than nested.  So results are a bit
> fit3 <- coxme(Surv(time, status) ~ age + trt + (1|inst) + (trt|inst),simdata,
+               vinit=list(.1, .2))
> mat3 <- diag(rep(0:1, 9))
> dimnames(mat3) <- list(idlist, idlist)
> fit3b <-  coxme(Surv(time, status) ~ age + trt + (1|inst/trt), simdata,
+                varlist=coxmeMlist(list(mat2, mat3), rescale=F, pdcheck=F),
+                vinit=c(.1, .2))
> 
> aeq(fit3$log, fit3b$log)
[1] TRUE
> aeq(fixef(fit3), fixef(fit3b))
[1] TRUE
> all.equal(unlist(VarCorr(fit3)), unlist(VarCorr(fit3b)), tolerance=1e-7, 
+           check.attributes=FALSE)
[1] TRUE
> # This function should map between coefficients
> map <- matrix(0, 20,20)
> for (i in 1:9) {
+     map[i, 2*i -1] <- 1
+     map[i+9, 2*i -1] <- -1
+     map[i+9, 2*i] <- 1
+     }
> map[19,19] <- 1
> map[20,20] <- 1
> 
> # Some of the random effects are very close to zero
> aeq(unlist(ranef(fit3)), c(map[1:18,1:18] %*% unlist(ranef(fit3b))),
+     tol=1e-7)
[1] TRUE
> aeq(as.matrix(fit3$var), map %*% as.matrix(fit3b$var) %*% t(map),
+     tol=1e-7)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   2.48    0.18    2.60