inst/testdata/glmmTMB_glmer_ar1_comparison.R

In lme4: Linear Mixed-Effects Models using 'Eigen' and S4

library(glmmTMB)

# Model 1; taken from github.com/lme4/lme4/issues/962
set.seed(101)
form <- out_bin_1 ~ ftime + trt + ar1(ftime + 0 | id_cluster) +
  (1 | id_individual)
sfun <- function(n) factor(sample(1:n, replace=TRUE, size = 1465))
dd <- data.frame(id_cluster = sfun(7), id_individual = sfun(486),
                 ftime = sfun(4), trt = sfun(2))
np <- list(beta = c(0, rep(0.1, 3), 1), theta = rep(0, 3))
dd$out_bin_1 <- simulate_new(form[-2], newdata = dd,
                             newparams = np,
                             family = binomial)[[1]]

dd$out_gauss <- simulate_new(form[-2], newdata = dd,
                             newparams = c(np, list(betadisp=0)),
                             family = gaussian)[[1]]

glmmTMB_1 <- glmmTMB(form, data = dd, family = binomial)

## store just results
glmmTMB_1_ref <- list(
  fixef_cond = unname(fixef(glmmTMB_1)$cond),
  sigma = unname(sigma(glmmTMB_1)),
  logLik = unname(c(logLik(glmmTMB_1))),
  AIC = unname(AIC(glmmTMB_1)),
  BIC = unname(BIC(glmmTMB_1)),
  nobs = nobs(glmmTMB_1),
  glmmTMB_version = packageVersion("glmmTMB")
)

glmmTMB_glmer_ar1_comparison <- list(
  glmer_ar1_dd = dd,
  glmmTMB_ar1_binomial = glmmTMB_1_ref
)

saveRDS(glmmTMB_glmer_ar1_comparison, "inst/testdata/glmmTMB_glmer_ar1_comparison.rds", version = 2)