data(bacteria,package="MASS")
bacteria$present <- as.numeric(bacteria$y)-1
## FIXME: restore when problems with new lme4 are sorted!
if (FALSE) {
library(lme4)
gfit <- glmer(present ~ trt + I(week > 2)+(1|ID),family = "binomial", data = bacteria,
optimizer="bobyqa", tolPwrss=1e-13, verbose=10)
}
library(glmmADMB)
if (!check_rforge()) {
bfit <- glmmadmb(present ~ trt + I(week > 2), random = ~ 1 | ID,
family = "binomial", data = bacteria)
if (!is.null(bfit$phi)) {
stopifnot(all.equal(bfit$phi,
glmmADMB:::make_phi(model.matrix(~trt+I(week>2),data=bacteria)),
tol=1e-4))
}
}
if (FALSE) {
gsd <- attr(lme4::VarCorr(gfit)[[1]],"stddev")
f <- lme4::fixef(gfit)
u <- unlist(lme4::ranef(gfit)[[1]])/gsd
bfit2 <-glmmadmb(present ~ trt + I(week > 2), random = ~ 1 | ID,
family = "binomial", data = bacteria,
start =list(fixed=f,RE_sd=log(gsd),u=u),
verbose=TRUE)
slist <- list(fixed=f,RE_sd=log(gsd),u=u)
bfit3 <-glmmadmb(present ~ trt + I(week > 2), random = ~ 1 | ID,
family = "binomial", data = bacteria,
start=slist,
extra.args="-phase 5",
verbose=TRUE)
}
## 9.6130683
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.