# [R-sig-ME] Poor convergence when using binomial response

Sundar Dorai-Raj sundar.dorai-raj at pdf.com
Wed May 23 03:15:11 CEST 2007

```Hi,

I'm seeing poor convergence of a model using the binomial family. In one
case, I have a binomial response for which I use the 'weights' argument.
In a second case, I expand the binomial response to Bernoulli trials and
refit. Theoretically, they should be the same model. However, that does
not appear to be the case because the residual scale for the binomial
case is unbelievably large. Could someone (Prof. Bates) please help
diagnose this problem?

And thank you so much for such wonderful software. I truly appreciate
the effort.

Thanks,

--sundar

tmp[2:4] <- lapply(tmp[2:4], factor)
library(lme4)
fit <- lmer(1 - y ~ z + (1 | A) + (1 | A:B), tmp,
binomial("cloglog"), weights = as.numeric(w))
## see below for expand.bin
tmp2 <- expand.bin(tmp, "x", "w")
fit2 <- lmer(x ~ z + (1 | A) + (1 | A:B), tmp2, binomial("cloglog"))

fit3 <- glm(1 - y ~ z, binomial("cloglog"), tmp, w)
fit4 <- glm(x ~ z, binomial("cloglog"), tmp2)

cbind(sapply(list(fit, fit2), fixef),
sapply(list(fit3, fit4), coef))
#                  [,1]       [,2]       [,3]       [,4]
#(Intercept) -2.8227711 -3.1247457 -2.8227711 -2.8227711
#z2          -0.2680992 -0.2694113 -0.2680992 -0.2680992
#z3           0.3109447  0.3233432  0.3109447  0.3109447

expand.bin <- function (data, x, n) {
char.x <- x
char.n <- n
x <- data[[x]]
n <- data[[n]]
i <- rep(seq(nrow(data)), n)
data <- data[i, , drop = FALSE]
expand <- function(z) c(rep(0, diff(z)), rep(1, z))
x <- apply(cbind(x, n), 1, expand)
data[[char.x]] <- if(is.matrix(x)) c(x) else unlist(x)
row.names(data) <- seq(nrow(data))
data
}

> sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
 "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
 "base"

other attached packages:
lme4      Matrix     lattice
"0.99875-0" "0.99875-1"    "0.15-6"

```