[R-sig-ME] Start values for glmer: Bug?

[Ben Bolker]

Adam D. I. Kramer wrote:
> Hello,
> 
>  	I'm fitting a model something like this:
> 
> s1d2.s <- glmer(chosen ~ rating + option + option2 + rating:option +
> rating:option2 + (distNum|studyID), data=cc2, family=binomial)
> 
> ...pretty straightforward. Of course, it doesn't converge...boo. So I turn
> on verbose, and see that it's starting with some really improbable values. 
> So I plug in some start values from other similar matrices that fit and some
> good guesses, and it chugs along and finishes, but gives me a warning I do
> not understand.
> 
> These are my start values:
> 
>> arg
> [[1]]
>              (Intercept) distNum
> (Intercept)         1.9     0.0
> distNum            -0.1     0.5
> 
>> fe
>     (Intercept)         rating         option        option2  rating:option
>         -7.5000         1.1000        -0.3000         0.0090         0.0500 
> rating:option2        distNum     condition1     condition2
>         -0.0025         0.2000         0.1000         0.1000
> 
> ...this is my call:
> s1d2.s <- glmer(chosen ~ rating + option + option2 + rating:option +
> rating:option2 + (distNum|studyID), data=cc2, family=binomial, verbose=TRUE,
> start=list(ST=arg,fixef=fe[1:6]))
> 
> ...and this is the eventual completion, with the warning message I do not
> understand:
> 
>   65:     1633.7847:  2.71240 0.719770 -0.228343 -8.32184  1.56395 -0.0683526
> 0.00144433 0.0226594 -0.000315729
> Warning message:
> In sort(names(start)) == sort(names(FL)) :
>    longer object length is not a multiple of shorter object length
> 
> ...the first-round verbose output does indeed use my provided start values,
> in the right order. The summary table, eventually, also uses names(fe)
> instead of the actual variable names passed to glmer...which I would argue
> is inappropriate behavior. But it's the problem with the length of the names
> of `start` that has me confused.
> 
> The help page says that I should be passing a list with items ST and fixef,
> and I'm doing that, and it's working...
> 
> Advice?

  Provide a reproducible example?
  (Not really meant to be snarky.  lme4 is still fairly bleeding-edge,
and it's quite possible that you have exposed a bug of some sort, but
without digging into it it's hard to tell.)

  or

debug(lme4:::glmer_finalize)

  and see what's going on (the test causing the warning is in the first
line of this function).

  In fact, digging around further suggests that this is indeed a bug I'm
not sure I've correctly reconstructed the logic of the test, which is
currently

  if (is.list(start) && all(sort(names(start)) == sort(names(FL))))
        start <- list(ST = start)

 FL comes from a call to lmerFactorList, which returns a list with
elements "trms" (terms), "fl" (factor list), and "dims" (dimensions &
auxiliary information).  Based on the logic of the help page, it seems
that perhaps the test should be

if (is.list(start) && length(start)==length(FL$fl) &&
all(sort(names(start)) == sort(names(FL$fl))))
        start <- list(ST = start)

  ?

  cheers
    Ben Bolker