I haven't been following the discussion too closely, but the default fixed effect prior used by blme makes the most sense if the various inputs are standardized to have a mean 0 and an sd of 0.5. I also just noticed that the default degrees of freedom for the t is off in the generalized case: it should be 3 instead of 5. You can use Gelman's default prior for logistic regression (http://www.jstor.org/stable/30245139) if you standardized the inputs and call bglmer with:

  bglmer(case~sex+PC1+PC2+PC3+PC4+(1|famid), family=binomial, data=test.dat.std, fixef.prior=t(df = 1), cov.prior = NULL)

There I also removed the default covariance prior because I'm not sure that it is intended in this case.

Vince

On Mar 18, 2014, at 10:34 PM, Ming-Huei Chen wrote:

> I just installed latest lme4. Here is the result... 
> 
>> 
> blme::bglmer(case~sex+PC1+PC2+PC3+PC4+(1|famid),family=binomial,data=test.da
> t,fixef.prior=t)
> Cov prior  : famid ~ wishart(df = 3.5, scale = Inf, posterior.scale = cov,
> common.scale = TRUE)
> Fixef prior: t(df = 5, scale = c(100, 0, 0, 0, ...), common.scale = FALSE)
> Prior dev  : 16.1703
> 
> Generalized linear mixed model fit by maximum likelihood (Laplace
>  Approximation) [bglmerMod]
> Family: binomial ( logit )
> Formula: case ~ sex + PC1 + PC2 + PC3 + PC4 + (1 | famid)
>   Data: test.dat
>      AIC       BIC    logLik  deviance  df.resid
> 3005.889  3052.986 -1495.944  2991.889      6168
> Random effects:
> Groups Name        Std.Dev.
> famid  (Intercept) 19.89
> Number of obs: 6175, groups: famid, 1592
> Fixed Effects:
> (Intercept)          sex          PC1          PC2          PC3          PC4
>   -10.2654       0.3371      -0.3533      -0.1078      -0.2225       0.1102
> 
> -----Original Message-----
> From: Ben Bolker [mailto:bbolker@gmail.com] 
> Sent: Tuesday, March 18, 2014 4:31 PM
> To: Ming-Huei Chen; 'Vincent Dorie'
> Cc: 'Yang, Qiong'; 'r-sig-mixed-models';
> 'lme4-authors@lists.r-forge.r-project.org'
> Subject: Re: [R-sig-ME] gee, geese and glmer
> 
> On 14-03-18 02:51 PM, Ming-Huei Chen wrote:
>> Is lme4_1.1-4 out-of-date? This is the version I used and encountered 
>> the error.
>> 
>> Best,
>> 
>> Ming-Huei
> 
>  Yes, 1.1-5 was released on CRAN recently (and blme did some updating to
> match).
> 
>  Ben Bolker
> 
>> 
>> -----Original Message-----
>> From: Vincent Dorie [mailto:vjd4@nyu.edu]
>> Sent: Tuesday, March 18, 2014 11:48 AM
>> To: Ben Bolker
>> Cc: Yang, Qiong; Ming-Huei Chen; r-sig-mixed-models; 
>> lme4-authors@lists.r-forge.r-project.org
>> Subject: Re: [R-sig-ME] gee, geese and glmer
>> 
>>>> 
>>>> blme::bglmer(case~sex+PC1+PC2+PC3+PC4+(1|famid),family=binomial,data
>>>> =
>>>> test.da
>>>> t,fixef.prior=t)
>>>> Error in get("checkConv", lme4Env)(attr(opt, "derivs"), opt$par, 
>>>> ctrl = control$checkConv,  :
>>>> unused argument (ctrl = control$checkConv)
>> 
>> I believe this can only happen if the installed version of lme4 is 
>> out-of-date. If there was a point where checkConv was added but didn't 
>> yet have the ctrl formal, you would see that error.
>> 
>> Vince
>> 
> 


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