[R-sig-ME] rare binary outcome, MCMCglmm, and priors

Thu Sep 9 00:00:33 CEST 2010

Hi Dave,
I was wondering if you happened to have finished these analyses and whether
the greater variance in the priors "worked". I coincidentally have a paper
in review (well, waiting on the AE recommendation actually-which I typically
assume means impending rejection!) which I now realize likely had a similar
problem to what you encountered. Like you I had some ridiculously large
odds-ratios and I only came across the Gelman et al. (2008, Annals) paper
after submission. I doubt the reanalysis would change the inferences but I'd
prefer to have the analysis done correctly.

Thanks a lot,
Ned

--
Ned Dochtermann
Department of Biology
University of Nevada, Reno

ned.dochtermann at gmail.com
http://wolfweb.unr.edu/homepage/mpeacock/Dochter/
--

Message: 2
Date: Tue, 31 Aug 2010 11:42:14 -0700
From: David Atkins <datkins at u.washington.edu>
To: Jarrod Hadfield <j.hadfield at ed.ac.uk>
Cc: "r-sig-mixed-models at r-project.org"
	<r-sig-mixed-models at r-project.org>
Subject: Re: [R-sig-ME] rare binary outcome, MCMCglmm, and priors
	(related to separation)
Message-ID: <4C7D4D06.2050507 at u.washington.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Jarrod--

Per usual, thanks for the input; I've got the Gelman et al. (2008) 
article and have some models running.  I'll update with what I find.

cheers, Dave

Dave Atkins, PhD
Research Associate Professor
Department of Psychiatry and Behavioral Science
University of Washington
datkins at u.washington.edu

Center for the Study of Health and Risk Behaviors (CSHRB)		
1100 NE 45th Street, Suite 300 	
Seattle, WA  98105 	
206-616-3879 	
http://depts.washington.edu/cshrb/
(Mon-Wed)	

Center for Healthcare Improvement, for Addictions, Mental Illness,
   Medically Vulnerable Populations (CHAMMP)
325 9th Avenue, 2HH-15
Box 359911
Seattle, WA 98104
http://www.chammp.org
(Thurs)

On 8/31/10 2:43 AM, Jarrod Hadfield wrote:
> Hi Dave,
>
> With respect to the prior specification for the fixed effects, you may
> want to make the variance larger. Perhaps something like:
>
> prior$B$V = diag(7)*(3+pi^2/3)
>
> The motivation behind this is to choose a prior for b, for which
> plogis(Xb+Zu+e) would be close to a uniform after marginalising the
> random effects u and e. pi^2/3 is the variance of the logistic
> distribution (the cdf of which is the inverse logit function) and 3 is
> the variance of Zu+e assuming Z is an identity matrix (1 for the
> residual variance + ~2 for the person variance). You can see it is
> pretty close for an intercept.
>
> priorB<-rnorm(1000, 0, sqrt(3+pi^2/3))
> priorMB<-1:1000
> for(i in 1:1000){
> priorMB[i]<-mean(plogis(priorB[i]+rnorm(1000,0,sqrt(3))))
> }
> hist(priorMB)
>
> This example works for a model with a single intercept, and when fitting
> a categorical predictor I usually remove the intercept (-1) so that the
> distribution is approximately uniform for all levels of the predictor.
> For continuous covariates and interactions it will be a bit more
> involved and you should probably read Gelman et. al. 2008 Annals of
> Applied Statistics 1360-1383.
>
> Using a prior with a variance of one will shrink the estimates to less
> extreme values and may explain some of the differences between models.
> However, if anything this new prior is likely to make the mixing worse
> rather than better. Two options that may speed up mixing are using
> slice=TRUE in the call to MCMCglmm. This will use slice sampling to
> update the latent variables rather then MH updates. You could also use
> parameter expanded priors for G, but from your output it does not look
> like the variance is hitting zero so it is unlikely to improve things.
>
> Cheers,
>
> Jarrod
>
>
>
>
>
> On 30 Aug 2010, at 21:37, David Atkins wrote:
>
>>
>> Some colleagues have collected data from 184 females in dating
>> relationships. Data were collected daily using PDAs; the outcome is a
>> binary indicator of whether any physical aggression occurred (intimate
>> partner violence, or IPV).
>>
>> They are interested in 3 covariates:
>>
>> -- alcohol use: yes/no
>> -- anger: rated on 1-5 scale
>> -- verbal aggression: sum of handful of items, with 0-15 scale
>>
>> Their hypothesis is that the interaction of all 3 covariates will lead
>> to the highest likelihood of IPV. As you might expect, the outcome is
>> very rare with 51 instances of IPV out of 8,269 days of data, and 158
>> women (out of 184) reported no instances of IPV.
>>
>> Question 1: Given that a GLMM will assume a normal distribution for
>> the person-specific baserate in IPV, is this data even appropriate for
>> GLMM or should they be looking elsewhere (perhaps GEE)?
>>
>> That said, for some (unknown) proportion of individuals, there
>> probably would be instances of IPV if the data collection period were
>> longer. Thus, perhaps there is some basis for assuming a distribution
>> across people, even if the observed data for some individuals are all
>> zeroes.
>>
>> To present some of the data (and I can check to see if it would be
>> okay to make the data available), I dichotomized both anger and verbal
>> aggression ("prov.cut" below):
>>
>> ang.cut prov.cut alc.cut ipv.yes ipv.no
>> 1 0 0 0 0 3918
>> 2 0 0 1 0 1
>> 3 1 0 0 5 2381
>> 4 1 0 1 1 292
>> 5 1 1 0 36 1471
>> 6 1 1 1 9 257
>>
>> Thus, the instances of IPV are more likely when there is anger and
>> verbal aggression; alcohol is a little less clear. (And, if the
>> association of anger and verbal aggression with IPV seems
>> tautological, there has been debate about different forms of IPV,
>> where some research has pointed to "cold" aggression.)
>>
>> Not surprisingly, analyses using either glmer() or MCMCglmm() show
>> signs of partial separation, with some whopping odds-ratios and 95% CI
>> spanning a couple orders of magnitude.
>>
>> I have read a bit about the problems of separation in logistic
>> regression and know that Gelman et al suggest Bayesian priors as one
>> "solution". Moreover, I see in Jarrod Hadfield's course notes that his
>> multinomial example has a "structural" zero that he addresses via
>> priors on pp. 96-97, though I confess I don't quite follow exactly
>> what he has done (and why).
>>
>> If I just let MCMCglmm cook on a regression with all 2-way
>> interactions for a long while:
>>
>> prior = list(R = list(V = 1, fix = 1),
>> B = list(mu = c(rep(0,7)), V = diag(7)),
>> G = list(G1 = list(V = 1, nu = 0.002)))
>> lr.mcmc <- MCMCglmm(ipv ~ (alc.cut + angc + log(provc + 0.03))^2, data
>> = ipv.df,
>> family = "categorical", verbose = TRUE,
>> prior = prior,
>> nitt = 2000000, burnin = 1000000, thin = 1000,
>> random = ~ person)
>>
>> The answers are less extreme than what I get with glmer, perhaps
>> suggesting this is wandering toward the "correct" solution, though
>> there are also plenty of indicators that we aren't there yet:
>>
>> > summary(lr.mcmc)
>>
>> Iterations = 1999001
>> Thinning interval = 1000001
>> Sample size = 1000
>>
>> DIC: 379.972
>>
>> G-structure: ~person
>>
>> post.mean l-95% CI u-95% CI eff.samp
>> person 2.287 0.6775 4.206 194.0
>>
>> R-structure: ~units
>>
>> post.mean l-95% CI u-95% CI eff.samp
>> units 1 1 1 0
>>
>> Location effects: ipv ~ (alc.cut + angc + log(provc + 0.03))^2
>>
>> post.mean l-95% CI u-95% CI eff.samp pMCMC
>> (Intercept) -2.58724 -3.49492 -1.65250 245.20 <0.001 ***
>> alc.cut 0.49512 -0.75268 1.99397 1000.00 0.464
>> angc 0.02664 -0.34227 0.41365 283.90 0.880
>> log(provc + 0.03) 1.36626 0.98743 1.70863 28.69 <0.001 ***
>> alc.cut:angc -0.16519 -0.79299 0.41949 683.56 0.590
>> alc.cut:log(provc + 0.03) -0.02631 -0.53118 0.55065 157.34 0.898
>> angc:log(provc + 0.03) -0.26132 -0.40141 -0.10407 74.98 0.004 **
>> ---
>> Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
>>
>> I haven't run multiple chains yet, but the effective sample sizes and
>> trace plots already suggest we ain't there yet. My specific question
>> is whether there would be an alternative prior specification for the
>> fixed-effects that would be more appropriate?
>>
>> I would appreciate any and all thoughts here, including if this just
>> doesn't seem like an appropriate data/question for GLMMs.
>>
>> sessionInfo below.
>>
>> cheers, Dave
>>
>> > sessionInfo()
>> R version 2.11.1 (2010-05-31)
>> i386-apple-darwin9.8.0
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats4 splines stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] MCMCglmm_2.06 corpcor_1.5.7 ape_2.5-3
>> [4] coda_0.13-5 Matrix_0.999375-44 lattice_0.19-10
>> [7] tensorA_0.35 Hmisc_3.8-2 modeltools_0.2-16
>> [10] mvtnorm_0.9-92 survival_2.36-1
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.13.1 coin_1.0-16 colorspace_1.0-1 gee_4.13-15
>> [5] grid_2.11.1 lme4_0.999375-35 nlme_3.1-96 party_0.9-9998
>> [9] rpart_3.1-46 tools_2.11.1
>>
>> --
>> Dave Atkins, PhD
>> Research Associate Professor
>> Department of Psychiatry and Behavioral Science
>> University of Washington
>> datkins at u.washington.edu
>>
>> Center for the Study of Health and Risk Behaviors (CSHRB)
>> 1100 NE 45th Street, Suite 300
>> Seattle, WA 98105
>> 206-616-3879
>> http://depts.washington.edu/cshrb/
>> (Mon-Wed)
>>
>> Center for Healthcare Improvement, for Addictions, Mental Illness,
>> Medically Vulnerable Populations (CHAMMP)
>> 325 9th Avenue, 2HH-15
>> Box 359911
>> Seattle, WA 98104
>> http://www.chammp.org
>> (Thurs)
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
>
>

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