R help - Aug 2006 - fixed effects following lmer and mcmcsamp - which to present?

Dear all,

I am running a mixed model using lmer. In order to obtain CI of 
individual coefficients I use mcmcsamp. However, I need advice which 
values that are most appropriate to present in result section of a 
paper. I have not used mixed models and lmer so much before so my 
question is probably very naive. However, to avoid to much problems with 
journal editors and referees addicted to p-values, I would appreciate 
advice of which values of the output for the fixed factor that would be 
most appropriate to present in a result section, in order to convince 
them of the p-value free 'lmer-mcmcsamp'-approach!

Using the example from the help page on lmer:

fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)

...I obtain the following for 'Days':


summary(fm1)
...
            Estimate Std. Error  t value

Days         10.4673     1.5458    6.771


...and from mcmcsamp:

summary(mcmcsamp(fm1 , n = 10000))

1. Empirical mean and standard deviation for each variable,
   plus standard error of the mean:

                        Mean     SD Naive SE Time-series SE
Days                 10.4695 1.7354 0.017354       0.015921

2. Quantiles for each variable:
                        2.5%       25%       50%       75%    97.5%
Days                  7.0227    9.3395   10.4712   11.5719   13.957



The standard way of presenting coefficients following a 'non-lmer' 
output is often (beta=..., SE=..., statistic=..., P=...). What would be 
the best equivalent in a 'lmer-mcmcsamp-context'? (beta=..., CI=...) is 
a good start I believe. But which beta? And what else?

I assume that the a 95% CI in this case would be 7.0227-13.957 (please, 
do correct me I have completely misunderstood!). But which would be the 
corresponding beta? 10.4673?, 10.4695? 10.4712? Is the t-value worth 
presenting or is it 'useless' without corresponding degrees of freedom 
and P-value? If I present the mcmcsamp-CI, does it make sense to present 
any of the three SE obtained in the output above? BTW, I have no idea 
what Naive SE, Time-series SE means. Could not find much in help and 
pdfs to coda or Matrix, or in Google.

Thanks in advance for any advice and hints to help-texts I have missed!


Best regards,

Henrik

On 8/8/06, Henrik Parn <henrik.parn at bio.ntnu.no>
wrote:
> Dear all,
>
> I am running a mixed model using lmer. In order to obtain CI of
> individual coefficients I use mcmcsamp. However, I need advice which
> values that are most appropriate to present in result section of a
> paper. I have not used mixed models and lmer so much before so my
> question is probably very naive. However, to avoid to much problems with
> journal editors and referees addicted to p-values, I would appreciate
> advice of which values of the output for the fixed factor that would be
> most appropriate to present in a result section, in order to convince
> them of the p-value free 'lmer-mcmcsamp'-approach!
>
> Using the example from the help page on lmer:
>
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
>
> ...I obtain the following for 'Days':
>
>
> summary(fm1)
> ...
>             Estimate Std. Error  t value
>
> Days         10.4673     1.5458    6.771
>
>
> ...and from mcmcsamp:
>
> summary(mcmcsamp(fm1 , n = 10000))
>
> 1. Empirical mean and standard deviation for each variable,
>    plus standard error of the mean:
>
>                         Mean     SD Naive SE Time-series SE
> Days                 10.4695 1.7354 0.017354       0.015921
>
> 2. Quantiles for each variable:
>                         2.5%       25%       50%       75%    97.5%
> Days                  7.0227    9.3395   10.4712   11.5719   13.957
>
>
>
> The standard way of presenting coefficients following a 'non-lmer'
> output is often (beta=..., SE=..., statistic=..., P=...). What would be
> the best equivalent in a 'lmer-mcmcsamp-context'? (beta=...,
CI=...) is
> a good start I believe. But which beta? And what else?
>
> I assume that the a 95% CI in this case would be 7.0227-13.957 (please,
> do correct me I have completely misunderstood!). But which would be the
> corresponding beta? 10.4673?, 10.4695? 10.4712? Is the t-value worth
> presenting or is it 'useless' without corresponding degrees of
freedom
> and P-value? If I present the mcmcsamp-CI, does it make sense to present
> any of the three SE obtained in the output above? BTW, I have no idea
> what Naive SE, Time-series SE means. Could not find much in help and
> pdfs to coda or Matrix, or in Google.
I would definitely report the REML value 10.4673 as the estimate.
This is a reproducible estimate - the other two are stochastic in that
you will get different values from different mcmcsamp runs.  However,
the reproducibility is high.  Notice that they all round to 10.47 and
two decimal places is quite enough precision for reporting this value
when you consider that  a 95% confidence interval is  [7.02,13.96].

Another way of evaluating a confidence interval using the coda package
is the HPDinterval function.  (HPD stands for "Highest Posterior
Density")  It returns the shortest interval with a 95% probability
content in the empirical distribution.

Here are values from a sample that I evaluated
> data(sleepstudy)
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> fs1 <- mcmcsamp(fm1, 10000)
> library(coda)
> summary(fs1)
...
1. Empirical mean and standard deviation for each variable,
   plus standard error of the mean:

                        Mean     SD Naive SE Time-series SE
Days                 10.4810 1.6910 0.016910       0.015762

2. Quantiles for each variable:

                        2.5%       25%       50%       75%    97.5%
Days                  7.0975    9.3971   10.4851   11.5751   13.810
> fixef(fm1)
(Intercept)        Days
  251.40510    10.46729
> HPDinterval(fs1)
                         lower       upper
Days                  7.038076   13.734493
attr(,"Probability")
[1] 0.95

If you would like to use a t-distribution to calculate a confidence
interval, I would argue that the degrees of freedom for the t should
be somewhere between n - p = 178 in this case (n = number of
observations, p = number of coefficients in the fixed effects or
rank(X) where X is the model matrix for the fixed effects) and n -
rank([Z:X]) = 144.  (there are 36 random effects and 2 fixed effects
but the rank of [Z:X] = 36)

If we use the lower value of 144 we produce a confidence interval of
> 10.4673 + c(-1,1) * qt(0.975, df = 144) * 1.5458
[1]  7.41191 13.52269

Notice that this interval is contained in the HPD interval and in the
interval obtained from the 2.5% and 97.5% quantiles of the empirical
distribution.  I attribute this to the fact that the standard errors
are calculated conditional on the variance of the random effects.
Thus the t-based confidence interval takes into account imprecision of
the estimate of \sigma^2 but it assumes that the variance of the
random effects is fixed at the estimated values.  (That's not quite
true - it is the relative variance that is assumed fixed - but the
effect is the same.) The MCMC sample allows all the parameters to vary
and I would claim is therefore a better measure of the marginal
variability of this parameter.

However, as stated above, the HPD interval is stochastic.  I would
create more than one sample to check the reproducibility of the
intervals.  In this case intervals based on a chain of length 10000
are not wonderfully consistent

Days                  6.9389037   13.851661
Days                  6.9968306   13.768851

and I might go to chains of length 50000 to check further

Days                  7.0880422   13.903068
Days                  7.0758948   13.965146

For the benefit of editors of a biological journal I think I would
report both the interval derived from the t-distribution and a
representative interval from the MCMC samples to show that the MCMC
samples show variation in excess of that reported by the t interval.



I hope this helps.

--Doug