[R-sig-ME] GLMM question

[Austin, Matt]

Thanks!

On 10/16/13 12:43 PM, "Jake Westfall" <jake987722 at hotmail.com> wrote:

>Hi Leena,
>
>Yes, p-values for tests of fixed effects can be found in various ways.
>See the FAQ here:
>
>http://glmm.wikidot.com/faq
>
>In particular see the sections "What is the best way to test hypotheses
>on effects in GLMMs?" and "Why doesn't lme4 display denominator degrees
>of freedom/p values? What other options do I have?"
>
>Note that most of these methods of obtaining p-values will *not* also
>come with an estimated degrees of freedom. My guess is that just having
>the p-value will satisfy the editor and the absence of DFs will not be a
>big deal. But if you decide that you do also want the degrees of freedom,
>you can use the Kenward-Roger procedure implemented in the pbkrtest
>package.
>
>Jake
>
>From: leena.hamberg at metla.fi
>To: r-sig-mixed-models at r-project.org
>Date: Wed, 16 Oct 2013 11:25:18 +0000
>Subject: [R-sig-ME] GLMM question
>
>Dear list members,
> 
>I would like to ask a question relating to generalized linear mixed
>models. I have used package lme4, function glmer to estimate my models
>(logit link for occurrences, log for counts and identity for height
>models). I presented the results of my models in our manuscript
>(coefficients with SE - significant ones highlighted). However, the
>editor asked me to add p-values, df:s, and test statistics to the result
>section every time I am presenting significant or insignificant results.
>I did as was asked and explained that degrees of freedom were not
>available for these models and that when normality was assumed (i.e., in
>the case of t statistics) p-values were not available. However, the
>editor answered as follows:
> 
>"In my previous e-mail I've requested you to add details of the
>statistical results in your MS (e.g., results of the GLM you've done,
>F-values, Chi2-values, df, P-values, etc.)... ...You did not take this
>comment fully into account and I disagree with your answer to this
>request. On the contrary to what you answered me, R (since you used R)
>provides all the detailed results you are requested to provide...
> 
>...Also, even if p-values, df and statistics are tightly interrelated,
>this does to prevent you to give the corresponding information in your
>published work, at least to help potential readers to verify what you
>wanted to say. P-values are always available in R - or can easily be
>found - for Gaussian or not normally distributed traits. So, you have to
>provide all the needed information is you MS. For example, every single
>t-test has to come with its df and P-value. If really you are not able to
>find this in R, then you have to use another program..."
> 
> 
>So how to proceed? Can df:s and p-values be found in any way using the R?
>If yes, how this can be done? Unfortunately I couldn't solve this problem
>by myself.
> 
>Here is an example of GLMMs estimated:
> 
>tyvivmaxp10P=glmer(Tkvmaxpit~käsittely+tyvilpm+m3haYHT+saastotKAIK+
>TKvHirvi+(1|ruutu),family=gaussian(link ="identity"), data=pihlajatE10)
> 
>summary(tyvivmaxp10P)
> 
>Linear mixed model fit by REML
>Formula: Tkvmaxpit ~ käsittely + tyvilpm + m3haYHT + saastotKAIK +
>TKvHirvi + (1 | ruutu)
>   Data: pihlajatE10
>   AIC  BIC logLik deviance REMLdev
>994.5 1015 -489.3    999.5   978.5
>Random effects:
>Groups   Name        Variance Std.Dev.
>ruutu    (Intercept)  207.25  14.396
> Residual             1255.73  35.436
>Number of obs: 100, groups: ruutu, 8
> 
>Fixed effects:
>             Estimate Std. Error t value
>(Intercept)  80.71047   17.52630   4.605
>käsittely2  -45.79590   13.98636  -3.274
>tyvilpm      22.06164    6.23251   3.540
>m3haYHT       0.11672    0.31592   0.369
>saastotKAIK   0.09566    0.11513   0.831
>TKvHirvi1    12.77524    8.55455   1.493
> 
>Correlation of Fixed Effects:
>            (Intr) ksttl2 tyvlpm m3hYHT ssKAIK
>käsittely2  -0.588
>tyvilpm     -0.662  0.126
>m3haYHT     -0.292  0.223  0.210
>saastotKAIK -0.408  0.199 -0.027 -0.192
>TKvHirvi1   -0.064 -0.124 -0.127 -0.029  0.006
> 
> 
> 
>Kind regards,
> 
>Leena Hamberg
> 
> 
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