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clustered data with glmer() and glmmPQL()

4 messages · Marsela Alvanopoulou, Thierry Onkelinx

Original
Marsela Alvanopoulou
# 
Hello,

I'm
? ?
a master student from
? ?
Greece. I?m trying to model count data with
? ?
GLMM (lme4
? ?
package), using as discrete response variable the number of parasites per
fish and as categorical predictor variable three
? ?
different species.
? ?
I'm using as random effect the three different tanks I used and as fixed
the infection level
??
.
?
?
This is the model I'm running:

mod
? ?
<-
? ?
glmer
? ?
(parasite~species+(1|tank),
? ?
family=poisson
??
, data=mydata)

I noticed that the estimate of the intercept does not give the mean of the
first species, so I ran a simple glm model to get the estimate. With
summary() I got the p values that allow me to reject my hypothesis and
continue
? ?
to the Tukey test. Is it legal to use
?
TukeyHSD(aov(parasite~species, data=mydata))
? ?
?
?
Finally I tested the assumptions
? ?
and
? ?
I found violation of normality and independence.

I also tried MASS package where the assumption of independent residuals was
not violated anymore but the histogram gave me a much more skewed
distribution, but also anova() is not available for QTLs.

mod2 <- glmmPQL (parasite~species, random=~1|tank, family=poisson,
data=mydata)

Thank you in advance for your help.

Maria
Thierry Onkelinx
# 
Dear Maria,

The assumption of normality is only required for the residuals of linear
(mixed) models, not for the residuals of generalised linear (mixed) models.

You can't use aov() for two reasons: it assumes a Gaussian distribution and
it assumes independent observations.

mod1 and mod2 are in principle the same model (but fitted differently).
Both assume the same correlation structure.

3 levels is not enough to get a sensible variance estimate for a random
effect. See glmm wiki faq for more details.

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-06-15 15:06 GMT+02:00 Marsela Alvanopoulou <marselalv at gmail.com>:

  
  


  


      

    

    

      
      

        


  

        

      Marsela Alvanopoulou
    

    

      
      #
    

  


  

      
Hi again,

Thank you very much for your response. I found most of the answers in glmm
wiki faq. I used MASS::glmmPQL for the model, car::Anova and multcomp::glht
for the hypothesis testing and I still need some work to check the effect
of the tank, if any.

I also want to check if there is a significant difference on the number of
parasites per gram (continuous response variable). I multiplied all values
by 100 to get a discrete variable like before. Does that affect the final
conclusions?

Thanks again!

On Mon, Jun 15, 2015 at 4:34 PM, Thierry Onkelinx <thierry.onkelinx at inbo.be>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Thierry Onkelinx
    

    

      
      #
    

  


  

      
You can use tank as a fixed effect instead of a random effect. In that case
your model reduces to a general linear model. Personally I prefer a
likelihood based model (glmer) over a penalised quasi-likelihood model
(glmmPQL) unless I need things that are not available with glmer.

You need to use the log(weight) of the fish as an offset factor instead of
calculating the ratio.

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-06-16 1:54 GMT+02:00 Marsela Alvanopoulou <marselalv at gmail.com>: