[R-sig-ME] Advice on GLMM with verIdent

[Diego Pavon]

Hello Thierry

Thanks for your answer!

I am interested in the interaction between period and phylogeny, to see
whether the trends differ between groups. If I understood correctly, I
shouldn't put something that I am interested in in the random part, am I
right?

Best

Di


2016-12-20 22:03 GMT+01:00 Thierry Onkelinx <thierry.onkelinx at inbo.be>:

> Dear Diego,
>
> The linear trend is required otherwise the optimum of the parabola is
> fixed a x = 0.
>
> You could try to fit the phylogeny effect as a random effect instead of a
> fixed effect. poly(Period, 2) | Phyloge ny and add species as a nested
> random intercept.
>
> If you have the individual latitudes you can try to use those instead of
> using only their average.
>
> 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
>
> 2016-12-20 17:49 GMT+01:00 Diego Pavon <diego.pavonjordan at gmail.com>:
>
>> Dear all,
>>
>> I write you because I need some advice about the model I want to fit to my
>> data, which I suspect it is not too 'correct'...
>>
>> My response variable is continuous (mean weighted latitude) of 24 species.
>> I have these mean latitudes calculated for 4 periods (95-99, 00-04, 05-09,
>> 10-13), for each species. Therefore I have 96 observations. I want to see
>> if there is a trend of the mean latitude over time (indicating a shift in
>> the population... all the species together). In this case, I would use
>> Period as a continuous varaible and not a factor. I want to fit a GLMM
>> with
>> random = SpeciesID. However, data exploration revealed a quadratic
>> relationship between my response (mean latitude) and Period (my continuous
>> covariate for time). But also, I am interested also to see whether there
>> are differences between functional groups (some species may move faster
>> than others). Thus I include the variable Phylogeny, which is a factor
>> with
>> 5 levels. Thus, the model in nlme notation is:
>>
>> lme(NEnessKM ~ Period_std + I(Period_std^2) + factor(Phylogeny)
>>           + Period_std : factor(Phylogeny) + I(Period_std^2) :
>> factor(Phylogeny),
>>           random = ~1| factor(Species),
>>           weights = varIdent(form =~ 1 | factor(Species)),
>>           control = ctrl2,
>>           method = "REML",
>>           data = NEness5y)
>>
>>
>> My concern is that this model might be too complicated. I have only 96
>> observation. If I follow the rule of 15 observation per parameter
>> estimated, this model i way to complex. I understand that in order to
>> include quadratic terms, one must include also the linear effect... and
>> that would also apply for the interactions. If the relationship between my
>> response (NEness = Mean Latitude) and Period is a parabola, I guess I
>> should include also the Period^2 in the interaction (Period^2 *
>> Phylogeny)?
>> But in that case, I have to include the interaction of Period * Phylogany?
>>
>> Is there a way to reduce the complexity? Is it totally wrong if I do not
>> include the linear effects and keep only Period^2?
>>
>> Thanks for sharing your knowledge and for the advice.
>>
>> Best
>>
>> Diego
>>
>>
>>
>>
>> --
>> *Diego Pavón Jordán*
>>
>> *Finnish Museum of Natural History*
>> *PO BOX 17 *
>>
>> *Helsinki. Finland*
>>
>> *0445061210https://www.researchgate.net/profile/Diego_Pavon-jordan
>> <https://www.researchgate.net/profile/Diego_Pavon-jordan>*
>>
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>>
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>
>
>


-- 
*Diego Pavón Jordán*

*Finnish Museum of Natural History*
*PO BOX 17 *

*Helsinki. Finland*

*0445061210https://www.researchgate.net/profile/Diego_Pavon-jordan
<https://www.researchgate.net/profile/Diego_Pavon-jordan>*

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