[R-sig-ME] GLMM for Combined experiments and overdispersed data

Juan Pablo Edwards Molina edwardsmolina at gmail.com
Mon Apr 24 17:27:36 CEST 2017


Yes, tree_id uses unique code over blocks and farms: ​each bk is
only present in one farm and each tree is present in only one bk. (tree_id
structure: farm_bk_tree)

By this way the model can handle the overdispersion (If I'm not mistaken)

Thank you all,

*Juan*

On Mon, Apr 24, 2017 at 11:46 AM, Thierry Onkelinx <thierry.onkelinx at inbo.be
> wrote:

> Dear Peter,
>
> Both models will yield identical results in case tree_id uses unique codes
> over the blocks.
>
> 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
>
> 2017-04-24 15:55 GMT+02:00 Peter Claussen <dakotajudo at mac.com>:
>
>> Juan,
>>
>> I would model this as
>>
>> m3 = glmer(resp ~ trt * farm +  (1| bk/tree), family = binomial, data=df)
>> or
>> m3 = glmer(resp ~ trt * farm +  (1| bk) +  (1| tree_id), family =
>> binomial, data=df)
>> (I can’t say off the top of my head if what the difference would be if
>> you’re dealing with over-dispersion).
>>
>> 1. I’m assuming that block is a somewhat uniform grouping of trees, so
>> that including block in the model gives you an estimate of spatial
>> variability in the response, and if that is important relative to
>> tree-to-tree variation.
>>
>> 2. You will most certainly want to include trt*farm to test for
>> treatment-by-environment interaction. If interaction is not significant,
>> you may choose to exclude interaction from the model. If there is
>> interaction, then you will want to examine each farm to determine if
>> cross-over interaction present.
>>
>> If your experiment is to determine the “best” fungicide spraying system,
>> and cross-over interaction is present, then you have no “best” system. You
>> might have cross-over arising because, say, system 1 ranks “best” on farm
>> 1, but system 2 ranks “best” on farm 2.
>>
>> There is extensive literature on the topic, mostly from the plant
>> breeding genotype-by-environment interaction side. Some of the associated
>> statistics implemented in the agricolae package, i.e. AMMI.
>>
>> Peter
>>
>> > On Apr 24, 2017, at 6:56 AM, Juan Pablo Edwards Molina <
>> edwardsmolina at gmail.com> wrote:
>> >
>> > I´m sorry... I´m new in the list, and when I figured out that the
>> question
>> > would suit best in the mixed model list I had already post it in general
>> > R-help. I don´t know if there´s a way to "cancel a question"... I will
>> take
>> > care of it from now on.
>> >
>> > Dear Thierry, thanks for your answer.
>> > Yes, I am not interested in the effect of a specific farm, they simply
>> > represent the total of farms from the region where I want to suggest the
>> > best treatments.
>> >
>> > I Followed your suggestions, but still have a couple of doubts,
>> >
>> > 1- May "farm" be include as a simple fixed effect or interacting with
>> the
>> > treatment?
>> >
>> > m3 = glmer(resp ~ trt * farm + (1|tree_id), family = binomial, data=df)
>> > m4 = glmer(resp ~ trt + farm + (1|tree_id), family = binomial, data=df)
>> >
>> > ​2 - ​
>> > In case of significant
>> > ​[ trt * farm ], should I report the results for each farm?​
>> >
>> > Thanks again Thierry,
>> >
>> > Juan Edwards
>> >
>> >
>> > *Juan*
>> >
>> > On Mon, Apr 24, 2017 at 4:29 AM, Thierry Onkelinx <
>> thierry.onkelinx at inbo.be>
>> > wrote:
>> >
>> >> Dear Juan,
>> >>
>> >> Use unique id's for random effects variables.
>> ​​
>> So each bk should only be
>> >> present in one farm. And each tree_id should be present in only one
>> bk. In
>> >> case each block has different treatments then each tree_id should be
>> unique
>> >> to one combination of bk and trt.
>> >>
>> >> Farm has too few levels to be a random effects. So either model is as a
>> >> fixed effect or drop it. In case you drop it, the information will be
>> >> picked up by bk. Note that trt + (1|farm) is less complex than trt *
>> farm.
>> >>
>> >> Assuming that you are not interested in the effect of a specific farm,
>> you
>> >> could use sum, polynomial or helmert contrasts for the farms. Unlike
>> the
>> >> default treatment contrast, these type of contrasts sum to zero. Thus
>> the
>> >> effect of trt will be that for the average farm instead of the
>> reference
>> >> farm.
>> >>
>> >> 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
>> >>
>> >> 2017-04-21 22:32 GMT+02:00 Juan Pablo Edwards Molina <
>> >> edwardsmolina at gmail.com>:
>> >>
>> >>> I am analyzing data from 3 field experiments (farms=3) for a citrus
>> flower
>> >>> disease: response variable is binomial because the flower can only be
>> >>> diseased or healthy.
>> >>>
>> >>> I have particular interest in comparing 5 fungicide spraying systems
>> >>> (trt=5).
>> >>>
>> >>> Each farm had 4 blocks (bk=4) including 2 trees as subsamples
>> (tree=2) in
>> >>> which I assessed 100 flowers each one. This is a quick look of the
>> data:
>> >>>
>> >>> farm      trt      bk    tree   dis   tot     <fctr>   <fctr>  <fctr>
>> >>> <fctr> <int> <int>
>> >>> iaras      cal      1      1     0    100
>> >>> iaras      cal      1      2     1    100
>> >>> iaras      cal      2      1     1    100
>> >>> iaras      cal      2      2     3    100
>> >>> iaras      cal      3      1     0    100
>> >>> iaras      cal      3      2     5    100...
>> >>>
>> >>> The model I considered was:
>> >>>
>> >>> resp <- with(df, cbind(dis, tot-dis))
>> >>>
>> >>> m1 = glmer(resp ~ trt + (1|farm/bk) , family = binomial, data=df)
>> >>>
>> >>> I tested the overdispersion with the overdisp_fun() from GLMM page
>> >>> <http://glmm.wikidot.com/faq>
>> >>>
>> >>>        chisq         ratio             p          logp
>> >>> 4.191645e+02  3.742540e+00  4.804126e-37 -8.362617e+01
>> >>>
>> >>> As ratio (residual dev/residual df) > 1, and the p-value < 0.05, I
>> >>> considered to add the observation level random effect (link
>> >>> <http://r.789695.n4.nabble.com/Question-on-overdispersion-td
>> 3049898.html
>> >>>> )
>> >>> to deal with the overdispersion.
>> >>>
>> >>> farm      trt      bk    tree   dis   tot tree_id    <fctr>   <fctr>
>> >>> <fctr> <fctr> <int> <int> <fctr>
>> >>> iaras      cal      1      1     0    100    1
>> >>> iaras      cal      1      2     1    100    2
>> >>> iaras      cal      2      1     1    100    3...
>> >>>
>> >>> so now was added a random effect for each row (tree_id) to the model,
>> but
>> >>> I
>> >>> am not sure of how to include it. This is my approach:
>> >>>
>> >>> m2 = glmer(resp ~ trt + (1|farm/bk) + (1|tree_id), family = binomial,
>> >>> data=df)
>> >>>
>> >>> I also wonder if farm should be a fixed effect, since it has only 3
>> >>> levels...
>> >>>
>> >>> m3 = glmer(resp ~ trt * farm + (1|farm:bk) + (1|tree_id), family =
>> >>> binomial, data=df)
>> >>>
>> >>> I really appreciate your suggestions about my model specifications...
>> >>>
>> >>>
>> >>>
>> >>> *Juan​ Edwards- - - - - - - - - - - - - - - - - - - - - - - -# PhD
>> student
>> >>> - ESALQ-USP/Brazil*
>> >>>
>> >>>        [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
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>> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >>
>> >>
>> >>
>> >
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>> >
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