[R] Nested variables
Mark Difford
mark_difford at yahoo.co.uk
Tue Jun 2 22:07:26 CEST 2009
Hi Daniel,
>> I read the chapter and it says that I can nest B in A by writing A/B. But
>> it doesnt seem to
>> work properly.
Then you need to read it again, and you need to play with some simple
models, so that you learn how to specify a model properly, using the formula
interface. (Achim Zeileis wrote the pscl function, which uses the formula
interface, so it almost certainly works as it should.)
It also is not at all clear what model you are trying to fit, since I only
have an R-specified model to go on, and your concept of what that means is
different from mine (and R's).
>> If I write Sps*Habitat/Site R somehow thinks that its a 3-way interaction
>> link and still
>> includes habitat as a single variable.
It will, because that is what you are specifying.
Reread this (from §11.1):
y ~ A*B
y ~ A + B + A:B
y ~ B %in% A
y ~ A/B
Two factor non-additive model of y on A and B. The first two specify the
same crossed classification and the second two specify the same nested
classification. In abstract terms all four specify the same model subspace.
And this (from §11.1):
y ~ (A + B + C)^2
y ~ A*B*C - A:B:C
Three factor experiment but with a model containing main effects and two
factor interactions only. Both formulae specify the same model.
What happens if you do something like the following?
zeroinfl(Visitation ~ Sps*Habitat/Site - Sps:Habitat:Site, data = data1)
zeroinfl(Visitation ~ Sps*Habitat/Site - Sps - Sps:Habitat:Site, data =
data1)
Regards,
Mark.
DanielWC wrote:
>
> Hi again
> I read the chapter and it says that I can nest B in A by writing A/B. But
> it doesnt seem to work properly. The package I use is pscl, I am trying to
> model zero inflated data. Here is the full model:
>
> zip1<-zeroinfl(Visitation ~ Habitat/Site + Sps + TP + Resource +
> Sps*Habitat/Site + Sps*Resource + Sps*TP + TP*Resource + TP*Habitat/Site |
> TP + Sps + Resource + Habitat/Site + TP*Sps + Sps*Resource + TP*Resource +
> TP*Habitat/Site, data = data1)
>
> where as you can see I have tried to include Habitat/Site. But it doesnt
> seem like its possible to create interaction links that way. I would like
> create the interaction link between say Sps and Habitat/Site. If I write
> Sps*Habitat/Site R somehow thinks that its a 3-way interaction link and
> still includes habitat as a single variable. Here is the summary just so
> you can see:
>
> Count model coefficients (poisson with log link):
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) 3.8643338 0.3450539 11.199 < 2e-16 ***
> Habitat -3.2757473 0.4871726 -6.724 1.77e-11 ***
> Sps -0.3332371 0.1117680 -2.982 0.00287 **
> TP -0.3857513 0.0975556 -3.954 7.68e-05 ***
> Resource 0.0130935 0.0009545 13.717 < 2e-16 ***
> Habitat:Site 0.2487012 0.0415908 5.980 2.24e-09 ***
> Habitat:Sps 0.5432845 0.1230434 4.415 1.01e-05 ***
> Sps:Resource -0.0041420 0.0002632 -15.738 < 2e-16 ***
> Sps:TP 0.0438085 0.0189411 2.313 0.02073 *
> TP:Resource -0.0009413 0.0002887 -3.260 0.00111 **
> Habitat:TP 0.1549435 0.1205884 1.285 0.19883
> Habitat:Site:Sps -0.0305628 0.0107794 -2.835 0.00458 **
> Habitat:Site:TP -0.0096408 0.0098497 -0.979 0.32768
>
> Zero-inflation model coefficients (binomial with logit link):
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) -1.3160850 0.8200631 -1.605 0.1085
> TP 0.2808474 0.2657544 1.057 0.2906
> Sps 0.8023648 0.1281520 6.261 3.82e-10 ***
> Resource -0.0075967 0.0035817 -2.121 0.0339 *
> Habitat -1.3122811 1.1348922 -1.156 0.2476
> Habitat:Site 0.1390498 0.0984716 1.412 0.1579
> TP:Sps -0.0189088 0.0406299 -0.465 0.6417
> Sps:Resource -0.0005548 0.0006843 -0.811 0.4175
> TP:Resource 0.0007100 0.0008454 0.840 0.4010
> TP:Habitat 0.7195254 0.3666809 1.962 0.0497 *
> TP:Habitat:Site -0.0782610 0.0314229 -2.491 0.0128 *
>
> Thanks again
>
>
> Mark Difford wrote:
>>
>> Daniel,
>>
>>>> Yes I am trying to model such data, and i need R to know that Site is
>>>> nested within Habitat.
>>>> Do I use some kind of command before running the model (like factor()
>>>> and so on) or do i
>>>> write it in the model formula. If so, how?
>>
>> You still are not telling the list enough, since nesting specifications
>> are sometimes package/program specific. You could help yourself by
>> reading some of R's basic documentation about how to specify a nested
>> model. Then "it" will tell you what to do.
>>
>> ?formula
>>
>> Or read §11.1 of "An Introduction to R" (one of R's manuals).
>>
>> Regards, Mark.
>>
>>
>> DanielWC wrote:
>>>
>>> Hi.
>>> Yes I am trying to model such data, and i need R to know that Site is
>>> nested within Habitat. Do I use some kind of command before running the
>>> model (like factor() and so on) or do i write it in the model formula.
>>> If so, how?
>>>
>>> Thanks
>>>
>>>
>>>
>>> Douglas Bates-2 wrote:
>>>>
>>>> On Fri, May 29, 2009 at 7:50 AM, DanielWC <daniel.carstensen at gmail.com>
>>>> wrote:
>>>>
>>>>> Hello
>>>>> I am working with a biological data including variables called Habitat
>>>>> and
>>>>> Site, example:
>>>>
>>>>> Habitat Site
>>>>
>>>>> Forest Low
>>>>> Forest Low
>>>>> Forest High
>>>>> Forest High
>>>>
>>>>> I want to tell R that the Site variable is nested within the Forest
>>>>> variable
>>>>> (that it is not a new variable).
>>>>> Does anyone know how to do this?
>>>>
>>>> If you could explain what you mean by "tell R", it would help. Are
>>>> you trying to model such data and you want to know how to express the
>>>> relationship between such factors in a model formula?
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>>
>>>
>>
>>
>
>
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