Dr. Stevens,
I've double-checked my variable lengths. All of my variables
(Total.vines, Site, Species, and DBH) came in at 549. I did correct
one problem in the data entry that had escaped my previous notice:
somehow the undergrad who entered all the data managed to make the
Acer negundo data split into two separate categories while still
appearing to use the same ACNE abbreviation. When I made that
correction and re-ran zicounts, R gave me the following error messages:
> vines.zip<-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site
+Species+DBH,distname=ZIP,data=sycamores.1)
Error in ifelse(y == 0, 1, y/mu) : dim<-: dims [product 12] do not
match the length of object [549]
In addition: Warning messages:
1: longer object length is not a multiple of shorter object length
in: eta + offset
2: longer object length is not a multiple of shorter object length
in: y/mu
In addition, zicounts would not run a normal poisson regression on
the data, giving me the same error messages as the ZIP regression.
Doing a poisson regression with glm did not show any error messages.
However, the glm model with full interactions was still over-dispersed.
Could the zicounts problem be that the individual sites and species
had different population sizes? For instance, Site A had 149 trees,
site B had 55 trees, site C had 270 trees, and site D had 75 trees.
The species had similar discrepancies in population sizes, with
Platanus occidentalis and Acer negundo forming the majority of the
trees.
Thanks for your help.
Jim Milks
Graduate Student
Environmental Sciences Ph.D. Program
136 Biological Sciences
Wright State University
3640 Colonel Glenn Hwy
Dayton, OH 45435
On Aug 15, 2007, at 5:58 AM, Martin Henry H. Stevens wrote:
> Hi Jim,
> With regard to same number, I simply wanted to make sure that each
> variable was the same length. The error message you show is what
> you would get if, for instance, you misspelled one of the variables
> and it doesn't exist, in which case it would be NULL, while your
> other variables would each be 550 elements in length.
> Hank
> On Aug 14, 2007, at 4:47 PM, James Milks wrote:
>
>> Dr. Stevens,
>>
>> Unfortunately, Poisson gives me an over-dispersed model with only
>> 3 out of 14 variables/interactions significant. Doing a step-wise
>> poisson regression still ended up with the same over-dispersed
>> model. Given the high number of zeros in the response variable,
>> Dr. Thad Tarpey (one of our statisticians on campus) suggested
>> zero-inflated poisson regression as a possible solution to the
>> over-dispersion problem.
>>
>> As for variables of the same length, there are different numbers
>> of trees for each species and site since we ran different numbers
>> of transects at each site (some sites were larger than others) and
>> there were different numbers of species and trees within each
>> transect. Acer negundo made up ~33% of all the trees we measured;
>> Platanus occidentalis had 25%; Fraxinus americana was another 12%
>> and ~11% was Ulmus americana. The remaining 25% was divided among
>> 16 other species, all of which were excluded from the analysis due
>> to singularities in the model when they were included (something
>> about glm not liking singularities in the model). So if the
>> zicounts requires that each species and site have the same length,
>> then I will not be able to use it unless I can get R to randomly
>> select x trees from each species and site combination.
>>
>> Thanks for your input.
>>
>> Jim Milks
>>
>> Graduate Student
>> Environmental Sciences Ph.D. Program
>> 136 Biological Sciences
>> Wright State University
>> 3640 Colonel Glenn Hwy
>> Dayton, OH 45435
>>
>>
>> On Aug 14, 2007, at 9:37 AM, Hank Stevens wrote:
>>
>>> Hi Jim,
>>> Two thoughts come to me, unencumbered by the thought process or
>>> knowledge of zicounts:
>>> 1. Is Poisson really NOT appropriate? (do you have to use zicounts?)
>>> 2. Are you 110% certain that all variables are the same length?
>>> Would NA's interfere?
>>> Cheers,
>>> Hank
>>> On Aug 13, 2007, at 5:10 PM, James Milks wrote:
>>>
>>>> I have data on number of vines per tree for ~550 trees. Over
>>>> half of
>>>> the trees did not have any vines and the data is fairly skewed
>>>> (median = 0, mean = 1.158, 3rd qu. = 1.000). I am attempting to
>>>> investigate whether plot location (four sites), species (I'm using
>>>> only the four most common species), or tree dbh has a significant
>>>> influence on the number of vines per tree. When I attempted to use
>>>> the zicounts function, R gave me the following error message:
>>>>
>>>>> vines.zip<-zicounts(resp=Total.vines~.,x=~Site+Species+DBH,z=~Site
>>>> +Species+DBH,distrname="ZIP",data=sycamores.1)
>>>> Error in ifelse(y == 0, 1, y/mu) : dim<- : dims [product 12] do not
>>>> match the length of object [549]
>>>> In addition: Warning messages:
>>>> 1: longer object length
>>>> is not a multiple of shorter object length in: x[good, ]
>>>> * w
>>>> 2: longer object length
>>>> is not a multiple of shorter object length in: eta + offset
>>>> 3: longer object length
>>>> is not a multiple of shorter object length in: y/mu
>>>>
>>>> I do not know enough about the calculations done in the function to
>>>> interpret the error messages. Is there a glitch in my data and if
>>>> yes, what is it?
>>>>
>>>> Thanks for your help.
>>>>
>>>> Jim Milks
>>>>
>>>> Graduate Student
>>>> Environmental Sciences Ph.D. Program
>>>> 136 Biological Sciences
>>>> Wright State University
>>>> 3640 Colonel Glenn Hwy
>>>> Dayton, OH 45435
>>>>
>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help@stat.math.ethz.ch 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.
>>>
>>>
>>>
>>> Dr. Hank Stevens, Associate Professor
>>> 338 Pearson Hall
>>> Botany Department
>>> Miami University
>>> Oxford, OH 45056
>>>
>>> Office: (513) 529-4206
>>> Lab: (513) 529-4262
>>> FAX: (513) 529-4243
>>> http://www.cas.muohio.edu/~stevenmh/
>>> http://www.muohio.edu/ecology/
>>> http://www.muohio.edu/botany/
>>>
>>> "E Pluribus Unum"
>>>
>>>
>>>
>>>
>>>
>>
>
> Dr. Hank Stevens, Associate Professor
> 338 Pearson Hall
> Botany Department
> Miami University
> Oxford, OH 45056
>
> Office: (513) 529-4206
> Lab: (513) 529-4262
> FAX: (513) 529-4243
> http://www.cas.muohio.edu/~stevenmh/
> http://www.muohio.edu/ecology/
> http://www.muohio.edu/botany/
> "E Pluribus Unum"
>
> If you send an attachment, please try to send it in a format anyone
> can read, such as PDF, text, Open Document Format, HTML, or RTF.
> Please try not to send me MS Word or PowerPoint attachments-
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>
>
>
>
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