R help - Jul 2015 - R wont accept my zero count values in the GLM with quasi_poisson dsitribution

Hello

I have count values for abundance which follow a pattern of over-dispersal
with many zero values.  I have read a number of documents which suggest that
I don't use data transforming methods but rather than I run the GLM with the
quasi poisson distribution.  So I have written my script and R is telling me
that Y should be more than 0.

Everything I read tells me to do it this way but I can't get R to agree. 
Did I need to add something else to my script to get it to work and keep my
data untransformed? The script I wrote is as follows:
> fit <- glm(abundance~Gender,data=teminfest,family=binomial())
then I get this error 
Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1

I don't use R a lot so I am having trouble figuring out what to do next.

I would appreciate some help

Many Thanks
Charlotte






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Sent from the R help mailing list archive at Nabble.com.

You have selected the binomial family in the call to glm.  You should
instead try something like

 family=quasipoisson(link = "log")

I hope this helps

Andrew

On Tue, Jul 28, 2015 at 4:33 PM, Charlotte <
charlotte.hurry at griffithuni.edu.au> wrote:
> Hello
>
> I have count values for abundance which follow a pattern of over-dispersal
> with many zero values.  I have read a number of documents which suggest
> that
> I don't use data transforming methods but rather than I run the GLM
with
> the
> quasi poisson distribution.  So I have written my script and R is telling
> me
> that Y should be more than 0.
>
> Everything I read tells me to do it this way but I can't get R to
agree.
> Did I need to add something else to my script to get it to work and keep my
> data untransformed? The script I wrote is as follows:
>
> > fit <- glm(abundance~Gender,data=teminfest,family=binomial())
>
> then I get this error
> Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1
>
> I don't use R a lot so I am having trouble figuring out what to do
next.
>
> I would appreciate some help
>
> Many Thanks
> Charlotte
>
>
>
>
>
>
> --
> View this message in context:
>
http://r.789695.n4.nabble.com/R-wont-accept-my-zero-count-values-in-the-GLM-with-quasi-poisson-dsitribution-tp4710462.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>


-- 
Andrew Robinson
Deputy Director, CEBRA, School of Biosciences
Reader & Associate Professor in Applied Statistics  Tel: (+61) 0403 138 955
School of Mathematics and Statistics                        Fax: +61-3-8344
4599
University of Melbourne, VIC 3010 Australia
Email: a.robinson at ms.unimelb.edu.au
Website: http://www.ms.unimelb.edu.au/~andrewpr

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SPuR: http://www.ms.unimelb.edu.au/spuRs/

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On 28/07/15 08:33, Charlotte wrote:
> Hello
>
> I have count values for abundance which follow a pattern of
> over-dispersal with many zero values.  I have read a number of
> documents which suggest that I don't use data transforming methods
> but rather than I run the GLM with the quasi poisson distribution.
> So I have written my script and R is telling me that Y should be more
> than 0.
No,  R  is telling you that you must have 0 <= y <= 1 (see below).
For count data you should not use the binomial family, but rather 
'poisson', or 'quasipoisson'.

?family

G?ran
> Everything I read tells me to do it this way but I can't get R to
> agree. Did I need to add something else to my script to get it to
> work and keep my data untransformed? The script I wrote is as
> follows:
>
>> fit <- glm(abundance~Gender,data=teminfest,family=binomial())
>
> then I get this error Error in eval(expr, envir, enclos) : y values
> must be 0 <= y <= 1
>
> I don't use R a lot so I am having trouble figuring out what to do
> next.
>
> I would appreciate some help
>
> Many Thanks Charlotte
>
>
>
>
>
>
> -- View this message in context:
>
http://r.789695.n4.nabble.com/R-wont-accept-my-zero-count-values-in-the-GLM-with-quasi-poisson-dsitribution-tp4710462.html
>
>
Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________ R-help at r-project.org
> mailing list -- To UNSUBSCRIBE and more, see
> 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.
>

On 7/28/2015 3:05 AM, G?ran Brostr?m wrote:
>
>
> On 28/07/15 08:33, Charlotte wrote:
>> Hello
>>
>> I have count values for abundance which follow a pattern of
>> over-dispersal with many zero values.  I have read a number of
>> documents which suggest that I don't use data transforming methods
>> but rather than I run the GLM with the quasi poisson distribution.
>> So I have written my script and R is telling me that Y should be more
>> than 0.
>
> No,  R  is telling you that you must have 0 <= y <= 1 (see below).
> For count data you should not use the binomial family, but rather
> 'poisson', or 'quasipoisson'.

With excess zeros, overdispersion is the symptom, but the quasipoisson
model is not the cure.
Even better than quasipoisson would be to use a ZIP (zero-inflated 
poisson) model or a hurdle model to explicitly model the
excess zeros.

These are handled by the countreg package, at present only
available on R-Forge.

  install.packages("countreg",
repos="http://R-Forge.R-project.org")

>
>> ______________________________________________ R-help at r-project.org
>> mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>

based on your code "fit <-
glm(abundance~Gender,data=teminfest,family=binomial())", i don't see
anything related to quasi_poisson. are you sure what you are doing
here?

On Tue, Jul 28, 2015 at 1:33 AM, Charlotte
<charlotte.hurry at griffithuni.edu.au> wrote:
> Hello
>
> I have count values for abundance which follow a pattern of over-dispersal
> with many zero values.  I have read a number of documents which suggest
that
> I don't use data transforming methods but rather than I run the GLM
with the
> quasi poisson distribution.  So I have written my script and R is telling
me
> that Y should be more than 0.
>
> Everything I read tells me to do it this way but I can't get R to
agree.
> Did I need to add something else to my script to get it to work and keep my
> data untransformed? The script I wrote is as follows:
>
>> fit <- glm(abundance~Gender,data=teminfest,family=binomial())
>
> then I get this error
> Error in eval(expr, envir, enclos) : y values must be 0 <= y <= 1
>
> I don't use R a lot so I am having trouble figuring out what to do
next.
>
> I would appreciate some help
>
> Many Thanks
> Charlotte
>
>
>
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/R-wont-accept-my-zero-count-values-in-the-GLM-with-quasi-poisson-dsitribution-tp4710462.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.


-- 
WenSui Liu
https://statcompute.wordpress.com/