[R] Predicted values for zero-inflated Poisson

Tue Jul 10 15:45:39 CEST 2012

On Tue, 10 Jul 2012, Laura Lee wrote:

> Alain-
>
> Thanks again for the response. I guess my question is more related to R, 
> which I'm learning as I go along. Could you provide guidance as to how I 
> would code this in R?

That depends on what exactly you want to predict.

As Alain said: The type="count" predictions are probably not interesting 
to you. In the JSS paper accompanying zeroinfl, these correspond to 
exp(x'b) in Equation 8.

More interesting is probably the mean (1 - pi) * exp(x'b) which is the 
expected mean mu_i in Equation 8. This can be obtained as type="response".

Additionally, you might be interested in the individual probabilities for 
counts of 0, 1, 2, ... etc. This corresponds to evaluating Equation 7 
for y = 0, 1, 2, ... which can be obtained via type="prob". And from this 
you could also get the mode or median rather than the mean of the 
distribution.

hth,
Z

> Thanks,
> Laura
>
> From: Alain Zuur [via R] [mailto:ml-node+s789695n4635920h92 at n4.nabble.com]
> Sent: Monday, July 09, 2012 5:20 PM
> To: Lee, Laura
> Subject: Re: Predicted values for zero-inflated Poisson
>
> Laura Lee laura.lee at ncdenr.gov
> Mon Jul 9 22:51:40 CEST 2012
>
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> Thanks for your reply. I do have a copy of "Zero Inflated Models and
> Generalized Linear Mixed Models with R" and have been using that as a guide.
> I applied the predict function (type="count") to the dataset for which I
> built the model to compare the predicted bycatch numbers to the observed to
> ensure I was doing things correctly. When I summed over the new predicted
> variable, the value is over 500 whereas there were less than 10 observed.
> I'd appreciate any advice regarding what I'm doing wrong.
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Predicted-values-for-zero-inflated-Poisson-tp4635861p4635916.html
> Sent from the R help mailing list archive at Nabble.com.
>
>
>
>
> AFZ:
> Laura....no...you don't want to compare the count part of the model with raw data....you need to compare
> the Exp(Y) = (1-pi) * mu with the raw data. Have a look at the Epilogue chapter....it shows the difference
> between mu and (1-pi) * mu.
>
>
>
> Alain
>
>
>
>
>
>
>
> --
>
> Dr. Alain F. Zuur
> First author of:
>
> 1. Analysing Ecological Data (2007).
> Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.
> URL: www.springer.com/0-387-45967-7<http://www.springer.com/0-387-45967-7>
>
>
> 2. Mixed effects models and extensions in ecology with R. (2009).
> Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.
> http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9
>
>
> 3. A Beginner's Guide to R (2009).
> Zuur, AF, Ieno, EN, Meesters, EHWG. Springer
> http://www.springer.com/statistics/computational/book/978-0-387-93836-3
>
>
> 4. Zero Inflated Models and Generalized Linear Mixed Models with R. (2012) Zuur, Saveliev, Ieno.
> http://www.highstat.com/book4.htm
>
> Other books: http://www.highstat.com/books.htm
>
>
> Statistical consultancy, courses, data analysis and software
> Highland Statistics Ltd.
> 6 Laverock road
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> Tel: 0044 1358 788177
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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> Dr. Alain F. Zuur
> First author of:
>
> 1. Analysing Ecological Data (2007).
> Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.
> URL: www.springer.com/0-387-45967-7<http://www.springer.com/0-387-45967-7>
>
>
> 2. Mixed effects models and extensions in ecology with R. (2009).
> Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.
> http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9
>
>
> 3. A Beginner's Guide to R (2009).
> Zuur, AF, Ieno, EN, Meesters, EHWG. Springer
> http://www.springer.com/statistics/computational/book/978-0-387-93836-3
>
>
> Other books: http://www.highstat.com/books.htm
>
>
> Statistical consultancy, courses, data analysis and software
> Highland Statistics Ltd.
> 6 Laverock road
> UK - AB41 6FN Newburgh
> Tel: 0044 1358 788177
> Email: highstat at highstat.com<mailto:highstat at highstat.com>
> URL: www.highstat.com<http://www.highstat.com>
> URL: www.brodgar.com<http://www.brodgar.com>
>
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> -----
> Laura M. Lee
> Senior Stock Assessment Scientist
> North Carolina Division of Marine Fisheries
> E-Mail: laura.lee at ncdenr.gov
> --
> View this message in context: http://r.789695.n4.nabble.com/Predicted-values-for-zero-inflated-Poisson-tp4635861p4635978.html
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