Re: [R-sig-eco] hurdle model

2010-08-19 Thread Ben Bolker
Yingjie Zhang wrote: > Dear all, > > Thanks for all your perspectives, I agree with Dr. Gavin Simpson's opinion > that the author cooked the model by themselves, and there is no Hurdle > function in package 'stats'. > > I got a data set of the abundance of microbial community, I think some of yo

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Yingjie Zhang
Dear all, Thanks for all your perspectives, I agree with Dr. Gavin Simpson's opinion that the author cooked the model by themselves, and there is no Hurdle function in package 'stats'. I got a data set of the abundance of microbial community, I think some of you will know how it looks like, i

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Peter Solymos
Dear All, I had a quick look at the internal functions used by pscl::hurdle to do the numerical optimization by optim. It clearly corresponds to the hurdle model defined in the paper/vignette, where the zero component is based on a right censored random variable, that is 0 if the original count da

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Jari Oksanen
On Thu, 2010-08-19 at 14:54 +0300, Gavin Simpson wrote: > On Thu, 2010-08-19 at 13:20 +0200, Yingjie Zhang wrote: > They fit several models and compare them: > > I. Poisson > II. Negative Binomial >III. Quasi-likelihood > IV. Hurdle model > V. zero-inflated model > > III sh

Re: [R-sig-eco] Warnings with Vegan radfit command

2010-08-19 Thread Marcus Cianciaruso
Hi Conrado and Jari, Indeed, using vegan 1.17.2 and R version 2.10.1 (32-bits), I got no warnings and the output Conrado sent above. All the best, Marcus On Thu, Aug 19, 2010 at 8:36 AM, Conrado Galdino wrote: > 2010/8/19 Jari Oksanen > > > On 19/08/10 01:07 AM, "Conrado Galdino" wrote: > >

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Gavin Simpson
On Thu, 2010-08-19 at 13:20 +0200, Yingjie Zhang wrote: > Thanks for the details, the paper is 'Comparing species abundance > models' by Joanne M.Potts, Jane Elith. Click the link... on page 158, > in the table, they compare 5 models, both Quasi-likelihood and Hurdle > are mentioned. > > http://w

Re: [R-sig-eco] Warnings with Vegan radfit command

2010-08-19 Thread Conrado Galdino
2010/8/19 Jari Oksanen > On 19/08/10 01:07 AM, "Conrado Galdino" wrote: > > > Thanks very much for your response Jari, > > > > Is good to know from you that there is nothing to worry. I'll surely > check > > the plots. Taking the opportunity I also like to inform that in newer > > versions of th

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Yingjie Zhang
Thanks for the details, the paper is 'Comparing species abundance models' by Joanne M.Potts, Jane Elith. Click the link... on page 158, in the table, they compare 5 models, both Quasi-likelihood and Hurdle are mentioned. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VBS-4KD5C2N-1&_

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Gavin Simpson
On Thu, 2010-08-19 at 11:14 +0200, Yingjie Zhang wrote: > Hi, > > There is a reason why am I addict to Quasi likelihood, since Hurdle > from 'pscl' use Zero Truncated Poisson regression for the non-zero > part, which incapable of handling the over-disperson comes from the > positive part of the da

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Yingjie Zhang
Hi, There is a reason why am I addict to Quasi likelihood, since Hurdle from 'pscl' use Zero Truncated Poisson regression for the non-zero part, which incapable of handling the over-disperson comes from the positive part of the data. Apparently, Quasi likelihood is at least a better choice. I

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Gavin Simpson
On Thu, 2010-08-19 at 10:30 +0200, Yingjie Zhang wrote: > I'd like to try the same way to my dataset, hurdle but estimated by > 'quasi-likelihood', but it's not in the standard 'pscl' package I > think, right? Please keep discussion on list; just because I replied doesn't give you a direct line to

Re: [R-sig-eco] hurdle model

2010-08-19 Thread Gavin Simpson
On Thu, 2010-08-19 at 09:52 +0200, Yingjie Zhang wrote: > Hello everyone, > > Does anyone of you using hurdle model? I am reading a paper which said > " Hurdle model removes effect of zero-inflation and over-dispersion in > the non-zero observations using a quasi-likelihood", I've checked the > he

[R-sig-eco] hurdle model

2010-08-19 Thread Yingjie Zhang
Hello everyone, Does anyone of you using hurdle model? I am reading a paper which said " Hurdle model removes effect of zero-inflation and over-dispersion in the non-zero observations using a quasi-likelihood", I've checked the help file from hurdle in R, which said differently that"for non-zer