[R-sig-eco] Zero inflated data on some levels of a random factor in mixed models
Dear all, I have a set of data on nectar volumes from four plant species. Two species have ample zeroes in the data (for one species almost 1/3 of the flowers had no nectar), but two species don’t have excessive zeroes in the data and have a normal distribution. I am trying to find out, what would be the correct way to model the trait responses in this situation. I would like to analyse all four species in one mixed model, but should I try to account for the zero inflated data, if the problem is only with half of the species? And if so, then how could I do it properly? An answer to an earlier question on the topic of zero inflated data (https://stat.ethz.ch/pipermail/r-help/2014-May/37.html) suggested to model the zero and non-zero data separately. With not too many zeroes in case of two species and wishing to combaine all four species, I probably cannot use this method in this case or could it be possible somehow? Till now I have used function glmmPQL (MASS) to model this trait with species/plant/flower as a random factor. However, as far as I know, this function does not allow to account for the zero inflated data. I found that MCMCglmm and glmmADMB would allow to account for zero inflated data, but before learning to use a new package I wanted to ask, whether this would be the correct way to approach this kind of data in the first place and whether there might be a way to do this using glmmPQL function? Could you give me some suggestions, what might be the best way to deal with this kind of data? Thank you in advance, Krista Takkis Department of Geography University of the Aegean ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Help obtaining f values
Hello, I am new using the R software and I am a little concerned about an apparently easy procedure which is done in R. When I perform a GLM analysis, I usually get the deviance, df and p values. Nevertheless, for publishing, reviewers require the F value. Although I have looked in several sources I have nott been able to find it, so I wanted to know if any of you knows how to find the exact f value using the deviance, df or p value. Any help will be welcome and this is an example of what I get. Thanks in advance Analysis of Deviance Table Model: quasipoisson, link: log Response: Count Terms added sequentially (first to last) Df Deviance Resid. Df Resid. DevFPr(F) NULL 26 3204.6 Sex 2 6.8924 3197.7 2.2640 0.1851036 Time153.9623 3143.8 35.4513 0.0010042 ** Behaviour 4 2356.3619 787.4 387.0562 2.295e-07 *** Sex:Time282.4917 704.9 27.0991 0.0009902 *** Sex:Behaviour 794.4210 610.5 8.8621 0.0083508 ** Time:Behaviour 4 601.27 69.3 98.7648 1.324e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Help obtaining f values
Well, I may have gotten your question over-simplified, but, isn't it the F in your table (*in bold*)? Df Deviance Resid. Df Resid. Dev*F*Pr(F) NULL 26 3204.6 Sex 2 6.8924 3197.7 *2.2640* 0.1851036 Time153.9623 3143.8 *35.4513* 0.0010042 ** Behaviour 4 2356.3619 787.4 *387.0562 *2.295e-07 *** Sex:Time282.4917 704.9 *27.0991* 0.0009902 *** Sex:Behaviour 794.4210 610.5 * 8.8621* 0.0083508 ** Time:Behaviour 4 601.27 69.3 *98.7648* 1.324e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 == Dr. Ricardo Ribeiro de Castro Solar (Curriculum Vitœ http://lattes.cnpq.br/9924177207371692) Pesquisador Associado (PNPD - Capes) Programa de Pós-Graduação em Ciências Biológicas Visit my blog! http://photographyandconservation.wordpress.com/ / Rede Amazônia Sustentável http://www.redeamazoniasustentavel.org Skype: rrsolar Universidade Estadual de Montes Claros - MG == On 15 September 2014 15:53, Luis Fernando García luysgar...@gmail.com wrote: Hello, I am new using the R software and I am a little concerned about an apparently easy procedure which is done in R. When I perform a GLM analysis, I usually get the deviance, df and p values. Nevertheless, for publishing, reviewers require the F value. Although I have looked in several sources I have nott been able to find it, so I wanted to know if any of you knows how to find the exact f value using the deviance, df or p value. Any help will be welcome and this is an example of what I get. Thanks in advance Analysis of Deviance Table Model: quasipoisson, link: log Response: Count Terms added sequentially (first to last) Df Deviance Resid. Df Resid. DevFPr(F) NULL 26 3204.6 Sex 2 6.8924 3197.7 2.2640 0.1851036 Time153.9623 3143.8 35.4513 0.0010042 ** Behaviour 4 2356.3619 787.4 387.0562 2.295e-07 *** Sex:Time282.4917 704.9 27.0991 0.0009902 *** Sex:Behaviour 794.4210 610.5 8.8621 0.0083508 ** Time:Behaviour 4 601.27 69.3 98.7648 1.324e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
