[R-sig-eco] Adonis and Random Effects

Hello List, Is adonis capable of modeling random effects? I'm analyzing the impact of a treatment on the microbial community in a split-plot design (2 treatments per plot, 4 plots per grassland, 3 grasslands total). I would like to quantify how much of the variance is due to the Treatment vers

Re: [R-sig-eco] proportion data with many zeros

Liz writes: > Hi Valerie, > The best advice I was ever given with regards to distribution was to choose > the one with the best fit i.e. no pattern in the residuals. > The 2 things to think about when fitting a GLM are the type of data you've > collected (binomial, counts etc) so that you can get

Re: [R-sig-eco] Very large dispersion parameter in a negative binomial model

Thank you very much Mollie. Best, Manuel 2013/2/3 Mollie Brooks > Hi Manuel, > This means that your data is closer to Poisson. > Here is an example where I simulate Poisson data and try to fit the NB > distribution. I get behavior from glm.nb that is similar to your results > (large dispersio

Re: [R-sig-eco] proportion data with many zeros

Hi Valerie, The best advice I was ever given with regards to distribution was to choose the one with the best fit i.e. no pattern in the residuals. The 2 things to think about when fitting a GLM are the type of data you've collected (binomial, counts etc) so that you can get an idea of which link

Re: [R-sig-eco] Very large dispersion parameter in a negative binomial model

Hi Manuel, This means that your data is closer to Poisson. Here is an example where I simulate Poisson data and try to fit the NB distribution. I get behavior from glm.nb that is similar to your results (large dispersion parameter and warning about iteration limit reached). x=rep(1:5, 10) y=rpo

[R-sig-eco] Very large dispersion parameter in a negative binomial model

Dear list members, I am fitting a negative binomial model but I get a very large dispersion parameter. Why is that? quine.nb2 <- glm.nb(Pt ~ Agua + Dist10, data = Abundancia) summary(quine.nb2) Deviance Residuals: Min1QMedian3Q Max -2.20911 -0.67157 0.04411

Re: [R-sig-eco] proportion data with many zeros

Thank you Liz, I don't know tweedie, I'll have a look at it, but I have indeed some high values. I know about the problems linked to the arcsine transformation. I won't consider it anyway. I'd like to use either the raw values of pollen grain counts or a logistic quasibinomial model. Best, Va

[R-sig-eco] adonis and negative F-values

Dear all, I used adonis to perform a test of the pairwise site dissimilarity indices proposed by Baselga (2010, 2012) in the package betapart. I am concerned about my results because I get some negative F-values. I read in another post that this may happen because of the presence of negative ei