[R-sig-eco] interpreting 0s and 1s from manyglm from mvabund

[David Warton]

Hi Elizabeth,
Wow, that's weird - could you send me the data/code (and R/mvabund version you used)?  I'll see if I can reproduce the problem.  My best guess at this stage is that there was something in the data that it didn't like and returned NaN's for everything (which were misleadingly translated into 0's and 1's in the anova table) 

Maybe we could sort it out communicating directly then get back to the mailing list with a report on how things went afterwards? (I assume that's the protocol?)
All the best
David


Date: Wed, 25 Feb 2015 13:43:40 -0500
From: Elizabeth Pringle <epringle at umich.edu>
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] interpreting 0s and 1s from manyglm from mvabund
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Hi,

I am using code that worked beautifully to analyze a previous dataset using manyglm in mvabund on a new dataset, and I am consistently getting results of Dev = 0 and Pr(>Dev)=1 for both multivariate and univariate tests. My plots do not indicate any particularly strong pattern in the data, so I am tempted to interpret this as a non-significant result...but I wanted to make sure it doesn't just indicate that I've somehow input the data incorrectly. Especially since I get a bunch of NAs and NaNs farther down the line if I go through my whole pipeline.

Code follows:
>glm.sug<-manyglm(dat~trtment,family="negative.binomial")
>results<-anova(glm.sug,resamp="pit.trap",p.uni="adjusted")
>results (here's where I see 0s and 1s)
>results$table
                 Res.Df Df.diff Dev Pr(>Dev)
(Intercept)          15      NA  NA       NA
trtment               14       1   0        1
> s=sort(results$uni.test[2,],index.return=T,decreasing=T)
> s$x[1:3]/sum(s$x)
        X..1          X.2        X..3
       NaN        NaN        NaN

Many thanks,
Beth

--
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Elizabeth G. Pringle
Michigan Society of Fellows
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