Re: [R-sig-eco] Specifying contrasts for an interaction in mvabund/manyglm

Sent: Wednesday, September 23, 2020 1:38:38 AM To: r-sig-ecology ; Kyle Tyler Subject: Specifying contrasts for an interaction in mvabund/manyglm Hi Kyle, from the bottom of your message it seems that what you have is a nested design, with Season nested within Site. If you specify your

[R-sig-eco] Specifying contrasts for an interaction in mvabund/manyglm

site 1 in season 1 is different from that at site 8 in season 4 etc. In mvabund, is there a way to specify/restrict the contrasts to only those that I am interested in? Thanks a lot for any help! Kyle Kyle J. Tyler PhD Candidate � Aquatic Ecology Charles Darwin University, Australia [[a

Re: [R-sig-eco] vegan RDA triplot species arrows

interesting to know, thanks. My apologies for conflating my textbook with universal standard practice! Cheers, Tyler ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

[R-sig-eco] vegan RDA triplot species arrows

-decision, and google, but I didn't find anything, (excepting the possibility of using biplot.rda, but only for unconstrained analyses). Thanks, Tyler ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] vegan RDA triplot species arrows

Gavin Simpson gavin.simp...@ucl.ac.uk writes: On Wed, 2011-05-04 at 15:44 -0400, Tyler Smith wrote: Why does vegan not plot species as arrows in plot? I know how to use scores() and arrows() to create my own arrows, but it seems odd that this feature is not built in. Is there ever a situation

Re: [R-sig-eco] Do we have to cut a dendrogramm at a specific level or not

; it is the user who decides if these structures are interesting and worth interpreting in ecological terms. HTH, Tyler Borcard, Gillet and Legendre. 2011. Numerical Ecology with R. Springer. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https

Re: [R-sig-eco] ordination and clustering with continous and categorical variables

is the relative niche position of each species, rather than their niche breadths. Regards, Tyler ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] how to calculate axis variance in metaMDS, pakage vegan?

) really make much sense. Please correct me if I'm wrong! Cheers, Tyler ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Intepreting a plot from a constrained NMDS

ordination, for example CCA? No, you're still doing an unconstrained ordination, also referred to as an indirect gradient analysis. Cheers, Tyler -- Friends don't let friends send Word documents http://www.nothingisreal.com/dfki/no-word ___ R-sig

Re: [R-sig-eco] Problems with vegdist in Vegan

to include the empty plots, you'll have to use a distance measure that appropriately quantifies their relationship to each other and the other non-empty plots. This would only really make sense if you have reason to believe that all the empty plots are empty for the same reason. HTH, Tyler -- Who

Re: [R-sig-eco] ANOVA Output

a function Anova (not to be confused with the anova function) that allows you to calculate type II or type III sums of squares. Cheers, Tyler ONKELINX, Thierry [EMAIL PROTECTED] writes: Dear Katrina, The F-value are different because you test different hypotheses since anova yields Type I SS

[R-sig-eco] classical statistics in R

. Is there a good standard text that covers the same breadth of material with a modern, R-compatible approach? Ben also recommended several books by Michael Crawley - any strong feelings on these, or other suggestions? Thanks! Tyler -- Research is what I'm doing when I don't know what I'm doing

Re: [R-sig-eco] classical statistics in R

functions, and wouldn't have to re-implement each variation of a test from scratch. But there's a conceptual gap between R and SR that I'm missing. Cheers, Tyler Seb On Mon, 10 Nov 2008 16:11:47 -0500, Brian Campbell [EMAIL PROTECTED] wrote: I conceded to R shift (mostly) last year

Re: [R-sig-eco] Improving efficiency in a simulation model

after time steps? I don't know if OO will make your programs run any faster, but it may make them easier to understand and maintain. Cheers, Tyler -- ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-eco] R 2.7.2 Issues

list: https://stat.ethz.ch/mailman/listinfo/r-sig-debian The package maintainers read that list and usually respond very promptly when issues arise. Cheers, Tyler This morning I upgraded to 2.7.2 via the Ubuntu package repository, and now when I go to run R via the command line it fails

Re: [R-sig-eco] Publication quality graphics in R

like the GIMP. If you have a low-res jpg (which will look pixelated), you can't fix it, you have to re-make it at higher res, or in another format. Of course, you can generate high-res tiff or jpg files to begin with, but they can be cumbersomely large to email around. my 2 cents! Tyler -- Tired