Re: [R-sig-eco] species richness, GLM and negative values

..or we could include 'Plot' as random variable? library(lme4) mod - glmm(DS ~ Time + 1|Plot) Yours, Kay Von meinem Smartphone gesendet Bob O'Hara boh...@senckenberg.de schrieb: On 10/29/2014 04:27 PM, Ludovico Frate wrote: Dear all,I'am trying to fit a very simple linear model. I am

[R-sig-eco] Issue with BiodiversityR::nested.npmanova

, permutations = 1000) Regards, Kay -- Kay Cichini, MSc Biol Grubenweg 22, 6071 Aldrans Tel.: 0650 9359101 E-Mail: kay.cich...@gmail.com Web: www.theBioBucket.blogspot.co.athttp://www.thebiobucket.blogspot.co.at/http://www.theBioBucket.blogspot.co.at -- [[alternative HTML version deleted

Re: [R-sig-eco] Issue with BiodiversityR::nested.npmanova

, Kay Cichini kay.cich...@gmail.com wrote: Hi all, Does anyone have a clue why this is not working: library(BiodiversityR) library(vegan) data(mite) mite - mite[1:60,] env - data.frame(Fac = rep(LETTERS[1:2], each = 30), NFac = rep(letters[1:4], each = 15)) nested.npmanova

Re: [R-sig-eco] Repeated Measures PERMANOVA

-- Kay Cichini, MSc Biol Grubenweg 22, 6071 Aldrans Tel.: 0650 9359101 E-Mail: kay.cich...@gmail.com Web: www.theBioBucket.blogspot.co.athttp://www.thebiobucket.blogspot.co.at/http://www.theBioBucket.blogspot.co.at -- [[alternative HTML version deleted

Re: [R-sig-eco] Package bio.infer: get.taxonomic() hangs R after editing taxa list

Hi, Maybe the ritis package does what you want? Regards, Kay Am 11.12.2012 23:46 schrieb Rich Shepard rshep...@appl-ecosys.com: On Mon, 10 Dec 2012, Sarah Goslee wrote: ... get.taxonomic() no longer has an outputFile argument. I've read the get.taxonomic() description in bio.infer.pdf

Re: [R-sig-eco] Help with function to webscrap

Hi, no need for RCurl - this should suffice: require(XML) input = panthera-uncia h - htmlParse(paste(http://api.iucnredlist.org/go/;, input, sep = )) (status - xpathSApply(h, '//div[@id=red_list_category_code]', xmlValue)) [1] EN Many thanks for pointing up the IUCN-API, Eduard

[R-sig-eco] Fwd: metaMDS - avoid species overlap in plots

Hi! library(vegan) data(dune) sol - metaMDS(dune) # use argument air! see ?orditorp: plot(sol, type = n) orditorp(sol, displ = sp, air = 1) # or use pointLabel() from maptools package. this should avoid overplotting of text - # here is an example where I added cex according to species

Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. On 26/04/2012, at 7:19, Kay Cichini kay.cich...@gmail.com

Re: [R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

Hi, thanks a lot - things are much clearer now! Then I will take the one you and Gavin suggested. Kind regards, Kay Am 26.04.2012 17:47 schrieb Jari Oksanen jari.oksa...@oulu.fi: On 26 Apr 2012, at 0:19, Kay Cichini wrote: Hello all, I'd like to test if total diversity differs

[R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

Hello all, I'd like to test if total diversity differs between two communities. For each community several samples were taken and abundances collapsed over groups to compute total diversity for each group. I tried to use vegan::oecosimu to test non-randomness of my statisitc (difference in

[R-sig-eco] ctree regression tree, interpretation of mean predicted values in terminal nodes

I can't grasp how it can be that the mean prediction at terminal nodes perfectly fit the true mean values of the observed variable at the terminal nodes - I'm afraid I'm missing something completely obviuos here: # make a regression tree: rt - ctree(Ozone ~ ., data = airq) # Validate: Prediction

[R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated, edit

Hello list members, I'm planning to model species presence / absence data (N = 523) that was collected over a geographic area. Samples come from preferential sites (sea level 1200 m, obligatory presence of permanent waterbodies, etc). I want to infere on environmental factors determining the

[R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated

thanks manuel, i'm afraid unmarked can not deal with spatial autocorrelation - see this post: http://groups.google.com/group/unmarked/browse_thread/thread/f45bd5ab12aa127d/26446409f3e2a140?lnk=gstq=spatial%23#26446409f3e2a140 best, kay 2012/3/20 Manuel Spínola mspinol...@gmail.com You need

Re: [R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated

, AIC and friends. contrary, ctree would yield an intuitive and simple result which i would fancy for this purpose! yours, kay 2012/3/21 Manuel Spínola mspinol...@gmail.com That is true, but it can deal with detectability, and I am afraid ctree cannot. Best, Manuel 2012/3/21 Kay Cichini

Re: [R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated

observations too close to each other. Maybe this is not the best and the most elegant solution, but it is often enough to see and get reassured that there is no problem of autocorrelation in the residuals. Best regards, Bálint On Wed, Mar 21, 2012 at 09:48, Kay Cichini kay.cich...@gmail.com

Re: [R-sig-eco] identifying groups in a cluster

hi, you also may be interested in this approach: library(vegan) library(sparcl) data(dune) dis - vegdist(dune) cluc - hclust(dis, complete) grp - cutree(cluc, 3) par(mfrow = c(2, 1)) plot(cluc) rect.hclust(cluc, 3) r - rect.hclust(cluc, 3) text(cumsum(sapply(r,length)),

Re: [R-sig-eco] Multivariate repeated measures ANOVA w 2 bs factors

Check this: http://thebiobucket.blogspot.com/2011/04/repeat-measure-adonis-lately-i-had-to.html Hope it helps, Kay Am 03.01.2012 16:26 schrieb Steve Brewer jbre...@olemiss.edu: Hey folks, I am ne Hey folks, I am new to R and am trying to modify my multivariate eco-statistics course by

Re: [R-sig-eco] Permutation: habitat diversity

hi, i don't exactly know what you want to do but this may serve as a starter: http://thebiobucket.blogspot.com/2011/04/test-difference-between-diversity.html if you want to test difference in habitat diversity between sites you just need to replace my species in the example with your habitats.

Re: [R-sig-eco] repeated measures with multivariate data

possible permutations. concluding, given a large enough nr. of possible permutations, i suppose one should be able to this kind of analysis with adonis - would you agree? yours, kay - Kay Cichini Postgraduate student Institute of Botany Univ. of Innsbruck

Re: [R-sig-eco] repeated measures with multivariate data

with two time points. concluding, given a large enough nr. of possible permutations, i suppose one should be able to this kind of analysis with adonis. would you agree? yours, kay - Kay Cichini Postgraduate student Institute of Botany Univ. of Innsbruck

Re: [R-sig-eco] repeated measures with multivariate data

- Kay Cichini Postgraduate student Institute of Botany Univ. of Innsbruck -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/repeated-measures-with-multivariate-data-tp5330819p5333603.html Sent from the r-sig-ecology mailing list archive

[R-sig-eco] repeated measures with multivariate data

be highly appreciated, kay - Kay Cichini Postgraduate student Institute of Botany Univ. of Innsbruck -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/repeated-measures-with-multivariate-data-tp5330819p5330819.html Sent