[R-sig-eco] PhD position in ecology and statistics at NTNU, Norway

to apply, and the formalities): https://www.jobbnorge.no/en/available-jobs/job/194344/phd-research-fellow-at-the-department-of-mathematical-sciences If any potential applicant have questions, they should feel free to ask me. Bob -- Bob O'Hara Institutt for matematiske fag NTNU 7491 Trondheim Norway

Re: [R-sig-eco] CI for stratified Cox PH model

9A 5H7 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Institutt for matematiske fag NTNU 7491 Trondheim Norway Mobile: +49 1515 888 5440 Homepage: http://www.ntnu.edu/employees

Re: [R-sig-eco] correlating three time-series in R

sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara NOTE: this email will die at some point, so please update you records to bob.oh...@ntnu.no Institutt for matematiske fag NTNU 7491 Trondheim Norway Mobile: +49 15

Re: [R-sig-eco] mixed effects in ordination (?)

est regards, Martin Weiser ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara NEW EMAIL: bob.oh...@ntnu.no NOTE NEW ADDRESS!!! Institutt for matematiske fag NTNU 7491 Trondheim Norway Mobile: +49 1515 888 5440 J

Re: [R-sig-eco] LMER: applying a random term to only one level of a factor

on deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 M

Re: [R-sig-eco] AIC in R: back-transforming standardized model parameters (slopes)

-0.38008 0.13722 -2.77 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___________ R-sig-

Re: [R-sig-eco] NMDS axes scores

ogy mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/i

Re: [R-sig-eco] best choice of GLMM for seed set data

-- Mehdi Abedi Department of Range Management Faculty of Natural Resources Marine Sciences Tarbiat Modares University (TMU) 46417-76489, Noor Mazandaran, IRAN mehdi.ab...@modares.ac.ir Homepage Tel: +98-122-6253101 Fax: +98-122-6253499 -- Bob O'Hara Biodiversity and Climate Research

Re: [R-sig-eco] Zero infalted model- T50

be, but I doubt that will be a big problem. I used to get data where the data would flip between 0 and 100 over a range of doses. In the end I gave up with those problems and became an ecologist Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am

Re: [R-sig-eco] mvabund SIMPER alternative

, you can use mvabund for OTUs: I've helped a colleague do this (e.g. dx.doi.org/10.1371/journal.pone.0053987). Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http

Re: [R-sig-eco] Association Routine?

with the original reference variable result[,1] = ref[,1] for (i in 1:nrow(ref)){ for (j in 1:nrow(assoc)) if (ref[i, 1] == assoc[j, 1]){ resultado[i, 2] == assoc[j, 2] } } col = ncol(dados) Any thoughts? Thanks in advance, Alexandre -- Bob O'Hara Biodiversity

Re: [R-sig-eco] Multivariate quasi-bionomial analysis of proportion data?

.12122/abstract Bob Thanks, Amanda [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre

Re: [R-sig-eco] SPEI index

list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id

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

R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219

Re: [R-sig-eco] EstimateR and Chao 1 standard deviation

On 10/17/2014 05:36 PM, Gavin Simpson wrote: On 17 October 2014 06:44, Bob O'Hara boh...@senckenberg.de mailto:boh...@senckenberg.de wrote: On 17/10/14 13:54, José M. Blanco Moreno wrote: Dear users I have been checking the values returned by the function estimateR

Re: [R-sig-eco] Binomial GLMM or GAMM with random intercept and temporal correlation

assumptions about how your system is behaving. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://blogs.nature.com

Re: [R-sig-eco] Question on unexpected regression results

[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main

Re: [R-sig-eco] deviance as a goodness of fit in GLM

to generate the plots too, so you have something to work from). Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http

Re: [R-sig-eco] Question about GLM post hoc and chi square (Angel)

-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://blogs.nature.com/boboh Journal of Negative Results - EEB

Re: [R-sig-eco] Question about GLM post hoc and chi square

://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://blogs.nature.com/boboh

Re: [R-sig-eco] mantel within mantel? multidimensional variance

Weiser -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://blogs.nature.com/boboh Journal of Negative Results - EEB

Re: [R-sig-eco] Help with a function

==which.casod], N, replace=F) e.g. SampledData=sapply(unique(Data$casod), blinding, df=Data) will sample for each value of casod Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 Mobile: +49 1515 888 5440 WWW: http

Re: [R-sig-eco] inference from GLMM fit using glmer

appreciated. Sincerely, Eric [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre

Re: [R-sig-eco] Bayesian analysis with MCMC

for convergence? If the chains are giving different marginal distributions, this suggests they haven't converged, so they are not sampling from the correct posterior distribution (or, at least, some chains aren't). Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D

Re: [R-sig-eco] This chains contains uninitialized variables and the trap report says undefined real result

, Kassahun [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage

Re: [R-sig-eco] Two-sided significant test for null models

? Let's say 'null.dist' the null distribution, 'obs' the observed value and 'alpha' the probability of Type I error. set.seed(10) rnorm(999)-null.dist obs-1.5 alpha-0.05 pval=mean(obsnull.dist) min(pval, 1-pval)0.05 Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D

Re: [R-sig-eco] interpretation of interaction between explanatory variables

* C.abundances:C.diversity 0.5367 0.1801 2.980 0.00489 ** Thanks a lot for your help! Iris [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob

Re: [R-sig-eco] GLM

model-checking plots (e.g. residuals). There is more advice in the links here: http://r.789695.n4.nabble.com/Checking-the-assumptions-for-a-proper-GLM-model-tp1559502p1560503.html. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany

Re: [R-sig-eco] patterns in weather data that could relate to pathogen prevalence

smaller. Of course, another temperature than 5°C might work better for you. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 7542 1863 / +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root

Re: [R-sig-eco] Spatial AND temporal correlation in linear mixed-effects models

appreciated! Best, A bit of googling brought up this, from 10 years ago: http://tolstoy.newcastle.edu.au/R/help/02b/2068.html I don't think lme has changed that much. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69

Re: [R-sig-eco] Using residuals as dependent variables

partial residuals (http://en.wikipedia.org/wiki/Partial_residual_plot). Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog

Re: [R-sig-eco] Multiple comparisons among predictors generated from same data

as well stick to the original analysis. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://blogs.nature.com/boboh

Re: [R-sig-eco] PCA as a predictive model

=Sigma) # Do PCA on new data. First do it wrong... PC.wrong=predict(PC, newdata=scale(NewData)) # Now scale correctly NewData.Sc=scale(NewData, center=attr(Data.Sc, scaled:center), scale=attr(Data.Sc, scaled:scale) PC.right=predict(PC, newdata=NewData.Sc) HTH Bob -- Bob O'Hara Biodiversity

Re: [R-sig-eco] gam

to fit a straight line rather than a smooth curve. The other thing to do is to define the maximum flexibility of the curve, e.g. model-gam(Sillaginidae~s(temperature, k=6)+s(salinity)+s(depth)) I hope this helps. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D

Re: [R-sig-eco] data normality

the best sort. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://blogs.nature.com/boboh Journal of Negative Results

Re: [R-sig-eco] ICC confidence intervals and power analysis for random effects in lmer?

://stat.ethz.ch/mailman/**listinfo/r-sig-ecologyhttps://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root

Re: [R-sig-eco] Which function would fit these data (Version 2)

to zero when x approaches infinity when at the same time y should equal 1 at infinity. It's not a big problem, though. Just use 1-y instead of y. Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49

Re: [R-sig-eco] ICC confidence intervals and power analysis for random effects in lmer?

effect. Any tips on how to approach that? Report the random effect and confidence intervals. Retrospective power analyses are pretty pointless (e.g. see http://beheco.oxfordjournals.org/content/14/3/446.full), unless you're planning to repeat the experiment. Bob -- Bob O'Hara Biodiversity

Re: [R-sig-eco] Output for interactions in models that do not include all main effects

interaction terms and not based on the term that was used as a main effect? Thanks very much for any insight. Kristen Gorman ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Bob O'Hara

Re: [R-sig-eco] Problem with R2WinBUGS packages

investigation IIRC, you just need to close WinBUGS, and it'll return to R. You only need to use debug=T if BUGS is trapping or throwing errors (and have fun understanding the traps). Bob -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany

Re: [R-sig-eco] Mixed model with zero truncated Poisson distributed data

-models https://stat.ethz.ch/mailman/options/r-sig-mixed-models/h.l.ward%40qmul.ac.uk list, so apologies if you've seen it twice! If an individual would have had pups, would you have seen it? I'm wondering if you could simply add the zeroes back into the data. Bob -- Bob O'Hara Biodiversity