Re: [R-sig-eco] Question regarding Bray Curtis and NMDS

Dne 10. 10. 23 v 18:26 Barton, Alana Charlotte napsal(a): Hello, I was recommended this email by another student for R help; I am currently analyzing differences in fish assemblages due to temperature extremes. I am looking at data over multiple years. I chose three sampling sites within a

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

he step up > to the multivariate model just needs some work understanding what the > relevant R package wants. > > HTH > > Bob > > On 12/01/17 14:12, Martin Weiser wrote: >> >> Dear friends, >> >> Could you please help me with analysis? I am a

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

-) ) are appreciated. With the best regards, Martin Weiser ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

[R-sig-eco] asymetric matrix - pairwise experiments

elegant one. I would appreciate your suggestions. With the best regards, Martin Weiser -- -- Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze: a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení

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

Hi Conny, AFAIK NMDS is *non-metric* and represents distances among objects, not gradients along axes (known or unknown): distances along axes are stretched as needed locally (NMDS works with rank order), even order of the elements along axes does not tell anything. NMDS is great if you want to

Re: [R-sig-eco] Morisita horn similarity index

moses selebatso píše v Pá 27. 11. 2015 v 03:55 +: > Hello > I am trying to analyse diet overlap (level of similarity) between two > species. I have diet composition in %. I have tried to find the best tool, > and thought Morisita horn will do, but I cant find the right package for. Is >

Re: [R-sig-eco] Morisita horn similarity index

moses selebatso píše v Pá 27. 11. 2015 v 03:55 +: > Hello > I am trying to analyse diet overlap (level of similarity) between two > species. I have diet composition in %. I have tried to find the best tool, > and thought Morisita horn will do, but I cant find the right package for. Is >

[R-sig-eco] glm(binomial) vs. logistf

Dear friends, Is there any reason why to run logistic regression (binomial response) by glm() and not by logistf() by default? In particular when having sparse data (e.g. 8 presences in 100 samples), frequently with quasi-separation (all presences at one level of the predictor, together with

Re: [R-sig-eco] cloglog logistic regression interpretation

-regression Best, Martin Weiser -- -- Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze: a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení důvodu, b) stanovuje, že smlouva musí mít písemnou formu, c) vylučuje

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

Ludovico Frate píše v St 29. 10. 2014 v 16:27 +0100: Dear all,I'am trying to fit a very simple linear model. I am analyzing the differences in the number of species (DS) found in several permanent plots in two year of observations. Firstly, I have calculated the differences per plot (i.e.

[R-sig-eco] variance partitioning: vegan

Dear friends, I have just looked at vegan:::varpart2, and it seems to me that in estimation of degrees of freedom for adjusted R2 calculation, it just uses number of columns in the constraining matrix/dataframe. Am I right? Is this appropriate if the constraining dataframe involves factors with

Re: [R-sig-eco] Regression with few observations per factor level

Hi, coefficients and their p-values are reliable if your data are OK and you do know enough about the process that generated them, so you can choose appropriate model. With 4 points per line, it may be really difficult to identify bad fit or outliers. For example: simple linear regression needs

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

Hi, just a minor comment below. Bob O'Hara píše v So 14. 06. 2014 v 09:45 +0200: On 06/14/2014 03:05 AM, Luis Fernando Garca wrote: Dear all, I am making an analysis using a GLM using three explanatory variables and a response variable. I need to obtain a table similar to this one,

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

be desirable for the overall test, but I simply do not know. Any advice? Best, Martin Weiser -- -- Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze: a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení důvodu, b

Re: [R-sig-eco] two nested conditioning factors in capscale()

Alicia Valdés píše v Čt 22. 05. 2014 v 15:47 +0200: Hi, I am using the function capscale() in vegan to perform a partial distance-based RDA. I would like to use not one, but two conditioning factors, A and B, in order to remove their effects out of the analysis. B is nested in A. I don't

Re: [R-sig-eco] Orthogonal contrasts and ANCOVA in R

Greg McClelland píše v Pá 04. 04. 2014 v 13:22 -0500: Hi everyone, Using the following data, I need to determine if, independent of mass, the observed response is associated with sex, location, and/or age

Re: [R-sig-eco] cross validation in CoCA and CCA

Besides, one can use (I hope) GNU Octave (free, libre, opensource) to do it with the original MatLab code, as Octave is compatible with MatLab. HTH. Martin Gavin Simpson píše v Pá 28. 03. 2014 v 20:44 -0600: In short, no. I haven't ported the rough code for LOO CV of CCA or CCA-PLS models. I

Re: [R-sig-eco] Plot question

Luis Fernando García píše v Ne 23. 03. 2014 v 21:32 -0300: Dear R friends, I have to produce a plot like the one attached on the file. The idea is to plot the time spent for a spider over several different prey, the spiders were repreated in the different trials. If any of you knows how to

Re: [R-sig-eco] R-sig-ecology (72-19): Plot question

Hi Claas, while this may be not the best plot one can imagine, I think it shows well behaviour of individual spider (results are grouped by spider identity, I guess). So yes, one could use specific symbol per spider, but this seems like a usable way how to to cope with the per-spider grouping,

Re: [R-sig-eco] SDM-model evaluation

Hi, I am not sure why AUC should be better than, say, AICc - second order Akaike criterion and AIC weights (comfortably calculated by AICcModavg package) or Nagelkerke's R2 in this case. Would anybody be so kind and explain this for me? I just want to make warning: do not put strong (or any)

Re: [R-sig-eco] how to detect different species among samples

Hi, I am not sure that I get what you wanted, but if you are interested in names, I propose something like this: is.there - dune is.there[is.there 1] - 1 #change counts to presence/absence data number.of.samples - colSums(is.there) single.occurrences-names(dune)[number.of.samples ==1]

[R-sig-eco] [Fwd: Re: how to detect different species among samples]

, but... if I would know which species are in common (and which not) between two particular selected samples? Thanks for the brainstorming :) Gian On 3 February 2014 17:01, Martin Weiser weis...@natur.cuni.cz wrote: Hi, I am not sure that I get what you wanted, but if you are interested

Re: [R-sig-eco] Ranked abundance distribution

Sol Noetinger píše v Út 17. 12. 2013 v 12:01 -0300: Hello, I am trying to apply different statistics methods in a field that traditionally is not very keen to it and in consequence I am trying to learn all that I can. To the point, I am studying a palynological succession from the

Re: [R-sig-eco] Data Frame Structure for vegdist()

:length(olddata)] rownames(newdata) - olddata[,1] HTH, Martin Weiser ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] GLM: calculate percentage deviance of factor

. Nagelkerke's R-squared, but be warned that these alternatives sometimes lack some usual properties of R2 like aditivity - sum of Your explained variances for individual factors would not be the same as the explained variance of the full model. I hope this helps. Martin Weiser

[R-sig-eco] Zuur or Pinheiro Bates

and Extensions in Ecology with R XOR b, Pinheiro Bates (2000/2009): Mixed-Effects Models in S and S-PLUS? Thank you for your patience. With the best regards, Martin Weiser (Dept. of Botany, Science Faculty, Charles University in Prague, Czech Rep.) ___ R

Re: [R-sig-eco] Use cor.test for multiple parameters?

not sure whether it is useful). Or forget testing, and just look at the matrix of correlation coefficients themselves - these numbers tell the story, p-values just say how likely are they lying in doing so. Best, Martin Weiser Wayne Richter píše v Pá 16. 11. 2012 v 12:59 -0500: Take a look at rcorr

Re: [R-sig-eco] Log transformed simple linear regression and Poisson regression

that as a measure of the variance explained by the particular model. (I hope someone corrects me if I am wrong). I hope this helps. Martin Weiser lgj200306 píše v Čt 02. 08. 2012 v 06:50 +0800: Thanks Liz, Brian and Mollie. Your replies are helpful for me. I have realized the complexity

Re: [R-sig-eco] [R] reception of (Vegan) envfit analysis by manuscript reviewers

) with undetermined something non-regularly stressed (NMDS). But this is just my feeling, I may be wrong easily, but in that case I hope someone will correct me. Best, Martin Weiser Alan Haynes píše v Čt 10. 05. 2012 v 13:17 +0200: Hi all, Im using envfit with some decomposition data currently

Re: [R-sig-eco] CCA and related ordination techniques

]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology Hi Marc, I personally like the website of Mike Palmer: http://ordination.okstate.edu/ I hope this helps. Best, Martin Weiser ___ R