Re: [R-sig-eco] mvpart alternatives and machine learning multivariate analysis

2017-07-01 Thread Gavin Simpson
If you want to stick with or at least compare a mulivariate tree with other approaches (like CCA or mvabund or boral) then the partykit package provides an implementation of a multivariate tree model, using conditional inference trees (i.e. you use conditional inference to decide if spits are

Re: [R-sig-eco] mvpart alternatives and machine learning multivariate analysis

2017-07-01 Thread Gavin Simpson
Right, but mvabund fits quite different types of model to that fitted in a multivariate tree, which can be seen as an unsupervised constrained clustering of the multivariate species response matrix. All the best Gavin On 24 June 2017 at 10:02, Torsten Hauffe wrote: >

Re: [R-sig-eco] accounting for linear sampling structure using PERMANOVA or dbRDA

2017-01-19 Thread Gavin Simpson
> Whiteman Laboratory > Integrative Biology > University of California, Berkeley > http://noahwhiteman.org/tim-oconnor.html > > > [[alternative HTML version deleted]] > > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.eth

Re: [R-sig-eco] RDA

2015-11-26 Thread Gavin Simpson
rda) will only have one data= argument. > However, in addition to variables in the data frame given in data=, you can > mix variables in the work environment in your formula. If you think you > need to have several data frames for the data= argument, please consider > cbind(). > > chee

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

2015-10-29 Thread Gavin Simpson
logy mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > ___ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] cross validated CCA

2015-08-24 Thread Gavin Simpson
[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted

Re: [R-sig-eco] biplot question: Error in 1L:n : argument of length 0

2015-07-29 Thread Gavin Simpson
/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] distances in NMDS ordination space

2015-07-16 Thread Gavin Simpson
of San Diego 5998 Alcala Park San Diego CA 92110 kateboer...@gmail.com http://www.oregonstate.edu/~boersmak/ ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD

Re: [R-sig-eco] Building glmms to handle zero-inflated continuous data in R - what options are available? (especially relating to hurdle/mixture models)

2015-06-19 Thread Gavin Simpson
-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Partitioning spatial effects using trend surface analysis or PCNM

2015-05-05 Thread Gavin Simpson
. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r

Re: [R-sig-eco] Using multiple species data for gam

2015-02-10 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r

Re: [R-sig-eco] Using multiple species data for gam

2015-02-10 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] GAM - Cyclic splines

2015-01-22 Thread Gavin Simpson
-- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Help in code for fitting a growth model in R

2014-11-16 Thread Gavin Simpson
., Karnataka Phone-Land: 08251-214336 Mobile: 9448780118 ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted

Re: [R-sig-eco] envfit permutation significance

2014-11-10 Thread Gavin Simpson
/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Logistic regression with 2 categorical predictors

2014-10-24 Thread Gavin Simpson
as is it is too complex for your data. You can;t test for an interaction but you could remove the interaction and just test for main effects, unless you can get some more data. G Andrew On 24 October 2014 04:08, Gavin Simpson ucfa...@gmail.com wrote: This all looks bogus to me; you've fit the data

Re: [R-sig-eco] Logistic regression with 2 categorical predictors

2014-10-23 Thread Gavin Simpson
419 473 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted

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

2014-10-23 Thread Gavin Simpson
...@oulu.fi wrote: On 23/10/2014, at 18:17 PM, Gavin Simpson wrote: On 22 October 2014 17:24, Chris Howden ch...@trickysolutions.com.au wrote: A good place to start is by looking at your residuals to determine if the normality assumptions are being met, if not then some form of glm

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

2014-10-17 Thread Gavin Simpson
___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R

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

2014-10-17 Thread Gavin Simpson
On 17 October 2014 10:04, Bob O'Hara boh...@senckenberg.de wrote: On 10/17/2014 05:36 PM, Gavin Simpson wrote: On 17 October 2014 06:44, Bob O'Hara boh...@senckenberg.de wrote: On 17/10/14 13:54, José M. Blanco Moreno wrote: Dear users I have been checking the values returned

Re: [R-sig-eco] SIMPER problem: invalid 'nrow' value (too large or NA)

2014-10-15 Thread Gavin Simpson
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

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

2014-06-06 Thread Gavin Simpson
[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted

Re: [R-sig-eco] calculating standard error of coefficients from adonis model

2014-05-09 Thread Gavin Simpson
-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted

Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER

2014-03-28 Thread Gavin Simpson
://home.olemiss.edu/~jbrewer/ FAX - 662-915-5144 Phone - 662-915-1077 On 3/27/14 10:47 AM, Gavin Simpson ucfa...@gmail.com wrote: Note that `betadisper()` only considers statistically dispersions about the group centroids. It might show the centroids and return their values, but it doesn't consider

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

2014-03-28 Thread Gavin Simpson
R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ 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-Adonis-NMDS-SIMPER

2014-03-27 Thread Gavin Simpson
-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Cosinor with data that trend over time

2014-03-26 Thread Gavin Simpson
it works with this data. I can't quite figure out how I would go about interrogating the fitted spline to deterine when the peak value happens with respect to DoY. Any suggestions? -Jacob On Tue, Mar 25, 2014 at 9:06 PM, Gavin Simpson ucfa...@gmail.com wrote: I would probably attack

Re: [R-sig-eco] Vegan-Adonis-NMDS-SIMPER

2014-03-26 Thread Gavin Simpson
-- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] Cosinor with data that trend over time

2014-03-26 Thread Gavin Simpson
- predict(mod$gam, newdata = newdat, type = terms) take - which(pred[,s(DoY)] == max(pred[,s(DoY)])) or take - as.numeric(which.max(pred[,s(DoY)])) Cheers, -Jacob On Wed, Mar 26, 2014 at 9:46 AM, Gavin Simpson ucfa...@gmail.com wrote: 1) Visually - unless it actually matters exactly on which

Re: [R-sig-eco] Cosinor with data that trend over time

2014-03-25 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] question about plot

2014-03-22 Thread Gavin Simpson
to do it, I would really appreciate it. Thanks in advance. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig

Re: [R-sig-eco] Fwd: How to label arrows in Ordiplot 3d graphs

2014-03-05 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-eco] Fwd: Error message while running anova in rda in r using vegan

2014-03-05 Thread Gavin Simpson
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Re: [R-sig-eco] plotting models with confidence bands from glmer

2014-02-27 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https

Re: [R-sig-eco] How to accommodate data with negative values for Canonical Correspondence Analysis in R using vegan Package

2014-02-26 Thread Gavin Simpson
___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-eco] partial ordination

2014-01-29 Thread Gavin Simpson
-rda(spe~1+Condition(env)) plot(partial.pca) Is this a reasonable approach? Some feedback would be great. Thanks, Duarte ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin

Re: [R-sig-eco] NA error in envfit

2013-12-06 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo

Re: [R-sig-eco] Erro in ordiR2step

2013-11-14 Thread Gavin Simpson
.n2.nabble.com/Erro-in-ordiR2step-tp7578520.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD

Re: [R-sig-eco] Missing species names in metaMDS object

2013-10-25 Thread Gavin Simpson
/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Re: [R-sig-eco] point color in NMDS (vegan)

2013-08-19 Thread Gavin Simpson
) # sites as text text(island.NMDS, display = 'sites') [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD

Re: [R-sig-eco] point color in NMDS (vegan)

2013-08-19 Thread Gavin Simpson
will the dune.env be in the case of metaMDS instead of rda? Thank you again Elaine On Tue, Aug 20, 2013 at 12:08 AM, Gavin Simpson ucfa...@gmail.com wrote: I have some posts on my blog that explain how to do this, ain the vein of Vit's reply (indexing via a factor). This way is preferable

Re: [R-sig-eco] Plotting adonis (vegan) results

2013-08-10 Thread Gavin Simpson
am wrong in any point, will be glad if someone corrects me. Cheers, Vit Dne 2013-08-09 19:25, Gavin Simpson napsal: What Jari meant was if you use `betadisper()` on your data then it will give you an object that has a `plot()` method which will give you something of relevance to what

Re: [R-sig-eco] Plotting adonis (vegan) results

2013-08-09 Thread Gavin Simpson
[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [[alternative HTML version deleted

Re: [R-sig-eco] mgcv:gam predicted class?

2013-07-18 Thread Gavin Simpson
[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor

Re: [R-sig-eco] Mixed effect (intercept) model with AR1 autocorrelation structure

2013-07-18 Thread Gavin Simpson
a mixed intercept model on the residuals to deal with the nested structure (and also the heterogeneity between plots). This runs, gives reasonable results that agree with the graphs, but is it statistically valid? Thanks, Jonathan From: Gavin Simpson

Re: [R-sig-eco] Mixed effect (intercept) model with AR1 autocorrelation structure

2013-07-17 Thread Gavin Simpson
-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w

Re: [R-sig-eco] Mixed effect (intercept) model with AR1 autocorrelation structure

2013-07-17 Thread Gavin Simpson
, hence it makes sense to model it this way. For the record, as simple AR1 model better account for the seasonal fluctuation than a gam, and my ARMA(2,0) model does an even better job. Hope this helps, J -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor

Re: [R-sig-eco] ordipointlabel with shortened names

2013-06-20 Thread Gavin Simpson
-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor

Re: [R-sig-eco] simple question about nmds

2013-06-10 Thread Gavin Simpson
list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute of Environmental Change Society [e] gavin.simp...@uregina.ca 523

Re: [R-sig-eco] Random Forest classification on species counts

2013-06-05 Thread Gavin Simpson
704.336.4110 Fax: 704.353.0473 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [t] +1 306

Re: [R-sig-eco] anova.cca question / missing data in constraining matrix

2013-06-05 Thread Gavin Simpson
___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute of Environmental

Re: [R-sig-eco] Mantel() with strata

2013-05-24 Thread Gavin Simpson
not to use it for `strata` in the permutation test if the null distribution you are testing needs to retain the archipelago-based clustering of samples. HTH G -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute

Re: [R-sig-eco] r2 values from envfit in NMDS

2013-05-17 Thread Gavin Simpson
is one of the machine learning tools that might usefully be applied. HTH G -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute of Environmental Change Society [e] gavin.simp...@uregina.ca 523 Research

Re: [R-sig-eco] NMDS and envfit

2013-05-15 Thread Gavin Simpson
. As for the species scores; metaMDS adds these as a convenience feature if the species data is available to it. They are added as a weighted average of the site scores and then possibly expanded. G thanks for any input on this! adrien -- Gavin Simpson, PhD [t] +1 306 337 8863

Re: [R-sig-eco] FW: betadisper

2013-05-14 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk

Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf

2013-04-22 Thread Gavin Simpson
Gillet [francois.gil...@univ-fcomte.fr] Date d'envoi : samedi 20 avril 2013 10:59 À : Gavin Simpson Cc: Aurélie Boissezon; r-sig-ecology@r-project.org Objet : Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf 2013/4/19 Gavin Simpson gavin.simp...@ucl.ac.ukmailto:gavin.simp...@ucl.ac.uk I

Re: [R-sig-eco] extract distance from betadisp {vegan}

2013-04-22 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology[f] +1 306 337 2410 Institute of Environmental Change

Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf

2013-04-19 Thread Gavin Simpson
A contrary view in-lined below: On Fri, 2013-04-19 at 15:19 +0200, François Gillet wrote: A lot of questions, some responses below... snip / Why not explore unconstrained ordination methods and went further with NMDS (V2 mission in Anderson et al 2011)? Just because your purpose is to

Re: [R-sig-eco] quantifying directed dependence of environmental factors

2013-03-11 Thread Gavin Simpson
On Thu, 2013-03-07 at 11:13 -0800, Rich Shepard wrote: On Thu, 7 Mar 2013, Philippi, Tom wrote: I would look at packages bio.infer, paltran, fossil, and analogue, and search to see if anyone has pushed them in the direction you want to go. To this list I would add Steve Juggins' excellent

Re: [R-sig-eco] quantifying directed dependence of environmental factors

2013-03-11 Thread Gavin Simpson
to *several* questions I've had already then I couldn't even have made it this far. Thank you! -- Gavin Simpson, PhD [t] +1 306 337 8863 Institute of Environmental Change Society [f] +1 306 337 2410 523 Research and Innovation Centre [e] gavin.simp

Re: [R-sig-eco] ordipointlabel for triplots

2013-03-07 Thread Gavin Simpson
On Thu, 2013-03-07 at 10:48 -0400, carolina monmany wrote: Hi all, I would like to use ordipointlabel() to plot a RDA but the function only displays species and sites. How can I include environmental variables as vectors? Thanks! You can use text(ord, display = bp) (where `ord` is

Re: [R-sig-eco] nMDS plot with points of different size

2013-03-07 Thread Gavin Simpson
On Thu, 2013-03-07 at 15:37 +, Mark Fulton wrote: There's probably something off the shelf, but I use a little function written in R: #A function for doing an xyz bubbleplot. bubbleplot - function(x, y, z, bmax=4, bmin=.5) { plot(x,y, type=n) z - z-min(z); z - z/max(z) for (i in

Re: [R-sig-eco] species scores for ordination in vegan

2013-02-25 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44

Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?

2013-02-25 Thread Gavin Simpson
On Mon, 2013-02-25 at 13:18 -0500, Sarah Loboda wrote: Hi, I have trouble to obtain the ordination graph I want. I want to have 4 RDA biplot on the same page and I don't want to have (or I want to modify) the axis numbers. I want the marks on the axis without numbers to maximize the space for

Re: [R-sig-eco] Vegan CCA - Problem in constraining variables

2013-01-18 Thread Gavin Simpson
! -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT

Re: [R-sig-eco] Error in La.svd(x, nu, nv) : error code 1 from Lapack routine 'dgesdd'

2013-01-16 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower

Re: [R-sig-eco] GCV in gam with mgcv

2013-01-16 Thread Gavin Simpson
/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London

Re: [R-sig-eco] betadisper() and variation in community change

2012-10-22 Thread Gavin Simpson
-vegdist(cen.si,method=euclidean) sites_main - factor(c(rep(1,4), rep(2,4)), labels = c(grazed,ungrazed)) mod3 - betadisper(time.dist,sites_main) boxplot(mod3) Cheers, Gustaf -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44

Re: [R-sig-eco] betadisper() and variation in community change

2012-10-22 Thread Gavin Simpson
if the within-site variation also differs. For example, a site may show little compositional variation over time overall, but the subplots may show large variation. Gustaf On 2012-10-22 13:57, Gavin Simpson wrote: betadisper() will give you a test of homogeneity of variance between groups

Re: [R-sig-eco] Question on block effect significance in 'adonis' PERMANOVA

2012-07-30 Thread Gavin Simpson
On Fri, 2012-07-27 at 09:45 +0100, Gavin Simpson wrote: On Mon, 2012-07-23 at 10:31 -0200, Alexandre Fadigas de Souza wrote: Dear friends, In performing a PERMANOVA in VEGAN's 'adonis' function, we can use strata to indicate a blocking variable. Contrary to standard statistical

Re: [R-sig-eco] Question on block effect significance in 'adonis' PERMANOVA

2012-07-27 Thread Gavin Simpson
-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http

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

2012-07-19 Thread Gavin Simpson
-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w

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

2012-05-25 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk

Re: [R-sig-eco] Poisson regression

2012-05-24 Thread Gavin Simpson
, append) : argument 2 (type 'list') cannot be handled by 'cat' what is meaning it? do i allow use it for continue? thanks -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f

Re: [R-sig-eco] CA

2012-05-11 Thread Gavin Simpson
[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t

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

2012-05-10 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679

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

2012-05-10 Thread Gavin Simpson
I've removed R-Help from this now... On Thu, 2012-05-10 at 10:13 +, Jari Oksanen wrote: On 10/05/2012, at 11:45 AM, Gavin Simpson wrote: snip / As you provide little or no context I'll explain what envfit() does etc. The idea goes back a long way (!) and is in my 1995 edition

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

2012-05-10 Thread Gavin Simpson
...@gmail.com Mobile: +41794385586 Skype: aghaynes On 10 May 2012 12:53, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: I've removed R-Help from this now... On Thu, 2012-05-10 at 10:13 +, Jari Oksanen wrote: On 10/05/2012, at 11:45 AM, Gavin Simpson wrote

Re: [R-sig-eco] bootstrapping gam models with multiple explanatory terms

2012-05-04 Thread Gavin Simpson
help that anyone can offer. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London

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

2012-04-26 Thread Gavin Simpson
-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson

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

2012-04-26 Thread Gavin Simpson
[[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson

[R-sig-eco] COURSE: Analysing Palaeolimnological Data with R

2012-04-08 Thread Gavin Simpson
have any further questions, please do not hesitate to contact me. We look forward to seeing you in August. Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565

Re: [R-sig-eco] MAFA function

2012-04-03 Thread Gavin Simpson
-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk

Re: [R-sig-eco] chronological clustering and dynamic factor analysis

2012-03-12 Thread Gavin Simpson
-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http

Re: [R-sig-eco] Co-correspondence analysis

2012-03-01 Thread Gavin Simpson
data, yes, presence absence data can be analysed using CoCA. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e

Re: [R-sig-eco] non-metric MDS comparison - vegan vs. ecodist packages

2012-02-20 Thread Gavin Simpson
-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http

Re: [R-sig-eco] non-metric MDS comparison - vegan vs. ecodist packages

2012-02-20 Thread Gavin Simpson
. You could always do a procrustes rotation on the two configurations to see how well they compare. G Gian 2012/2/20 Gavin Simpson gavin.simp...@ucl.ac.uk On Mon, 2012-02-20 at 16:28 +0100, Gian Maria Niccol Benucci wrote: Hi r-sig-ecology Members, I would please you to examine

Re: [R-sig-eco] non-metric MDS comparison - vegan vs. ecodist packages

2012-02-20 Thread Gavin Simpson
can find it, maybe it escapes me... Thank you very much for your aid, Gian 2012/2/20 Gavin Simpson gavin.simp...@ucl.ac.uk On Mon, 2012-02-20 at 17:24 +0100, Gian Maria Niccol Benucci wrote: Dear Gavin, Thank you very much. I tried with your advice but the result

Re: [R-sig-eco] singletons and doubletons in vegan

2012-02-01 Thread Gavin Simpson
___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679

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

2011-12-23 Thread Gavin Simpson
-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK

Re: [R-sig-eco] envfit calculation

2011-12-20 Thread Gavin Simpson
deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522

Re: [R-sig-eco] Problem with a loop

2011-11-28 Thread Gavin Simpson
://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk

Re: [R-sig-eco] interpreting adonis results

2011-11-25 Thread Gavin Simpson
,SIMa,SIMb,SZV,BM,BRE)) levels(groups) [1] SIG BA SIMa SIMb SZV BM BRE Do check that code you use creates the expected results! HTH G Gian 2011/11/17 Gavin Simpson gavin.simp...@ucl.ac.uk On Thu, 2011-11-17 at 10:01 +0100, gabriel singer wrote: ... dangerous wording

Re: [R-sig-eco] interpreting adonis results

2011-11-25 Thread Gavin Simpson
diversity, in the vegan tutorial at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf. best, kay Zitat von Gavin Simpson gavin.simp...@ucl.ac.uk: On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccolò Benucci wrote: Hi all, I had 84 samples

Re: [R-sig-eco] interpreting adonis results

2011-11-17 Thread Gavin Simpson
of a dispersion effect using the function betadisper(), then you know a bit more about the type of effect. Indeed, and as the author of that function I too would suggest that the homogeneity assumption be tested. G gabriel On 11/16/11 11:02 PM, Gavin Simpson wrote: On Wed, 2011-11-16 at 03

Re: [R-sig-eco] interpreting adonis results

2011-11-16 Thread Gavin Simpson
-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson

Re: [R-sig-eco] aov vs. glm

2011-11-11 Thread Gavin Simpson
-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson

Re: [R-sig-eco] aov vs. glm

2011-11-11 Thread Gavin Simpson
-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E

Re: [R-sig-eco] Question on using strata in a pRDA

2011-11-08 Thread Gavin Simpson
/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w

Re: [R-sig-eco] Dynamic factor analysis

2011-11-07 Thread Gavin Simpson
]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL

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