Re: [R-sig-eco] Clustering large data

2008-10-24 Thread Dave Roberts
Thierry and Hadley, Sorry to be late coming into this (I forgot I subscribed to sig-eco). package labdsv has a function called matrify() which takes a three column data.frame (sample,taxa,abundance) and creates a full (sparse) matrix representation. I've never tried it on a data set

Re: [R-sig-eco] Teaching materials

2009-08-26 Thread Dave Roberts
Volker, You're welcome to take look at my site: It's primarily for multivariate analysis in community ecology, bit does also have some stuff on GLMs and GAMS in an ecological context. You might also visit with Hank Stevens at Miami as he's just next

Re: [R-sig-eco] multivariate smoothing and gradient estimation

2009-09-16 Thread Dave Roberts
Chris, One (sub-optimal) solution would be to fit GAMS and then have the gam.predict estimate values immediately near your data points which you could use to calculate a local gradient. If the GAM is reasonably smooth, I would think you could get estimates that were reasonable. Dave --

Re: [R-sig-eco] Dissimilarity ranking

2010-12-09 Thread Dave Roberts
of a # plot to itself apply(as.matrix(demodis),1,mean) # calcualte the mean dissimilarity # of every plot to the others This is all done as part of function disana() in package labdsv along with some other simple dissimilarity analyses. Dave Roberts

Re: [R-sig-eco] The final result of TWINSPAN

2011-04-26 Thread Dave Roberts
Dear List, Earlier this year on an (undoubtedly ill-advised) lark I coded up an R version of TWINSPAN. It's far from a polished package at this point, but the code does run. One of the interesting features is that you can partition a PCO or NMDS in addition to the traditional CA. To be

Re: [R-sig-eco] The final result of TWINSPAN

2011-04-27 Thread Dave Roberts
Modified TWINSPAN classification in which the hierarchy respects cluster heterogeneity Journal of Vegetation Science 20(4): 596–602 Zoltan 2011.04.26. 23:40 keltezéssel, Dave Roberts írta: Dear List, Earlier

Re: [R-sig-eco] controlling the species displayed on a biplot

2011-05-25 Thread Dave Roberts
Thanks Gavin. That's actually very nice and I suspect just what Andy was looking for. Dave On 05/23/2011 04:33 AM, Gavin Simpson wrote: require(vegan) require(labdsv) data(dune) data(dune.env) ## Indicators of Management type set.seed(38) inds- with(dune.env, indval(dune, Management)) ##

Re: [R-sig-eco] help with analysis

2011-08-19 Thread Dave Roberts
Hi Kátia, Sorry to be so late; just back in the office. Pedro is correct that adonis will help establish statistical significance to potential differences, but I think NMDS could still be very helpful. One approach would be to code the sites by glyph (e.g. site 1 = circle, site 2 =

Re: [R-sig-eco] Multivariate ANOVA/repeated measures

2011-10-10 Thread Dave Roberts
On 10/07/2011 08:51 AM, Dr N.A. Cutler wrote: Dear All, I have a query about multivariate analysis of community data. In my experiment, 24 microbial communities in different locations were sampled using Sampling Technique 1 (ST1). A site X species matrix was then derived by molecular

Re: [R-sig-eco] Multivariate ANOVA/repeated measures

2011-10-10 Thread Dave Roberts
On 10/10/2011 02:15 PM, Gavin Simpson wrote: On Mon, 2011-10-10 at 09:11 -0700, Rich Shepard wrote: On Mon, 10 Oct 2011, Dave Roberts wrote: I want to compare the results of the two sampling exercises in order to test the performance of the two sampling techniques. I would try

Re: [R-sig-eco] The problems on BIO-ENV procedure by [R]

2011-12-05 Thread Dave Roberts
the duplicate plots you can change the zero to a small value d[d==0] - 0.0001 and run the isoMDS on the resulting revised dissimilarity matrix. Undoubtedly someone from the vegan group will respond to your second question. Dave Roberts On 12/05/2011 01:28 AM, 坪井 隼 wrote: Dear Madam / Sir, I have two

Re: [R-sig-eco] Recommended R package for analyzing community data set? - nested design, stratified random sampling, covariates

2012-01-17 Thread Dave Roberts
in. Dave Roberts On 01/15/2012 12:10 PM, Laura S wrote: Dear all: May you recommend an R package for analyzing this data set? I would greatly appreciate any thoughts you can provide. I. Study goals This study examines soil crust (lichens and bryophytes) recovery and succession in fields

Re: [R-sig-eco] [R] Component analysis / cluster analysis of multiple sites based on soil characteristics

2012-01-23 Thread Dave Roberts
is available in the ecodist package you already have loaded. Dave Roberts On 01/23/2012 05:51 AM, Sacha Viquerat wrote: Hello dear list! Maybe I am demanding too much, but I am having problems finding the right way to tackle a seemingly trivial problem: We counted fish at different sites. In order

Re: [R-sig-eco] IndVal groups Plotting an RDA with labels

2012-07-03 Thread Dave Roberts
(clustid) and see if cluster size is unique. Dave Roberts On 07/03/2012 07:12 AM, Caitlin Porter wrote: Dear all, I am working with a large data set to examine plant community structure on barrens habitats and have a couple of questions regarding Indval (labdsv package) on Wards Clusters (hclust

Re: [R-sig-eco] Zuur / Pinierho / Faraway

2012-11-30 Thread Dave Roberts
Philip, IS there an online errata,or do you just have to be smart and diligent? Thanks, Dave On 11/29/2012 07:30 AM, Dixon, Philip M [STAT] wrote: I agree with all the previous comments and second Tom's recommendations of Faraway as an 'in between' Zuur and Piniehro Bates. One thing to

Re: [R-sig-eco] fonction spc.pres in labdsv package

2013-04-26 Thread Dave Roberts
=;, header=TRUE) any( newveg[1:10,1:10] and then spc.pres- apply(newveg0,2,sum) any( Dave Roberts On 04/19/2013 06:49 AM, lisa couet wrote: Hi, I have an issue concerning the fonction spc.pres in package labdsv. the message is: Erreur dans plot.window