search for: vegdist

---------- Forwarded message ---------- From: <r-help-owner@r-project.org> Date: 2013/2/8 Subject: vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande To: caro.bello58@gmail.com Message rejected by filter rule match ---------- Mensaje reenviado ---------- From: caro bello <caro.bello58@gmail.com> To: r-help@r-project.org Cc: Date: Fri, 8 Feb 2013 15:18:40 -08...

hello, i'd be happy if someone could provide help with the following problem: i have a dist.matrix that comes from vegdist() function of the vegan package. the used method = "horn" is not accepted as argument in hvcluster(...,dist.method="..."). is there a way to incorporate the method "horn" in hvcluster()? thanks in advance! yours, kay -- View this message in context: http://n4.nabb...

...ot about this question, but I do not get the answer about it. Although I know that the R function is adonis () (vegan package), it does not work: adonis(Pha.env~SPha, data=Pha, permutations=10) The error message: Error: cannot allocate vector of size 334.2 Mb In addition: Warning messages: 1: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 2: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 3: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 4: I...

Hi I have just (finally) started to poke around in R and wanted to analyse a stream fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an error message saying that: Error in isoMDS(vare.dis) : zero or negative distance between objects 14 and 15 i.e. the two sites w...

..."maximum", full=TRUE, sq=F) ~ beers + slope_dem + elev_dem+ plc_dem + pr_curv+ +curv+max_depth+doc_rocks+ abandon+land_use+ca_old, data=ba12, xv="p") This works fine. Now I would like to use other dissimilarity measures as can be found in the function dist (STATS) or vegdist (VEGAN). De'Ath notes that gdist should be interchangeable with dist - but I receive following error message: > fit21 <- mvpart(dist (ba12[,18:29], meth="minkowski", diag=T, upper=T p=2) ~ beers + slope_dem + elev_dem+ plc_dem + pr_curv+ curv+max_depth+doc_rocks+ ab...

...ed to look at similar problems but I get error messages. Any ideas? #NMDS step1<-read.delim2("day20.txt", row.names=1) library(clusterSim) step2<-data.Normalization(step1,type="n10") step3<-asin(sqrt(step2))*57.3 step4<-t(step3) library(vegan) step5<-data.matrix(vegdist(step4,method="bray")) step6<-metaMDS(step5, autotransform=FALSE) plot(step5) Warning message: In ordiplot(x, choices = choices, type = type, display = display, : Species scores not available #PerMANOVA step1<-read.delim2("day20.txt", row.names=1) library(clusterSim) s...

Hi, I need to run a PCoA (PCO) for a data set wich has both positive and negative values for variables. I  could not find any distancecoefficient other than euclidean distace running for the data set. Are there any other coefficient works with negtive values.Also I cannot get summary out put (the eigen values) for PCO as for PCA.   Thanks. Dilshan [[alternative HTML version deleted]]

...-O2 -pipe -c ordering.f -o ordering.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c pnpoly.c -o pnpoly.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c stepacross.c -o stepacross.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c vegdist.c -o vegdist.o *gcc -shared -o vegan.dll cepin.o data2hill.o decorana.o goffactor.o monoMDS.o nestedness.o ordering.o pnpoly.o stepacross.o vegdist.o -lgfortran -lcygwin -luser32 -lkernel32 -ladvapi32 -lshell32 -L/usr/lib/R/lib -lR /usr/lib/libintl.dll.a -L/usr/lib/ncursesw /usr/lib/libiconv.dll.a...

...results[["significantclusters"]] <- simprof.results$samples return(results) } <environment: namespace:clustsig> I tried to trick the function by bypassing the input of a raw community matrix (sites x species) by inputing instead a distance matrix already calculated with vegdist (vegan package) (Jaccard distance is available in vegdist, but not in the function dist used in simprof...) I therefore modified the function as follow: simprof2=function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average", alpha = 0.05, sample.orientation = &...

Hello I have 2 rows in a matrix and I want to calculate the Gower Distance between the 2 , how can I do it? I searched and found nothing that can help me, and my program doesn't know the gdist function and I couldn't find it on the R help site. Can anyone help me plz Thank u all [[alternative HTML version deleted]]

...p26288610/cor.coef.R cor.coef.R . As it is now, it is extremely long, and for the future I was hoping to find a more efficient way of doing this sort of thing. To give you an outline of the function, first I create the dissimiarity matrices using all possible methods in the VEGAN command "vegdist", then create the clusters using all possible algorithms in "hclust" and the dissimilarity matrices I crated, then create a table, and in one column, list all combinations, and in the other, compute and put the cophenetic correlation. Any help would be appreciated! I'm pretty n...

...trix of Spearman's `rho' rank correlation coefficients for all possible pairs of columns of a matrix. What if I want a matrix of rank correlation coefficients for pair of columns of two different matrices? I have the same question about distance metrics in package Vegan. The function 'vegdist' computes distance indexes for all possible pairs of row of a matrix. What if I am interested in comparing each single row of matrix A with the correspondent row of matrix B? Any help would be appreciated. Luca

How to calculate sorensen (bray-curtis) distance by dist function within the vegan package? Cheers Duccio

Hello, I am attempting to assign significance levels to a UPGMA cluster analysis as part my doctoral research. The pvclust function works well but doesn't include the similarity index I need (morisita's) as an option for computing a distance matrix. Morisita's is available in vegdist in the VEGAN library but I am having a hard time getting the vegdist function to "direct drop" into pvclust as the vegdist documentation suggests. I would appreciate any suggestions. Thank you Brad Bradley N. Strobel Department of Natural Resource Management Texas Tech Universit...

Dear r-helpers! How can I integrate other distances (in the form of a dist object) into function metaMDS? The problem: metaMDS needs the original data.frame for the calculation and only the default distances of function vegdist are allowed. Any suggestions are greatly appreciated! Thank you, Kim -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 - sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser

...a way to 'print' the results to a table that shows which plots were in what group, correct? I've attached the matrix I'm working with (the whole thing since the point is its large size). I've been able to run the following code to get the groups I need: > VTM.Dist<- vegdist(VTM.Matrix) > VTM.HClust<- hclust(VTM.Dist, method="ward") > plot(VTM.HClust, hang=-1) It takes a while, but it does run. Then, I can extract 8 groups, which I'd like to experiment with, but is about how many I'd like: rect.hclust(VTM.HClust, 8) > VTM.8groups<...

Hi folks, I tried for the first time hclust. Unfortunately, with missing data in my data file, it doesn't seem to work. I found no information about how to consider missing data. Omission of all missings is not really an option as I would loose to many cases. Thanks in advance Holger -- View this message in context:

Hello, I am a relatively new user of R. I have written a basic function to calculate the Gower similarity function. I was motivated to do so partly as an excercise in learning R, and partly because the existing option (vegdist in the vegan package) does not accept missing values. I think I have succeeded - my function gives me the correct values. However, now that I'm starting to use it with real data, I realise it's very slow. It takes more than 45 minutes on my Windows 98 machine (R 2.0.1 Patched (2005-03-29))...

...vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe, spe.chwo) spe is the dataframe spe.chwo came from: spe.norm <- decostand(spe, "normalize") spe.ch <- vegdist(spe.norm, "euc") spe.ch.UPGMA <- hclust(spe.ch, method = "average") spe.chwo <- reorder.hclust(spe.ch.UPGMA, spe.ch) and the error is Error in vegemite(spe, spe.chwo) : Cowardly refusing to use longer than 1 char symbols: Use scale The data in the dataframe is bio...

Hi, I'm having some trouble with a bit of combined C & R code. I'm trying to write a C function to handle the for loops in a function I'm working on to calculate a similarity matrix. Jari Oksanen has kindly added the necessary changes to the vegan package so that I can use the vegdist function, so this isn't absolutely necessary. However, I'm stubborn and want to know why Jari's code works and mine doesn't! Other than, of course, the obvious - one of us knows what their doing and the other doesn't. I would appreciate any help. What I've done is: pass...