search for: vegdist

Displaying 20 results from an estimated 30 matches for "vegdist".

2013 Feb 08
vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande
---------- Forwarded message ---------- From: <> Date: 2013/2/8 Subject: vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande To: Message rejected by filter rule match ---------- Mensaje reenviado ---------- From: caro bello <> To: Cc: Date: Fri, 8 Feb 2013 15:18:40...
2010 Feb 02
hvcluster() with distance method from vegdist(), package = vegan
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://...
2010 Mar 16
memory failure in adonis function (permanova)
...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...
2006 Mar 08
function gdist, dist and vegdist in mvpart
..."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...
2011 Sep 09
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
...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...
2011 May 17
simprof test using jaccard distance
...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 = &...
2008 Apr 14
Vegan R^2 and tau values for metaMDS
I am using the function metaMDS with jaccard distances to ordinate a set of constituent by site matrix. I can post this data if it would be helpful, but it is large to include in an email. I can also provide reproducable code if necessary. I would like to get an R^2 value for the axes of the ordination configuration that I get with metaMDS in the vegan package is there a way to do this- is it
2007 Aug 22
distance by vegan
How to calculate sorensen (bray-curtis) distance by dist function within the vegan package? Cheers Duccio
2008 Jun 16
pvclust distance matrix
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...
2012 Oct 11
extracting groups from hclust() for a very large matrix
...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<...
2013 Jul 23
Heat Map for species - code from Numerical Ecology with R
...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") <- vegdist(spe.norm, "euc") <- hclust(, method = "average") spe.chwo <- reorder.hclust(, 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...
2005 Nov 09
how to convert strings back to values?
...eading the dataset. When I transpose the dataset, the original values become strings (instead of 0,1,0,0,1 I have "0","1","0","0","1"). The distance matrix cannot be counted from the transposed dataset, I have 2 error messages: <Warning in vegdist(tdf1, method = "jaccard", binary = FALSE, diag = FALSE, : results may be meaningless because input data have negative entries> <Error in rowSums(x, prod(dn), p, na.rm) : 'x' must be numeric> I do not understand the first, since I have only 1 and 0 in the dataset. I...
2005 Nov 10
error in rowSums:'x' must be numeric
...a comma separated file. I would like to calculate the Jaccard distance of the dataset. I have the following error message: Error in rowSums(x, prod(dn), p, na.rm) : 'x' must be numeric In addition: Warning message: results may be meaningless because input data have negative entries in: vegdist(t2, method = "jaccard", binary = FALSE, diag = FALSE, Do you have any idea what can be the problem? I have only 0 and 1 in the dataset. Thank you very much! All the best: Eszter _______________________________________________________________________ KGFB 2006 - Garant??ltan a le...
2004 Sep 07
heatmap help
Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried >heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in
2018 Apr 18
nMDS with R: missing values
...Message----- From: Jessie Woodbridge <jessie.woodbridge at> Sent: Wednesday, April 18, 2018 3:42 AM To: David L Carlson <dcarlson at> Subject: RE: nMDS with R: missing values Dear Prof Carlson, Thank you for your reply. I'm using 'vegan' with 'vegdist' and 'bray'. I have a selection of datasets that cover different time periods (converted to z-scores), so a record that starts 5000 years ago would have missing data before this date when other records cover the last 8000 years. I need to build into the nMDS the fact that this isn't...
2013 Jan 30
betadisper plot
Hello, I tried to make a betadisper plot; however, it is quite messy at the moment with lines and symbols. I made two plots, one focusing on sites and the other on treatments. This is the code that I used: plot(betadisper(vegdist(y.nth,method="euclidean"),site)) plot(betadisper(vegdist(y.nth,method="euclidean"),treatment)) I have a few questions pertaining to how I could clean up the figures for interpretation purposes: How would I be able to place labels on the centroids, which would enable me to ident...
2013 Jun 11
'Boolean Index too long'
#Hi, I am trying to run an MRPP with community data (spp-site-matrix). I use the following code: mzbtaxa_mrpp <- mrpp(mzbdist,mzbsites$Site) #mzbdist being a distance object (Bray-Curtis similarity matrix) derived from my sqrt transformed community data set, created with function 'vegdist', mzbsites$Site refers to factors structuring my community. #when I run this code, I get the following error message: error in dmat[ind == x, ind == x] : (subscript) boolean index too long #What does that mean? How can I solve this problem? #thanks a lot for your help, #Claudia [[alterna...
2018 Apr 17
nMDS with R: missing values
Dear All, I was wondering whether anyone might be able to provide some advice with an nMDS / R problem. I?m trying to run nMDS on a dataset that contains many missing values and was wondering how I can account for the missing values when running nMDS? It seems as though the data are being grouped depending on where the zero values appear. Any suggestions greatly appreciated. Thank you very
2005 Mar 14
Significance of Principal Coordinates
...he eigenvalues > > nEigen <- round(ncol(Data*0.8)) > > # Calculate Weights for Principal Coordinates Analysis > > Total <- apply(Data,1,sum) > Weight <- round(Total/max(Total)*1000) > > > # Calculate Chord Distance > > library(vegan) > Chord <- vegdist(decostand(Data, "norm"), "euclidean") > > # Calculate Principal Coordinates, including distance matrix row weights > > library(ade4) > PCoord.Eigen <- dudi.pco(Chord,row.w=Weight,scann=F,full=T)$eig[1:nEigen] > > # Randomization of Principal Coordinates A...
2013 Dec 17
What is the formula of Pseudo-F statistic in capscale in vegan?
...and Clarke 2008, Chapter 4. Pg. 129, and based on pseudo-F equation in Legendre and Anderson (1999), Ecological Monographs vol. 69): F= (SSFull - SSReduced)/(qFull-qReduced) (SSTotal-SSFull)/(N - qFull - 1) (3) R code ## creating Bray-Curtis of Biodiversity data H.BC <- vegdist(H.Full [,14:211], "bray") ## Distance based redundancy analysis (dbRDA) m1<-capscale(H.BC ~ GroupSize + Board + MtgStyle + DmStyle + DifView + VolAuton, SScomp [,14:19], distance = "euclidean", add = TRUE) ### NOTE: pseudo-F values are the same with or without correctin...