search for: bray

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2004 Mar 16
2
bray-curtis?
Does R have a function to calculate Bray-Curtis distance measures, which is probably one of the most frequently used and recommended dissimilarity measures in ecology? It isn't mentioned in dist().
2013 Jun 22
1
metaMDS Error, Nan similar or negative values
...0 0 0 0 0 0 0 96 0 D30M1A 60 0 0 0 0 0 0 0 0 0 74 0 169 When I tried to perform metaMDS, it was not working, with the error > ord1 <- metaMDS( X ="bray") Square root transformation Wisconsin double standardization Error in if (any(dist < -sqrt(.Machine$double.eps))) warning("some dissimilarities are negative -- is this intentional?") : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In distfun(comm, meth...
2004 Dec 10
1
How to circumvent negative eigenvalues in the capscale function
Dear All I am trying to do a partial canonical analysis of principal coordinates using Bray-Curtis distances. The capscale addin to R appears to be the only way of doing it, however, when I try and calculate a Bray-Curtis distance matrix either using Capscale or Vegedist (capscale I understand uses Vegedist anyway to calculate its distance matrix), R uses up all available memory on the co...
2008 May 12
1
inserting mathematical symbols in lattice strip
...xyplot(adjusted_Rand_index~cluster|distance_measure, main="Level of agreement between partitions: Wards Method", ylab="Coefficient value (adjusted rand index)", xlab="number of clusters", type="l", data=randA1, strip=strip.custom(varnames=c(expression(sqrt(Bray-Curtis))) Is there a way of generating the square root symbol inside the strip or am I wasting my time. i.e. converting Bray-Curtis to ... [sqrt symbol] Bray-Curtis. Thank you very much Regards Andrew http://www.nabble.com/file/p17188291/randA1.csv randA1.csv -- View this message in conte...
2011 Feb 16
0
y-axis slightly cut-off after printing plots to tiff
...e could help me a bit. I have plotted the following: ########################################### tiff("plot7.tiff",units="cm",width=15,height=36,res=700) layout(matrix(c(1,2,3,4,5,6),3,1),widths=lcm(c(15)),heights=lcm(c(12,12,12)),respect=TRUE) plot.t1<-plot(data.dist,flot1.bray.hell,xlab="",ylab="Bray-Curtis dissimilarity index",cex.lab=2,cex.axis=1.7,pch=20,cex=2,col="darkgray",font=2,font.lab=2);text(0,0.34,"a",font=2,cex=1.7);text(1.5,0.07,"y=0.041x + 0.113",cex=1.7,font=2);text(1.3,0.05,"R2=0.1785",cex=1.7,fo...
2010 Apr 18
8
[Bug 27720] New: Hard Hang on suspend - 8600M GS
https://bugs.freedesktop.org/show_bug.cgi?id=27720 Summary: Hard Hang on suspend - 8600M GS Product: xorg Version: git Platform: x86-64 (AMD64) OS/Version: Linux (All) Status: NEW Severity: normal Priority: medium Component: Driver/nouveau AssignedTo: nouveau at lists.freedesktop.org
2010 Feb 26
2
Error in mvpart example
Dear all, I'm getting an error in one of the stock examples in the 'mvpart' package. I tried: require(mvpart) data(spider) fit3 <- rpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method="dist") #directly from ?rpart summary(fit3) ...which returned the following: Error in apply(formatg(yval, digits - 3), 1, paste, collapse = ",", sep = "") : dim(X) must have a positive length...
2007 Aug 22
1
distance by vegan
How to calculate sorensen (bray-curtis) distance by dist function within the vegan package? Cheers Duccio
2008 Aug 13
1
re placing default labels in lattice
...4)~factor(distance),aspect=1.0,cex=1.0,xlab="Distance",ylab="Residuals",data=meanAG, span=1, panel=function(x,y,span){ panel.grid(h=0, v=-1) panel.xyplot(x,y,cex=1.0,points="jitter") panel.loess(x,y, span) panel.axis(side="bottom",at=TRUE, labels=c(expression(Bray-Curtis^{1}),expression(Bray-Curtis^{2}),expression(Canberra),expression(Gower),expression(Hellinger),expression(Kulczynski))) }) http://www.nabble.com/file/p18964008/meanAG.csv meanAG.csv -- View this message in context: http://www.nabble.com/replacing-default-labels-in-lattice-tp18964008p1896400...
2011 Oct 03
4
distance coefficient for amatrix with ngative valus
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]]
2011 Sep 09
2
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
...ems 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) step2<-data.Normalizat...
2006 Nov 10
2
Problems with metaMDS from vegan
...version 1.8-3 on both machines. On the new Ubuntu machine I even tried to regress to the Vegan 1.6-10, but to no avail, as the error remains the same: As soon as a I try to process an R matrix (see below) to obtain the MDS I am confronted with: > meta <- metaMDS(distab.dist, distance="bray", k, trymax=50) Fehler in rowSums(x, na.rm = TRUE) : 'x' muss ein Array mit mindestens zwei Dimensionen sein Ausf?hrung angehalten ( translated: error in rowSums(x, a.rm = TRUE) : 'x' must be an array of at least two dimensions. Execution stopped ) This error is not appearing...
2013 Dec 17
1
What is the formula of Pseudo-F statistic in capscale in vegan?
...ence that provides this formula? We ask because we are doing the exact same analysis in another program (using distLM in PRIMER 6 v 6.1.13 and PERMANOVA+ v 1.0.3 from PRIMER-E), but we are getting very different pseudo-F ratios despite specifying the exact same order of model terms, using the same Bray-Curtis distance measure (distance matrices produced by the two programs are the same), and using the same sequential test for significance. Below is a table displaying the order of the model terms and the pseudo-F values computed by R and by PRIMER (we also ran the same analysis in CANOCO which sho...
2009 Sep 01
3
Strange error returned or bug in gam in mgcv????
Dear friends, what is this error message in gam???? I cannot understand what it means .... is it a bug? gam_bray_scot24_pc_0505<gam(bray~s(PC1,PC2,PC3,PC4,PC5, PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate) Error in if (length(data) != vl) { : missing value where TRUE/FALSE needed Calls: gam ... smooth.construct -> smooth.construct.tp.smooth.spec -> array In addition: Warning...
2007 Aug 14
0
Comparing long species lists via Sorenson’s dissimilarity
...to interpret the above results? I have read a paper that states that when comparing two samples if QS is less than 50% than the samples are considered dissimilar, what is 100%? I mean 50% of what? There are a number of other tests that I can run using R. These are squared euclidan, manhattan, bray-curtis, jaccard, ruzicka, (dis)similarity ratio, ochiai, cosine compliment, and Raup-crick. Would it be advantageous to run these now that I have my sorensons result? It is especially easy for me to run the Bray-Curtis all I would need to do is change the terms from ‘binary’ to ‘minimum’ and re-run...
2008 May 12
1
Mathematical annotation in lattice strip: Is it possible?
.... xyplot(adjusted_Rand_index~cluster|distance_measure, main="Level of agreement between partitions: Wards Method", ylab="Coefficient value (adjusted rand index)", xlab="number of clusters", type="l", data=randA1, strip=strip.custom(varnames=c(expression(sqrt(Bray-Curtis))) Is there a way of generating the square root symbol inside the strip or am I wasting my time. Thank you very much Regards Andrew http://www.nabble.com/file/p17187888/randA1.csv randA1.csv -- View this message in context: http://www.nabble.com/Mathematical-annotation-in-lattice-str...
2010 Dec 01
1
procrustes results affected by order of sites in input file
..., I am using a Procrustes analysis to compare two NMDS ordinations for the same set of sites. One ordination is based on fish data, the other is based on invertebrate data. Ordinations were derived using metaMDS() from the {vegan} library as follows: fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100, wascores=TRUE, trace=TRUE, zero="add") invert.mds<-metaMDS(bugcal.a, distance="bray", k=3, trymax=100, wascores=TRUE, trace=TRUE, zero="add"), where fish.data and invert.data are site-by-abundance matrices for fish and invertebrates, respe...
2010 Feb 09
1
Bug#569014: logcheck kernel rules don't match [<blank><number>.<number>]
...of "[[:digit:]]+\.[[:digit:]]", giving the following re: ^\w{3} [ :0-9]{11} [._[:alnum:]-]+ kernel:( \[ +?[[:digit:]]+\.[[:digit:]]+\])? tun: Universal TUN/TAP device driver, [.[:digit:]]+$ I am using Debian GNU/Linux "lenny" 5.0.4 with kernel 2.6.26-2-amd64. -- Daniel Le Bray Centre de Ressources Informatiques Universite du Havre
2004 May 13
2
BIO-ENV procedure
I've been unable to find a R package that provides the means of performing Clarke & Ainsworth's BIO-ENV procedure or something comparable. Briefly, they describe a method for comparing two separate sample ordinations, one from species data and the second from environmental data. The analysis includes selection of the 'best' subset of environmental variables for explaining
2012 May 09
1
reception of (Vegan) envfit analysis by manuscript reviewers
...ion in the Vegan package. Has anyone else struggled to effectively explain this analysis? If so, can you share any helpful tips? The most recent comment I've gotten back: "What this shows is which NMDS axis separates the communities, not the relationship between the edaphic factor and the Bray-Curtis distance." Thanks for any suggestions! Matt