search for: decostand

Hi: I do not know why the function decostand is not found in my vegan library, I have downloaded the package recently, and it seems to work well..Do you have any suggestion? Rosa. [[alternative HTML version deleted]]

...a matrix *My code is like * library(vegan) library(ggplot2) library(dplyr) rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv", header=T, stringsAsFactors=T) rassevee<-read.csv("C:/Users/hp/Desktop/R_data/rassenv.csv", header=T, stringsAsFactors=T) sptrans <- decostand(rassspec, "hellinger") envtrans <- decostand(rassevee, "hellinger") vare.cca <- cca(sptrans, envtrans) Any kind of help will be appreciable Thanking you regards Shailendra Pal Research Scholar Plant Ecology Lab (Prof. S.C. Garkoti) School of Environmental Sciences JNU...

...hat I can't seem to figure out. I am using the 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 s...

...igenvalues > > 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 Analysis &g...

Hi every body: I need some help with kendall.global. The example in the manual seems not working well, and cannot used with my data, always the same error. data(mite) > mite.hel <- decostand(mite, "hel") > > # Reproduce the results shown in Table 2 of Legendre (2005), a single group > mite.small <- mite.hel[c(4,9,14,22,31,34,45,53,61,69),c(13:15,23)] > kendall.global(mite.small) Errore in FUN(newX[, i], ...) : .Random.seed is not an integer vector but of ty...

Hi, I would like to calculate the RELATIVE euclidean distance. Is there a function in R which does it ? (I calculated the abundance of 94 chemical compounds in secretion of several individuals, and I would like to have the chemical distance between 2 individuals as expressed by the relative euclidean distance. Some compounds are in very low abundance whereas others are in high abundance,

...al community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <- decostand(gotu,"hell") G.var <- varpart(gotud,~Depth,~CH4_oxidation,~d13C_DIC+Temperature+Spec.Conductivity+DO+CH4+N2O+pH, data=ge) plot(G.var) Sample depth T SpCond DO pH Chl CH4 CH4oxidation N2O TA POC BP SO4 Gi25Feb12 25 24.46 1104 4.42 8.94 1.6 40.00174578 1.1 6.683260809 12.723 41.98...

...on definition for ?panel.abline? plot3d.prcurve: no visible global function definition for ?rda? prcurve: no visible global function definition for ?rda? tran.default: no visible global function definition for ?wisconsin? tran.default: no visible global function definition for ?decostand? I realise that I don't importFrom all of those functions in NAMESPACE - I've missed some so this list is actually very handy. But also I Depend on packages that provide some of the function complained about. Is that the cause of these NOTEs? Is the expectation that if I am using a functi...

Hello I am using Jari Oksanen's CCA routine from the Vegan package on some estuary data, following a technique applied in (Anderson, M.J. & Gribble, N.A., 1998, Partitioning the variation among spatial, temporal and environmental components in a multivariate data set, Australian Journal of Ecology 23, 158-167). Some steps in the process require that the dependent matrix be constrained by

..."plafem", "plafos", "placom", "tacfim", "cicsex", "spsK"), row.names = c("AP-0", "AP-100", "AP-200", "AP-300", "ST-0", "ST-100"), class = "data.frame") apst.log <- decostand(apst, "log") apst.bray <- vegdist(apst.log) apst.clusters <- hclust(apst.bray, method = "average") vegemite(apst, apst.clusters)

Hello, everybody, I hope somebody could help me with a dist() function. I have a data frame of size 2*4087 (col*row), where col corresponds to the treatment and rows are species, values are Hellinger distances, I should reconstruct a distance matrix with a dist() function. I know that "euclidean" method should be used. When I type: dist(dframe,"euclidean") it gives me a

...erl ../../../share/perl/build-help-windows.pl -txt -html -example -latex C:/R/rw1040/src/gnuwin32/vegan C:/R/rw1040/library >>> Building/Updating help pages for package `vegan' Formats: text html latex example decorana text html latex example decostand text html latex example diversity text html latex example initMDS text html latex example postMDS text html latex example procrustes tex...

Hello, i have a xls file. I will read it in r, what library-command i use for this?? any ideas?? Thanks Michele [[alternative HTML version deleted]]

...s a wunderkind when > it comes to transformation, but in the package vegan type > ?wisconsin > and that should give you a start,  but if you know what > transformations you would like to preform then apply should do what > you need with whatever transformation you are trying to use. decostand provides (mostly) standardisations not transformations, it even says so. What Holger is looking for is something like a Box Cox transform for bivariate normality but to instead achieve multivariate normality. That is a different kettle of fish to what decostand tries to do. HTH G > > Step...