search for: varespec

If you submit these lines, you end up with variable "vare.dis". I want to export vare.dis to csv. Stuck I am. library(vegan,logical.return = TRUE) #return=true verifies package is available library(MASS,logical.return=TRUE) #return=true verifies package is available data(varespec) #varespec is an example data file in the vegan package vare.dis <- vegdist(varespec) vare.dis #this is the triangular matrix I'd like to export x=format.data.frame(vare.dis) #nope, don't work x=format(vare.dis) #nope x=data.frame(vare.dis) #ditto x=unknown.function(vare.dis)...

Dear r-help users, I have just downloaded the package vegan and I have problems accessing the data to go through the examples in the tutorial. I can see the data when I type "data()" but I am told that the data doesn't exist when I type the name of one of the variables e.g.: > varespec Error: object 'varespec' not found I suspect this could be a way I have my files organised or that I have not set a working directory? I am new to R so I suspect I have probably made a simple mistake. Thanks for your help, Craig. ______________________________________________...

Hi all, I have been using princomp() recently, its very useful indeed, but I have a question about how to specify the rows of data you want it to choose. I have a set of variables relating to bird characteristics and I have been using princomp to produce PC scores from these. However since I have multiple duplicate entries per individual (each bird had a varying number of chicks), I only want

Dear all, I realised a correspondence analysis with function cca() of vegan library. Just like in Okansen (2010) in the example of R help: library(vegan) data(varespec) data(varechem) vare.cca<-cca(varespec~ Al + P + K, varechem) With plot.cca() function I represented the species matrix in the next way: plot(vare.cca,display="species") Being similar to: plot((c(-2,2)),(c(-2,2)), type="n", xlab="AXIS 1", ylab="AXIS 2")...

Hi After trying a simple decorana analysis (from the vegan package) on a simple data frame which contains no NA's the following error was returned: > tt_decorana(covN) Error in decorana(covN) : NA/NaN/Inf in foreign function call (arg 1) Have any vegan users come across this error and know what can be done about it? Cheers, J

...anonical correspondence analysis (cca) with the example data of vegan, but I'm not able to obtain a table like scores() for the constraining variables. I can see them in the summary() mode, but it would be great to have in a separate table. Any suggestion?, thanx Gianandrea require(vegan) data(varespec) data(varechem) vare.cca<-cca(varespec,varechem) scores(vare.cca) summary(vare.cca) -- View this message in context: http://www.nabble.com/cca-constraining-variables-table-tp19688215p19688215.html Sent from the R help mailing list archive at Nabble.com.

Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to

Hello This is a simple question but I couldn't google an answer. In the procrustes function of the vegan package, one uses plot(procrustes_object, kind=2) to obtain a plot of the residual differences. For instance: data(varespec) vare.dist <- vegdist(wisconsin(varespec)) library(MASS) mds.null <- isoMDS(vare.dist, tol=1e-7) mds.alt <- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7) vare.proc <- procrustes(mds.alt, mds.null) plot(vare.proc, kind=2) In the resulting plot 3 horizontal lines (1 con...

Hi, I have used Vegan to construct an NMDS ordination plot. I plotted sites of three forest types with the site number in it. My reviewer has asked me to use different symbols for each of the forest types. Can anyone send me how I can do this in R in simple steps. I have used the options like ordiplot, sel and pl syntaxes that are not working for the question that I asked for. Best, Sinu --

Estimados, Buenas Tardes, Estoy teniendo problema para testar la significancia de los ejes del RDA. NO se cual seria el error. Alguien me podría ayudar? Desde ya muchas gracias. Saludos, Luis # Tests of all canonical axes anova.cca(ssp.rda.hel, by="axis", step=1000)#Para saber la significancia de cada eje Error in anova.cca(ssp.rda.hel, by = "axis", step = 1000) :

Hi all, I have site data with plant species cover and am looking for trends. I'm kind of new to this, but have done lots of reading and can't find an answer. I tried decorana (I know it's been replaced by ca.) and see a trend, but I'm not sure what it means. Is there a way to get the loadings/eigenvectors of the axes (like in PCA)? Is there a way to do this with rda() too? How

Hello R experts, I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data

I'm trying to place labels so as to avoid covering points (and other labels) in an ordination plot. I've been trying to use orditkplot() for this purpose, but get an error message, even when I try to replicate the example: >require("vegan") >data(varespec) > ord <- cca(varespec) > orditkplot(ord, mar = c(4,4,1,1)+.1, font=3) Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : [tcl] invalid command name "tk". In addition: Warning message: In fun(libname, pkgname) : couldn't connect to display &qu...

Hi, I'm using nmds command (library vegan) to analyze some fishing data. I'd like to plot not only points, but also the names of species and stations in a specified position. I used the command text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds $points),pos=3,cex=0.5) But the labels are sometimes overlapped. Is there any way to use identify, or a similar command, to plot the

hello, i'd like to extract values from stressplot, but as this should happen within a long run of code, which also does a multiple plot, i need to prevent stressplot to print to the device. i tried ..,plot=F), but this is useless. any advise on this? thanks, kay ----- ------------------------ Kay Cichini Postgraduate student Institute of Botany Univ. of Innsbruck

Dear r-helpers, I just read in an article by Virtanen et al. (2006) where vegetation-environment relationships are studied by fitting smoothed surfaces on an NMDS ordination using GAMs (Wood 2000). The authors describe, that they used R? as goodness-of-fit statistic, which they compare to the R? of fitted vectors. Calculations were carried out using the package vegan (Oksanen). I know that I can

Hi, I have a couple questions about fitting environmental (land use factors, plant species presence-absence, and soil variables) constraints to my CCA biplot. 1. After successfully plotting species and site scores in my CCA, I have been trying to insert the biplot arrows of the environmental constraints in my data set using the text() function. When I do that, the plot changes completely. Is there

....arrows to work as I wish when conditioning. The attached file contains the function definitions for the xyplot method and the custom panel and prepanel functions I am using. This example, using data and functions from the vegan package illustrates the problem. require(vegan) require(lattice) data(varespec) vare.dist <- vegdist(wisconsin(varespec)) library(MASS) ## isoMDS mds.null <- isoMDS(vare.dist, tol=1e-7) mds.alt <- isoMDS(vare.dist, initMDS(vare.dist), maxit=200, tol=1e-7) vare.proc <- procrustes(mds.alt, mds.null) vare.proc groups <- factor(c(rep(1,16), rep(2,8)), labels = c(&...

...rop = FALSE] : subscript out of bounds I googled but I couldn't find an answer. Could anyone tell me why this error msg and what to do? Here is the command I used: mod=capscale(as.dist(dist)~mydataset$Var1+Condition(mydataset$Var2)) My dataset looks like the output of column-binding the 'varespec' and 'varechem' datasets, and has 92 rows and about 3500 columns. I also fed capscale a similarity matrix in the formula. Here is more info on the R version and the OS: R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Thanks a lot for any help or comment, Zhao -...

Hi all, ok, i know i can cut a dendrogram, which i did. all i get is three objects that a dendrograms itself. for example: myd$upper, myd$lower[[1]], myd$lower[[2]] and so on. of course i can plot them seperately now. but the lower parts still have hundreds of branches. i?ll need a 30 " widescreen to watch the whole picture. what i?d like to is group the lower branches , so that i get a