search for: varechem

...pondence 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.

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") points(vare.cca...

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) :

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

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

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

...t 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 -- Zhao JIN Ph.D. Candi...

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

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

Dear r-helpers! Jan Thiele asked r-help-list in february, but I could not find an answer to his question. I have the same problem: While preparing figures of 'envfit' plots with vegan for publication, I ran into a layout problem, that I found no solution for in the literature or the help archive: The labels of the vectors that indicate correlations of environental variables sometimes

Hello, I am using vegan to do an NMDS plot and I would like to suppress the labels for the loading vectors. Is this possible? Alternatively, how can I avoid overlap? Many thanks for the help. Example code: #perform NMDS using metaMDS() function spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS", autotransform=F, trymax=1000) #calculate the loading (i.e.,

Dear all, Does anyone knows why the results of a BIOENV (PRIMER v. 6.1.15) are diferent of the bioenv() + mantel() in vegan? Not the spearman correlation, indeed the pseudo-p value. I know that the approach bioenv() + mantel() is biased. So, how the BIOENV (PRIMER) ends with larger p values (permutated). Acctualy how the permutation test in BIOENV (PRIMER) is conducted. The user guide does not

...html latex example initMDS text html latex example postMDS text html latex example procrustes text html latex example rankindex text html latex example varechem text html latex example vectorfit text html latex example vegdist text html latex example wascores text html latex example make[1]: Leaving directory `/cygdrive/...