search for: capscale

Displaying 12 results from an estimated 12 matches for "capscale".

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 computer, stops and then comes ba...
2013 Jul 12
2
vegan capscale 'subscript out of bounds' error
Hi list, I am using the capscale function in vegan_2.0-7 to do a constrained principal coordinates analysis, and I kept getting the following error message: Error in Y.r[, oo, drop = 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 c...
2006 Nov 16
2
question about capscale (vegan)
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' an...
2008 Sep 13
2
Symbols on a capscale object plot
Hi, I'm a beginner with R, but I'm getting excellent results with it. Well I've got an capscale object (vegan package) and I want to made a biplot with symbols representing six groups of areas. With the plot.cca function and some par attributes (like 'labels') I was able to substitute the samples names for keyboard symbols ('x','o','#',ect), but it's far fr...
2008 Sep 13
0
Symbols On a Capscale Object Biplot
Hi, I'm a beginner with R, but I'm getting excellent results with it. Well I've got an capscale object (vegan package) and I want to made a biplot with symbols representing six groups of areas. With the plot.cca function and some par attributes (like 'labels') I was able to substitute the samples names for keyboard symbols ('x','o','#',ect), but it's far...
2013 Mar 05
0
permutest
I'm working with capscale and permutest for the first time, and having trouble getting statistical analyses for more than one constraining variable. I've read the documentation, but setting first=FALSE or using by="axis" doesn't seem to be helping. capscale seems to be fine, I receive output for more than...
2013 Dec 17
1
What is the formula of Pseudo-F statistic in capscale in vegan?
Dear R-help, We are conducting a distance-based redundancy analysis using capscale and then testing for statistical significance for six terms in the model for the constrained ordination using anova.cca in the vegan package. The significance test is sequential, i.e., testing for significance of a term only after accounting for all preceding terms. Could someone please provide us...
2010 Sep 21
1
partial dbRDA or CCA with two distance objects in Vegan.
I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et...
2013 Apr 03
2
Ask help
Hello! I am eager to learn if I only have a data about the relationship between otu and sample, could I use the function capscale, and final make a point plot that x-axis is CAP1 and y-axis is CAP2? Besides, what function could I use to make the different rarefaction curve with different color in the a plot in R? Appreciate very much....
2008 Oct 23
2
Avoiding Biplot Labels Overllaping
Hi everybody, I'm trying, without success, to avoid some variables labels to overlap on a capscale (vegan package) object graph. I was able to move the labels with the coding below, but it moves the entire vector... CAPobj<-CAPpotiFT for(i in c(2:8))CAPobj$CCA[[i]][,1]<-CAPpotiFTI$CCA[[i]][,1] CAPpotiFTI$CCA[[i]][,1][2]<-0.85 And here the graphic script ScoresCAPFT<-scores(CAPpot...
2009 Nov 26
2
Multivariate problems . . . with 200 resposes variables and 1 explanatory variable
How should I analysis it in R ???? all the resposes variables are ordinal from 0 to 10. and the explanatory variable is a factor ... -- View this message in context: http://old.nabble.com/Multivariate-problems-.-.-.-with-200-resposes-variables-and-1-explanatory-variable-tp26522912p26522912.html Sent from the R help mailing list archive at Nabble.com.
2009 Sep 09
2
"predict"-fuction for metaMDS (vegan)
Dear r-Community, Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data. Step2: Then I want to plot environmental variables over it, using function envfit. The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I