search for: envfit

Displaying 11 results from an estimated 11 matches for "envfit".

2011 Sep 23
1
Envfit, inconsistant result?
Hi R-experts, I am using the envfit function over an ordination of floristic data. The problem is that every time that I run it changes the results. Sometimes dramatically, selecting variables that the first time were not significant. I do not get what could be the problem or if is normal given the permutations are different. # the...
2011 Sep 09
1
envfit vector labels with ordiplot3d
Hi R experts, I'm looking for some help with plotting vectors from envfit in vegan, onto a 3d plot using ordiplot3d. So far I have data.mds <- metaMDS(data, k=3,trace = FALSE) vect_data<-envfit(data.mds,vegdata[,3:21],choices=1:3,permu=9999) ordiplot3d(data.mds,envfit=vect_data) ordixyplot(data.mds,pch=pts,envfit=vect_data) (my data's not really called data,...
2009 Nov 05
1
plot.envfit/move labels
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 overlap with each other or with other content of the figure. Hence, I wou...
2012 Dec 29
2
Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical subscript too long
Hello there, I'm trying to plot vectors with p<0.1 in a NMDS ordination plot using p.max. Below the scripts I'm using. I guess I'm missing something! could you please give me a hand? species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species, dis="sites")plot(ef,p.max=0.1) Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical subscript too long Many thanks! Laura [[alternative HTML version deleted]]
2009 Apr 02
0
Plots of envfit (vegan) - placing of vector labels
Dear R folks 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 overlap with each other or with other content of the figure. Hence, I...
2011 Mar 28
1
ordination in vegan
...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 about with cca()? I know I can do scores() or summary() but that's not exactly the info I need. I basically want to interpret the axes. Also after doing envfit() and plotting, is there a way to label sites based on certain environmental factors? For instance, I want to highlight plots that have a certain treatment (or have different colored points for the different treatments. I don't know if it matters but I used downweight() before applying de...
2010 Feb 13
2
NMDS ordination
Hi Im currently trying to plot my NMDS data together with fitted variables (envfit funct) on an ordination plot. The plot function shows two displays="sites" and "sp". I was wondering how to plot it so that the sites come up as different points for different sites but the species come up as actual names? It looks a little busy at the moment with everything in....
2004 May 10
1
environmental data as vector in PCA plots
Hi, I want to include a vector representing the sites - environmental data correlation in a PCA. I currently use prcomp (no scaling) to perform the PCA, and envfit to retrieve the coordinates of the environmental data vector. However, the vector length is different from the one obtained in CAnoco when performing a species - environmental biplot (scaling -2). How can I scale the vector in order to be in accordance with Canoco, or which other scaling options ar...
2010 Nov 23
1
RDA Triplot
Hi Im using the VEGAN package to do an RDA ordination. In my plot I get my environmental scores as arrows/vectors, but my species scores as points. I would like to get the species scores as arrows as well. I tried the envfit function, and this creates arrows, but the lenght is not proportionate to the strengh of the correlation and the point is still there (so I both have point and arrow). fit <- envfit(rdawal, dat.one, perm = 999, display = "wa") ordiplot(rdawal, type = "p") plot(fit, col = &...
2006 Apr 20
2
PCA biplot question
Hi everyone, I'd like to project two pcas onto one device window. I plot my first PCA: biplot(prcomp(t(cerebdevmat)), var.axes=FALSE, cex=c(1,.1), pc.biplot=TRUE) Now I'd like to project the features of another PCA onto this graph. Any suggestions? I know this is easily done in MatLab but haven't figured it out in R. Thanks, Tanya [[alternative HTML version deleted]]
2013 Apr 11
1
Ordination Plotting: Warning: Species scores not available
Hi, I am working with a species-by-trait .csv file (columns=traits, rows=species) and get the following warning message when trying to plot results of both metaMDS and pcoa:  "Warning message: In ordiplot(x, choices = choices, type = type, display = display,  :   Species scores not available" I am using a Gower's transformation in both procedures within the metaMDS or pcoa