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
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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
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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