Displaying 20 results from an estimated 3000 matches similar to: "Problem with Species x Site matrix please help"
2008 Apr 23
1
problem with data for metaMDS analysis please help
am at my wit's end. I am not sure what is wrong with this data matrix. It
is sparse because it is a matrix of species, but I have looked at the row
totals and column totals and they are positive.
rmetaMDS(x.d)
Error in if (autotransform && xam > 50) { :
missing value where TRUE/FALSE needed
What is wrong? And in the future how in God's name do I easily diagnose
whatever
2007 Aug 24
1
Adding new points to a metaMDS ordination ("vegan" pkg)
Hi, I've been using R for a while now but I've got a problem with
metaMDS (in the vegan package) that I can't quite figure out.
I have a set of proportion data (from 0-1, rows sum to 1) that I apply
metaMDS to using the command:
nMDS.set=metaMDS(sqrt(test.set),distance="euclidean",k=3,zerodist="add",autotransform=FALSE)
I am using a squared-chord distance
2013 Apr 26
1
NMDS in Vegan: problems in stressplot, best solution
Hello,
I can draw a basic stress plot for NMDS with the following code in package
Vegan.
> stressplot(parth.mds, parth.dis)
When I try to specify the line and point types, it gives me error message.
> stressplot(parth.mds, parth.dis, pch=1, p.col="gray", lwd=2, l.col="red")
Error in plot.xy(xy, type, ...) : invalid plot type
In the above code, if I removed line type,
2013 May 27
1
metaMDS with large dataset produces 'insufficient data' warning
Greetings everyone,
I am running MDS on a very large dataset (12 x 25071 - 12 model runs with 25071 output values each), and also on a very much reduced version of the dataset (randomly select 1000 of the 25071 output values). I would like to look at similarities/dissimilarities between the 12 model runs. When I use metaMDS on the full dataset, I get a warning message:
Warning message:
In
2012 Jul 27
1
labeling loading vectors in vegan
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.,
2008 Dec 30
1
why stress value remains so high after invoking of metaMDS
Hello everyone!
metaMDS(cm, distance = "euclidean", k = 2, trymax = 50, autotransform
=TRUE, trace = 1, plot = T)
(cm is a similarity matrix, in which values are positive integers or 0)
I use this command to run NMDS on my matrix "cm". But the stress is very
high after analysis. About 14.
Actually, there is no improvment comparing with using isoMDS.
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 NMDS ordination
gap_flor_NMDS_chord <- metaMDS(gaps_flor,
2008 Dec 29
0
stress value remains so high(metaMDS)
metaMDS(cm, distance = "euclidean", k = 2, trymax = 50, autotransform =TRUE,
trace = 1, plot = T)
(cm is a similarity matrix, in which values are positive integers or 0)
I use this command to run NMDS on my matrix "cm". But the stress is very
high after analysis. About 14.
Actually, there is no improvment comparing with using isoMDS.
2011 Mar 10
1
3 dimensional MDS plots
Hi,
I am trying to create 3 mds plots: one with axis 1 vs axis 2, one with axis 2 vs axis 3, and one with axis 1 vs axis 3. When inputting my code, I only end up with one diagram and when inputting
mdsg.mds$dims, the program returns 2 for 2 dimensions. How can I create the other two plots?
Any help would be greatly appreciated,
Calla Carbone
The table I use is number of each taxa on each
2009 May 27
1
vegan metaMDS question
The design decision in metaMDS says that it uses:
Minchin, P.R. (1987) An evaluation of relative robustness of
techniques for ecological ordinations. Vegetatio 71, 145-156.
This is the paper that I found by the same name. Is this the correct reference?
Minchin, Peter R.1987. An Evaluation of the Relative Robustness of
Techniques for Ecological Ordination. Vegetatio. Vol. 69, No. 1/3:
89-107.
2008 Apr 14
1
Vegan R^2 and tau values for metaMDS
I am using the function metaMDS with jaccard distances to ordinate a
set of constituent by site matrix. I can post this data if it would
be helpful, but it is large to include in an email. I can also
provide reproducable code if necessary. I would like to get an R^2
value for the axes of the ordination configuration that I get with
metaMDS in the vegan package is there a way to do this- is it
2013 Feb 27
1
best ordination method for binary variables
Dear all,
I'm analyzing a dataset (A) of 400 cases with 11 binary variables.
Unfortunately, several (actually a lot) of cases are identical. NA are also
present.
I want to to plot distances between cases.
For this, I obtained a distance matrix by dist(A, method="binary"). I then
analyzed the obtained distance via Principal coordinate analysis with
cmdscale(). Results are fine.
2011 Sep 09
2
NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity
Hi!
Thanks for providing great help in R-related statistics. Now, however I'm
stuck. I'm not a statistics person but I was recommended to use R to perform
a nmds plot and PerMANOVA of my dataset.
Sample(treatment) in the columns and species (OTU) in the rows. I have 4
treatments (Ambient Temperature, Ambient temperature+Low pH, High
temperature, High temperature+low pH), and I have 16
2011 Nov 24
4
I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?
Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account.
I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such
2008 Apr 11
1
Vegan plotting- color help
I have looked all over the internet for being able to color sites
differently in a plot of an MDS (metaMDS)- I would like to color the
different sites in the ordination plot (plot or ordiplot). I have set
the matrix up so that my site code is 1 .... 296 (first column). is
there a way to make 1-23 blue, 24-40 red etc.
thanks
Stephen
--
Let's not spend our time and resources thinking
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
2010 Jan 06
1
positive log likelihood and BIC values from mCLUST analysis
My question is with respect to mCLUST and the values of BIC and log
likelihood. The relevant part of my R script is:
######################### BEGIN MDS ANALYSIS #########################
#load data
data <- read.table("Ecoli33_Barry.dis", header = TRUE, row.names = 1)
#perform MDS Scaling
mds <- metaMDS(data, k = Dimensions, trymax = 20, autotransform =TRUE,
noshare = 0.1,
2011 May 22
0
Manipulating rownames for nMDS
I am trying to plot an nMDS plot using ggplot2. My rownames are coded so
that they can be broken down by Site, Species, Treatment, or Replicate based
on unique separators. There are no column headers. I am having trouble
coding ggplot2 to plot by Site -or- Species -or- Treatment and NOT by all
unique row names. This is probably a simple question but I'm still very new
with command line
2012 Apr 25
1
fill a dataframe with zeros where the rows are a smaller subset of a larger dataframe (species by site)
row <- c("a","b","c","d","e","f","g") #rows from larger data frame
row.1 <- c("a","b","c","g") #rows of smaller data frame because d, e,
and f don't contain any of the species, but the zeros are important
x <- data.frame(sp1=rnorm(4), sp2=rnorm(4), sp3=rnorm(4),
2010 Mar 11
1
uid fetch/store always use the last uid when range is invalid
hello all;
one colleague found a strange behavior, that can be annoying :
-bash-3.1$ telnet 0 143
Trying 0.0.0.0...
Connected to 0 (0.0.0.0).
Escape character is '^]'.
* OK [CAPABILITY IMAP4rev1 LITERAL+ SASL-IR LOGIN-REFERRALS ID ENABLE
AUTH=PLAIN AUTH=CRAM-MD5] Dovecot ready.
l login login pass
l OK [CAPABILITY IMAP4rev1 LITERAL+ SASL-IR LOGIN-REFERRALS ID ENABLE
SORT SORT=DISPLAY