Displaying 13 results from an estimated 13 matches for "trymax".
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2006 Nov 10
2
Problems with metaMDS from vegan
...n both machines. On the new
Ubuntu machine I even tried to regress to the Vegan 1.6-10, but to no
avail, as the error remains the same:
As soon as a I try to process an R matrix (see below) to obtain the MDS
I am confronted with:
> meta <- metaMDS(distab.dist, distance="bray", k, trymax=50)
Fehler in rowSums(x, na.rm = TRUE) : 'x' muss ein Array mit mindestens
zwei Dimensionen sein
Ausf?hrung angehalten
(
translated:
error in rowSums(x, a.rm = TRUE) : 'x' must be an array of at least two
dimensions.
Execution stopped
)
This error is not appearing on identical dat...
2010 Dec 01
1
procrustes results affected by order of sites in input file
...rocrustes analysis to compare two NMDS ordinations for the
same set of sites. One ordination is based on fish data, the other is based
on invertebrate data. Ordinations were derived using metaMDS() from the
{vegan} library as follows:
fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100,
wascores=TRUE, trace=TRUE, zero="add")
invert.mds<-metaMDS(bugcal.a, distance="bray", k=3, trymax=100,
wascores=TRUE, trace=TRUE, zero="add"),
where fish.data and invert.data are site-by-abundance matrices for fish and
invertebrates, respectively.
I have th...
2011 Sep 23
1
Envfit, inconsistant result?
...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, distance = "euclid", k = 2, trymax
= 20, autotransform =TRUE,
noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
plot = FALSE, old.wa = FALSE, zerodist = "add")
# the environmental variables to use with enfit
explain1<- site[c("Tipo", "Gap.size", "Gap diameter (m)", "Size.cat...
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 iso...
2011 May 10
3
metaMDS and envfit: Help reading output
...rent dimensions). I then used envfit to correlate a predictor dataset of environmental variables with the NMDS results, using the following code.
>Fish<-as.data.frame(read.csv("Fish.csv",header=TRUE, sep = ","))
>Fish.mds<-metaMDS(Fish,zerodist = "add",k=3,trymax=20)
>Predictors<-as.data.frame(read.csv("Predictors.csv",header=TRUE, sep = ","))
>Fish.fit <- envfit(Fish.mds$points, Predictors, k=3, 1000, na.rm = TRUE)
>Fish.fit
The output of Fish.fit was as follows (table truncated):
Dim1...
2013 Apr 26
1
NMDS in Vegan: problems in stressplot, best solution
...not I define both line and point at the same time?
If I have 100 iterations for metaMDS, then when I plot the result, does it
give me result from best solution? How do I know that. Can you plot the
Stress by Iteration number?
parth.mds <- metaMDS(WorldPRSenv, distance = "bray", k = 2, trymax = 100,
engine = c("monoMDS", "isoMDS"),
autotransform =TRUE, wascores = TRUE, expand = TRUE, trace = 2)
plot(parth.mds, type = "p")
Thanks in advance,
Kumar
--
Section of Integrative Biology
University of Texas at Austin
Austin, Texas 78712, USA
[[alternative HTM...
2012 Jul 27
1
labeling loading vectors in vegan
...ld like to suppress the labels
for the loading vectors. Is this possible? Alternatively, how can I avoid
overlap?
Many thanks for the help.
Example code:
#perform NMDS using metaMDS() function
spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS",
autotransform=F, trymax=1000)
#calculate the loading (i.e., variable weights) on each NMDS axis
vec.sp<-envfit(spe.nmds$points, data, perm=1000, choices=c(1:2))
#plot data in ordination
ordiplot(spe.nmds, choices=c(1:2), type='text', display="sites", xlab="Axis
1", ylab="Axis 2"...
2013 Sep 06
1
Fwd: calculating dissimilarity index of islands (vegan and betapart)
...compare species presence/absence between a pair of island?
Should the two islands be specifically located or close to each other?)
Thank you
Elaine
Code
# NMDS
library(MASS)
library(vegan)
island.NMDS <- metaMDS(island,k=2, distfun = betadiver, distance =
"sim",trymax=100,zerodist="add")
plot(island.NMDS, type = "n")
#Simpson Dissimilarity Index
library(betapart)
island.dist<-beta.pair(island, index.family="sor")
class(island.dist)
[[alternative HTML version deleted]]
2010 Jan 06
1
positive log likelihood and BIC values from mCLUST analysis
...ues 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, wascores = TRUE, expand = TRUE, trace = FALSE, plot = FALSE,
old.wa = FALSE)
######################### BEGIN EM ANALYSIS #########################
#Use the points determined by MDS to perform EM clustering.
#Allow only the unconstrained models. Sometimes...
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 is...
2011 May 22
0
Manipulating rownames for nMDS
...D.1 0 0 0 0
ST9_MF..CC.3 1 0 0 1
ST9_MF..CC.4 1 0 0 1
FX9_MF..CH.1 1 1 0 0
FX9_MF..CH.2 1 0 0 0
This is the code I have thus far:
datum <- read.csv(q, header=F)
datum2 <- datum[,2:ncol(datum)]
rownames(datum2) <- datum[,1]
fit <- metaMDS(datum2, distance = "jaccard", k = 3, trymax=20,
autotransform=F)
fit. <- data.frame(sample=rownames(datum2), fit$points)
p <- qplot(X1,X2, col=sample, data=fit.)
print(p)
dev.off()
Thanks for your help!
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Sent from t...
2011 Mar 10
1
3 dimensional MDS plots
...n 3 stress 10.61520
... New best solution
... procrustes: rmse 0.005646588 max resid 0.009332332
Run 4 stress 10.61520
... New best solution
... procrustes: rmse 0.0001009763 max resid 0.0001754211
*** Solution reached
> mdsg.mds.ALT<- metaMDS(mdsg, distance="euclidean", k=3, trymax=50, autotransform=FALSE)
Run 0 stress 3.020817
Run 1 stress 0.00673153
... New best solution
... procrustes: rmse 0.09349157 max resid 0.2443702
Run 2 stress 0.008861757
... procrustes: rmse 0.08275172 max resid 0.1932439
Run 3 stress 0.006908548
... procrustes: rmse 0.0447681 max resid 0....
2010 May 25
2
Calculation time of isoMDS and the optimal number of dimensions
Dear all,
I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS,
on a 800x800 distance matrix. I noticed that setting the parameter k to
larger numbers seriously increases the calculation time. Actually, with k=10
it calculates already longer than for k=2 and k=5 together. It's now
calculating for 6 hours, and counting...
There is quite a difference between the