Displaying 20 results from an estimated 30 matches for "vegdist".

2013 Feb 08

1

vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande

---------- Forwarded message ----------
From: <r-help-owner@r-project.org>
Date: 2013/2/8
Subject: vegdist Error en double(N * (N - 1)/2) : tama?o del vector
especificado es muy grande
To: caro.bello58@gmail.com
Message rejected by filter rule match
---------- Mensaje reenviado ----------
From: caro bello <caro.bello58@gmail.com>
To: r-help@r-project.org
Cc:
Date: Fri, 8 Feb 2013 15:18:40...

2010 Feb 02

2

hvcluster() with distance method from vegdist(), package = vegan

hello,
i'd be happy if someone could provide help with the following problem:
i have a dist.matrix that comes from vegdist() function of the vegan
package. the used method = "horn" is not accepted as argument in
hvcluster(...,dist.method="...").
is there a way to incorporate the method "horn" in hvcluster()?
thanks in advance!
yours,
kay
--
View this message in context: http://...

2010 Mar 16

1

memory failure in adonis function (permanova)

...ot
about this question, but I do not get the answer about it. Although I know
that the R function is adonis () (vegan package), it does not work:
adonis(Pha.env~SPha, data=Pha, permutations=10)
The error message:
Error: cannot allocate vector of size 334.2 Mb
In addition: Warning messages:
1: In vegdist(lhs, method = method, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In vegdist(lhs, method = method, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
3: In vegdist(lhs, method = method, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
4: I...

2006 Mar 08

1

function gdist, dist and vegdist in mvpart

..."maximum", full=TRUE,
sq=F) ~ beers + slope_dem + elev_dem+ plc_dem + pr_curv+
+curv+max_depth+doc_rocks+ abandon+land_use+ca_old,
data=ba12, xv="p")
This works fine. Now I would like to use other dissimilarity measures as
can be found in the function dist (STATS) or vegdist (VEGAN).
De'Ath notes that gdist should be interchangeable with dist - but I
receive following error message:
> fit21 <- mvpart(dist (ba12[,18:29], meth="minkowski", diag=T,
upper=T p=2) ~
beers + slope_dem + elev_dem+ plc_dem + pr_curv+
curv+max_depth+doc_rocks+ ab...

2011 Sep 09

2

NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity

...ed to look at similar problems but I get error messages.
Any ideas?
#NMDS
step1<-read.delim2("day20.txt", row.names=1)
library(clusterSim)
step2<-data.Normalization(step1,type="n10")
step3<-asin(sqrt(step2))*57.3
step4<-t(step3)
library(vegan)
step5<-data.matrix(vegdist(step4,method="bray"))
step6<-metaMDS(step5, autotransform=FALSE)
plot(step5)
Warning message:
In ordiplot(x, choices = choices, type = type, display = display, :
Species scores not available
#PerMANOVA
step1<-read.delim2("day20.txt", row.names=1)
library(clusterSim)
s...

2011 May 17

1

simprof test using jaccard distance

...results[["significantclusters"]] <- simprof.results$samples
return(results)
}
<environment: namespace:clustsig>
I tried to trick the function by bypassing the input of a raw community matrix (sites x species) by inputing instead a distance matrix already calculated with vegdist (vegan package) (Jaccard distance is available in vegdist, but not in the function dist used in simprof...)
I therefore modified the function as follow:
simprof2=function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average",
alpha = 0.05, sample.orientation = &...

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

2007 Aug 22

1

distance by vegan

How to calculate sorensen (bray-curtis) distance by dist function
within the vegan package?
Cheers
Duccio

2008 Jun 16

0

pvclust distance matrix

Hello,
I am attempting to assign significance levels to a UPGMA cluster analysis as part my doctoral research. The pvclust function works well but doesn't include the similarity index I need (morisita's) as an option for computing a distance matrix. Morisita's is available in vegdist in the VEGAN library but I am having a hard time getting the vegdist function to "direct drop" into pvclust as the vegdist documentation suggests. I would appreciate any suggestions.
Thank you
Brad
Bradley N. Strobel
Department of Natural Resource Management
Texas Tech Universit...

2012 Oct 11

2

extracting groups from hclust() for a very large matrix

...a
way to 'print' the results to a table that shows which plots were in
what group, correct?
I've attached the matrix I'm working with (the whole thing since the
point is its large size). I've been able to run the following code to
get the groups I need:
> VTM.Dist<- vegdist(VTM.Matrix)
> VTM.HClust<- hclust(VTM.Dist, method="ward")
> plot(VTM.HClust, hang=-1)
It takes a while, but it does run. Then, I can extract 8 groups, which
I'd like to experiment with, but is about how many I'd like:
rect.hclust(VTM.HClust, 8)
> VTM.8groups<...

2013 Jul 23

1

Heat Map for species - code from Numerical Ecology with R

...vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe, spe.chwo) spe is the dataframe spe.chwo came from: spe.norm <- decostand(spe, "normalize") spe.ch <- vegdist(spe.norm, "euc") spe.ch.UPGMA <- hclust(spe.ch, method = "average") spe.chwo <- reorder.hclust(spe.ch.UPGMA, spe.ch) and the error is Error in vegemite(spe, spe.chwo) : Cowardly refusing to use longer than 1 char symbols: Use scale The data in the dataframe is bio...

2005 Nov 09

2

how to convert strings back to values?

...eading the dataset.
When I transpose the dataset, the original values become strings
(instead of 0,1,0,0,1 I have "0","1","0","0","1"). The distance matrix
cannot be counted from the transposed dataset, I have 2 error
messages:
<Warning in vegdist(tdf1, method = "jaccard", binary = FALSE, diag =
FALSE, : results may be meaningless because input data have
negative entries>
<Error in rowSums(x, prod(dn), p, na.rm) : 'x' must be numeric>
I do not understand the first, since I have only 1 and 0 in the dataset. I...

2005 Nov 10

2

error in rowSums:'x' must be numeric

...a comma
separated file. I would like to calculate the Jaccard distance of the
dataset. I have the following error message:
Error in rowSums(x, prod(dn), p, na.rm) : 'x' must be numeric
In addition: Warning message:
results may be meaningless because input data have negative entries
in: vegdist(t2, method = "jaccard", binary = FALSE, diag = FALSE,
Do you have any idea what can be the problem? I have only 0 and 1 in
the dataset.
Thank you very much! All the best:
Eszter
_______________________________________________________________________
KGFB 2006 - Garant??ltan a le...

2004 Sep 07

3

heatmap help

Dear R wizards,
Hopeful someone can help me with what I believe is a pretty simple task. I
pretty new to R so some (much) of the obvious escapes me. How do I get a
distance matrix into heatmap? What do I tell distfun if what I'm trying to
map is already an ordered distance matrix? I tried >heatmap(x,
distfun=as.dist(x)) where x is the distance matrix but R gave me an error.
Thanks in

2018 Apr 18

0

nMDS with R: missing values

...Message-----
From: Jessie Woodbridge <jessie.woodbridge at plymouth.ac.uk>
Sent: Wednesday, April 18, 2018 3:42 AM
To: David L Carlson <dcarlson at tamu.edu>
Subject: RE: nMDS with R: missing values
Dear Prof Carlson,
Thank you for your reply. I'm using 'vegan' with 'vegdist' and 'bray'. I have a selection of datasets that cover different time periods (converted to z-scores), so a record that starts 5000 years ago would have missing data before this date when other records cover the last 8000 years. I need to build into the nMDS the fact that this isn't...

2013 Jan 30

0

betadisper plot

Hello,
I tried to make a betadisper plot; however, it is quite messy at the moment with lines and symbols.
I made two plots, one focusing on sites and the other on treatments.
This is the code that I used:
plot(betadisper(vegdist(y.nth,method="euclidean"),site))
plot(betadisper(vegdist(y.nth,method="euclidean"),treatment))
I have a few questions pertaining to how I could clean up the figures for interpretation purposes:
How would I be able to place labels on the centroids, which would enable me to ident...

2013 Jun 11

1

'Boolean Index too long'

#Hi, I am trying to run an MRPP with community data (spp-site-matrix). I
use the following code:
mzbtaxa_mrpp <- mrpp(mzbdist,mzbsites$Site)
#mzbdist being a distance object (Bray-Curtis similarity matrix) derived
from my sqrt transformed community data set, created with function
'vegdist', mzbsites$Site refers to factors structuring my community.
#when I run this code, I get the following error message:
error in dmat[ind == x, ind == x] : (subscript) boolean index too long
#What does that mean? How can I solve this problem?
#thanks a lot for your help,
#Claudia
[[alterna...

2018 Apr 17

2

nMDS with R: missing values

Dear All,
I was wondering whether anyone might be able to provide some advice with an nMDS / R problem. I?m trying to run nMDS on a dataset that contains many missing values and was wondering how I can account for the missing values when running nMDS? It seems as though the data are being grouped depending on where the zero values appear. Any suggestions greatly appreciated. Thank you very

2005 Mar 14

1

Significance of Principal Coordinates

...he eigenvalues
>
> nEigen <- round(ncol(Data*0.8))
>
> # Calculate Weights for Principal Coordinates Analysis
>
> Total <- apply(Data,1,sum)
> Weight <- round(Total/max(Total)*1000)
>
>
> # Calculate Chord Distance
>
> library(vegan)
> Chord <- vegdist(decostand(Data, "norm"), "euclidean")
>
> # Calculate Principal Coordinates, including distance matrix row weights
>
> library(ade4)
> PCoord.Eigen <- dudi.pco(Chord,row.w=Weight,scann=F,full=T)$eig[1:nEigen]
>
> # Randomization of Principal Coordinates A...

2013 Dec 17

1

What is the formula of Pseudo-F statistic in capscale in vegan?

...and
Clarke 2008, Chapter 4. Pg. 129, and based on pseudo-F equation in Legendre
and Anderson (1999), Ecological Monographs vol. 69):
F= (SSFull - SSReduced)/(qFull-qReduced)
(SSTotal-SSFull)/(N - qFull - 1)
(3) R code
## creating Bray-Curtis of Biodiversity data
H.BC <- vegdist(H.Full [,14:211], "bray")
## Distance based redundancy analysis (dbRDA)
m1<-capscale(H.BC ~ GroupSize + Board + MtgStyle + DmStyle + DifView +
VolAuton, SScomp [,14:19], distance = "euclidean", add = TRUE)
### NOTE: pseudo-F values are the same with or without correctin...