Displaying 20 results from an estimated 100 matches similar to: "extract values from summary of function indval of the package labdsv"
2005 Sep 19
4
indicator value in labdsv
Hi,
I'm trying to find out what threshold of indicator value in labadsv should be
used to accept a specie as an indicator one? So far I assumed that indval=0.5
is high enough to avoid any mistakes but it was based only in my intuition.
I'd be greatful for any advise
best regards
Agnieszka
2005 Aug 08
2
INDVAL and mvpart
Hi,
I'd like to perform Dufrene-Legendre Indicator Species Analysis for
a multivariate regression tree. However I have problems with arguments
of duleg(veg,class,numitr=1000)function. How to obtain a vector of
numeric class memberships for samples, or a classification object
returned from mvpart?
thanks in advance
--
Best regards,
Agnieszka Strzelczak
2006 May 15
0
labdsv won't install with Mac OS X, R 2.3.0
I am trying to install labdsv from CRAN binaries (or source) to use
with R 2.3.0 from Mac OS X, but the package fails to install
properly. Here is the message that I receive from R when I type
library(labdsv):
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library '/Library/Frameworks/R.framework/
Resources/library/labdsv/libs/ppc/labdsv.so':
2011 Oct 17
1
plotting issues with PCA
Hi Listers,
This has a simple answer but it has been eluding me nonetheless.
I have been building a PCA plot from scratch with the ability to plot
predefined groups in different colors. This has worked fine but when I try
to get a polygon drawn around each of the groups it is not recognising my
colour file correctly and is only printing the first colour in the
file....code is below
2010 Apr 02
2
Biplot for PCA using labdsv package
Hi everyone,
I am doing PCA with labdsv package. I was trying to create a biplot graphs
in order to observe arrows related to my variables. However when I run the
script for this graph, the console just keep saying:
*Error in nrow(y) : element 1 is empty;
the part of the args list of 'dim' being evaluated was:
(x)*
could please someone tell me what this means? what i am doing
2002 May 13
5
installing labDSV library
I am trying to install labDSV from http://labdsv.nr.usu.edu/ into
R-Windows 1.5.0.
It only comes as a TAR file which extracts into folders that seem to match
those for other libraries DATA, MAN, R and SRC. I have manually copied
these folders into a folder called labDSV under the Library directory
under R.
However when I load the library I get a message that the library contains
no R code.
2008 Nov 20
1
gam and ordination (vegan and labdsv surf and ordisurf)
I have a general question about using thin plate splines in the surf
and ordisurf routines. My rudimentary knowledge of a gam is that with
each predictive variable there is a different smooth for each one and
then they are added together with no real interaction term (because
they don't handle this well?). Now, If I have two variables that
have a high D^2 score and a low GCV score (I am
2016 Apr 18
3
Indicator Species analysis; trouble with multipatt
Hello,
*Error in tx %*% comb : non-conformable arguments*
Suggestions greatly appreciated. I am a beginner and this is my first time
posting.
I would like to get the summary for indicator species analysis, using
package indicspecies with multipatt. I am getting errors, I believe, do to
my data organization. After reorganizing and reorganizing, nothing has
helped.
> data<-
2016 Apr 19
0
Indicator Species analysis; trouble with multipatt
Hi Ansely,
As Jim points out we really need some sample data to go with the code.
Have a look at ?dput which is the best way to supply sample data here or have a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and/or http://adv-r.had.co.nz/Reproducibility.html for some general suggestions on asking questions here---including discussions of using
2016 Apr 19
0
Indicator Species analysis; trouble with multipatt
Hi Ansley
It looks good to me but I did not run the analysis as I am too lazy to install "indicspecies". The inclusion of the raw data is a great help.
John Kane
Kingston ON Canada
-----Original Message-----
From: daily.puja at gmail.com
Sent: Tue, 19 Apr 2016 08:16:54 -0400
To: jrkrideau at inbox.com
Subject: Re: [R] Indicator Species analysis; trouble with multipatt
Thanks for the
2005 Mar 08
1
Multidimensional Scaling (MDS) in R
Hi;
I am working with the similarity matrix below and I would like to plot
a two-dimensional MDS solution such as each point in the plot has a
label.
This is what I did:
data <- read.table('c:/multivariate/mds/colour.txt',header=FALSE)
similarity <- as.dist(data)
distance <- 1-similarity
result.nmds <- nmds(distance)
plot(result.nmds)
(nmds and plot.nmds as defined at
2007 Jun 20
1
Dissimilarity
Hello Stephen,
I am happy that you help me. Thanks a million.
It is a good feeling that you confirm my assumption that dsvdis is
not able to deal with missing data, because it says me that I am not
completely incapable.
Okay now I have the problem what to do.
I used this function ´cause there is an option to weight columns
differently what I haven´t found in other functions.
But now I
2007 Jun 19
1
Dissimilarity Analysis
Hello you all!
I am a completely new user of R and I have a problem to solve.
I am using Mac OS X on a PowerBook.
I have a table that looks like this:
species X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14
X15 X16 X17 X18 X19 X20 X21
1 Anth_cap1 1 0 0 1 0 1 0 0 1 0 0 0 0 0
0 0 1 0 0 0 1
2 Anth_crin1 1 0 0 1 0 1 0 0 1 0 1
2005 Nov 04
1
Stress in multidimensional scaling
Hello,
We are trying to find a function to compute "stress" in our
multidimensional scaling analysis of a dissimilarity matrix. We've used
"dist()" to create the matrix and "cmdscale()" for the scaling. In order
to determine the number of dimensions we would like to plot stress vs.
dimensions. However, we cannot find a pre-made command. It seems that
other
2011 Oct 03
4
distance coefficient for amatrix with ngative valus
Hi,
I need to run a PCoA (PCO) for a data set wich has both positive and negative values for variables. I could not find any distancecoefficient other than euclidean distace running for the data set. Are there any other coefficient works with negtive values.Also I cannot get summary out put (the eigen values) for PCO as for PCA.
Thanks.
Dilshan
[[alternative HTML version deleted]]
2008 Jan 25
4
Function for translation of a list into a matrix as used by ordination?
Hello.
Does anyone know of an existing function that takes a list in the form of:
Plot1 Species1 Abundance1
Plot1 Species2 Abundance2
Plot2 Species1 Abundance1
Plot2 Species3 Abundance3
.
.
.
PlotN SpeciesN AbundanceN
and translates into a matrix in the form of
Species1 Species2.... SpeciesN
Plot1 Abundance1 Abundance2... AbundanceN
Plot2 Abundance1
2008 May 19
3
Rank Values in a Matrix
Dear All,
a short and maybe simple question:
I have to rank all values in a matrix from 0 to X,
[1] [2] [3] [4]
[1] 0.1 2 0 3
[2] 50 3 3 1
[3] 100 1 1 0
[4] 100 2 2 0
0->0
0.1->1
2->2
3->3
50->4
100->5 (X=5)
is there any function for this? i have looked in several packages
(vegan, labdsv etc.) because I am working with species by site tables,
2008 Oct 24
4
gfortran optimization problems
Colleagues,
I have a routine in package labdsv that calls a FORTRAN subroutine.
Recently, I was informed that it sometimes gives different results on a
PC and Mac, and that the PC version is clearly wrong. I tested it on
linux (because I don't have a PC), and I get the same (incorrect)
behavior as the PC.
Simply by inserting debug WRITE statements in the FORTRAN I would get
different,
2010 Feb 04
1
mgcv problem to load
Dear friends,
I cannot load the pachkages labdsv...which i do not understand is linked to 'mgcv' package. Anyway neither the last is loadable in my new R 2.10 version. Th emessage on the screen is the following:
This is mgcv 1.6-1. For overview type `help("mgcv-package")'.
Error in runif(1) :
.Random.seed is not an integer vector but of type 'list'
Error :
2009 Jan 29
1
Multidimensional scalling
Dear R developers and users!
I have calculated metric MDS by cmdscale from matrix of distances
(dissimilarities).
I would like to ask you how can I estimate how well this new mapping
represents characteristic features of my data set?
Thank you for any suggestions.
Best,
tomek