Displaying 20 results from an estimated 2000 matches similar to: "Subsetting matrices"
2005 Nov 09
2
how to convert strings back to values?
Dear All,
It's Eszter from Hungary, a total beginner with R. My problem is the
following:
I have a dataset with binary values as a comma separated textfile. The
samples are in the coloumns and the species are in the rows.
I have to transpose it for the further PCoA analysis. There is no
problem with reading the dataset.
When I transpose the dataset, the original values become
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
2011 May 17
1
simprof test using jaccard distance
Dear All,
I would like to use the simprof function (clustsig package) but the available distances do not include Jaccard distance, which is the most appropriate for pres/abs community data. Here is the core of the function:
> simprof
function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average",
method.distance = "euclidean", method.transform =
2012 Dec 06
1
clustering of binary data
Good morning,
I am analyzing a dataset composed by 364 subjects and 13 binary variables
(0,1 = absence,presence).
I am testing possible association (co-presence) of my variables. To do
this, I was trying with cluster analysis.
My main interest is to check for the significance of the obtained clusters.
First, I tried with the pvclust() function, by using method.hclust="ward"
and
2005 Nov 10
2
error in rowSums:'x' must be numeric
Dear All,
It's Eszter again from Hungary. I could not solve my problem form
yesterday, so I still have to ask your help.
I have a binary dataset of vegetation samples and species as 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:
2006 Mar 08
1
function gdist, dist and vegdist in mvpart
Dear R community,
I am analyzing plant communities with the function mvpart, using a
dissimilarit matrix as input. The matrix is calculated with the funtion
gdist.
fit <- mvpart(gdist (ba12[,18:29], meth="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
2008 Mar 19
0
Table for clustering dendrogram
Dear all,
I am using the hclust method in R. I am building nice dendrograms with it.
Actually for my further analysis I want to get the number of bifurcations
(bif) for each object (labels) in the dendrogram. That has to be calculated
by the colums merge, height and order.
http://www.nabble.com/file/p16142989/Sc2Mown_Pred.txt Sc2Mown_Pred.txt
Sc2Mpred<-
2010 Jan 20
0
putting labels back on a matrix.
I did not post this question to the ecology list, even though it is about an analysis using Vegan, since my question is based more on basic data manipulation in R. I think this is a fairly simple question but for the life of me I cannot find a reference for in the archives.
I have an analysis using a matrix in which I needed to strip the ID variable off the input data to run the analysis. Now I
2005 Mar 14
1
Significance of Principal Coordinates
Dear all,
I was looking for methods in R that allow assessing the number of
significant principal coordinates. Unfortunatly I was not very
successful. I expanded my search to the web and Current Contents,
however, the information I found is very limited.
Therefore, I tried to write code for doing a randomization. I would
highly appriciate if somebody could comment on the following approach.
2010 Dec 28
3
Jaccard dissimilarity matrix for PCA
Hi
I have a large dataset, containing a wide range of binary variables.
I would like first of all to compute a jaccard matrix, then do a PCA on this
matrix, so that I finally can do a hierarchical clustering on the principal
components.
My problem is, that I don't know how to compute the jaccard dissimilarity
matrix in R? Which package to use, and so on...
Can anybody help me?
Alternatively
2024 Oct 13
1
The RV coinertia coefficient to interpret multivariate analysis plots
Dear all community,
My issue is related to the R package (made4) that permits me to calculate
the RV coefficient of co-inertia. However, it is a theoretical question.
And if I am not mistaken, the list Usenet groups sci.stat.consult is not
currently active.
Let me explain briefly:
Through different microbiota datasets, I have plotted PCoA, db-RDA and
sPLS-DA using 3 different types of
2009 Mar 25
1
how to calcualte Jaccard Coefficient
Does anyone have a good method for calculating Jaccard coefficients now that the dissimilarity() function is no longer an option?
Wen Gu
John Jay College of Criminal Justice445 West 59 StreetNew York, NY 10029
wgu@gc.cuny.edu
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2003 May 11
2
rank correlation and distance between two different matrices
Dear all,
in package Hmisc `rcorr' computes a matrix of Spearman's `rho' rank
correlation coefficients for all possible pairs of columns of a matrix.
What if I want a matrix of rank correlation coefficients for pair of
columns of two different matrices?
I have the same question about distance metrics in package Vegan. The
function 'vegdist' computes distance indexes for all
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]]
2013 Jan 19
0
Cluster Analysis and PCoA (mixt variables)
Hello everyone,
I mail you because of my lake of knowlegde regarding statistics.
I'm using the CA and PCoA (but maybe should I use some other techniques) to
determine the differences and similarities between a large sample of plants
using different kind of traits through matrix of mixte variables.
I understood that the daisy() function using the gower metric and defining
the different type
2005 Sep 18
0
How to test homogeneity of covariance matrices?
Dear Group Members,
Forgive me if I am a little bit out of subject. I am looking for a good
way to test the homogeneity of two variance-covariance matrices using R,
prior to a Hotelling T test. Youll probably tell me that it is better
to use a robust version of T, but I have no precise idea of the
statistical behaviour of my variables, because they are parameters from
the harmonics of
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
2012 Feb 14
1
[LLVMdev] Static slicer and other useful stuff
On 02/14/2012 07:26 AM, Evan Cheng wrote:
> Hi js,
>
> On Feb 13, 2012, at 8:49 AM, Jiri Slaby <jirislaby at gmail.com> wrote:
>
>> Hello,
>>
>> we, at the Masaryk University, have developed an interprocedural static
>> slicer with other useful stuff. This includes Andersen's points-to
>> analysis, accurate call-graph, modifies relations.
2007 Sep 24
1
save 3dplot to file
I think it is an easy question but i haven´t found a solution since I
am r beginner.
I did this
plot3d(PCoA, type="p", col=rainbow(1000),size=5)
text3d(PCoA, text=Nam)
How can I save it including the labels to a jpg-file?
Thanks in advance.
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
2007 Oct 22
1
plot3d with more than 8 colors
Hello R user and helper!
I would like to get a 3d plot with coloured points.
I did that:
colors<-c(rep("2",7), rep("3",12), rep("4", 24), rep("5", 13), rep
("6", 8), rep("7", 51), rep("8", 1), rep("9", 15), rep("10", 53), rep
("11",3), rep("12",3), rep("13", 8),