Displaying 20 results from an estimated 2000 matches similar to: "Similarity matrix"

2011 Oct 07

1

R equivalent of proc varclus

Dear List
What is the R package equivalent of Proc Varclus or Information Value. ANy
assistance in determining R equivalents of f Oblique Component Analysis
(PROC VARCLUS), Information Value
(IV) and Weight Of Evidence (WOE) analysis, and business intelligence
http://www.nesug.org/proceedings/nesug06/an/da23.pdf
Regards,
Ajay
Websites-
http://decisionstats.com

2001 Dec 19

2

How to create a data.frame "like" another, but longer?

Hello,
does anyone know of a quick way to create a data frame "like" another, but
with more rows?
What I'd like to do is this:
if mydata is a data.frame like
a b c
1 TRUE yes
2 FALSE no
3 TRUE yes
I'd like to get mydata2 with the same column names and column types, but
without the values and with more rows.
All I could think of was to manually do

2005 Mar 24

2

font sizes for row.names of dendograms

Dear R
I recently performed a cluster analysis. It produced the dendogram no
problem but unfortunately the font size of the row.names were all cluttered
due to their large size
So I tried to change the font size using
plclust(cluster.results, labels=iris$specie, cex=0.8)
and R came back to me saying
Error in plclust(cluster.results, labels = iris$specie, cex = 0.8) :
unused argument(s)

2003 May 06

1

S's plclust and R's hclust

Hello everyone,
Does anyone know how to implement the argument "unit" in R's plclust
function ? I used to use Splus where this argument exists but it has not
been implemented in R's plclust. The reason why I switched from Splus to
R is that Ward's method is not implemented for S's hclust whereas it is
implemented for R's hclust. What I would need is S's plclust

2000 Apr 11

2

xgobi interface

i just installed the xgobi interrface,
and this is what i get
when i try to run the example
things don't work
> xgobi(laser)
xgobi -title 'laser' -std mmx -dev 2 /tmp/unixR3e07S15fb &
> Neither the file 2 nor 2.dat exists
what am i doing wrong?
p.s.: xgobi is installed and works
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2000 Apr 10

2

Newbie: how to calculate group averagege?

Dear R-List,
I?m new in R, so I hope my question is not to primitive, but I haven?t
found a solution in the R-help. I?ve got a datatframe with 3 factors,
called xf (9 levels), yf (9 levels), zf (3 levels) and one variable
(rt):
> xf yf zf rt
> 1 1 1 67
> 1 1 1 56
> 1 1 1 60
[...]
> 1 1 2 58
> 1 1 2 61
[...]
> 9 1

2004 Jan 04

5

Analyzing dendograms??

I have used heatmap to visualize my microarray data. I have a matrix of
M-values. I do the following.
#The distance between the columns.
sampdist <- dist(t(matrix[,]), method="euclidean")
sclus <- hclust(sampdist, method="average")
#The distance between the rows.
genedist <- dist(matrix[,], method="euclidean")
gclus <- hclust(genedist,

2005 May 31

1

Loading matrices and other things

Hi all,
I'm new to R, so needless to say I have a couple questions (which I hope
I haven't missed through the documentation).
I have several files in lower triangular matrix form. For each of these
matrices, I want to perform some form of hierarchical clustering on each
matrix and capture the output of the clustering.
The first problem I run into is actually loading the matrix file

2010 Nov 15

2

hclust, does order of data matter?

Hello,
I am using the hclust function to cluster some data. I have two separate
files with the same data. The only difference is the order of the data in
the file. For some reason, when I run the two files through the hclust
function, I get two completely different results.
Does anyone know why this is happening? Does the order of the data matter?
Thanks,
RC
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2013 Dec 12

2

method default for hclust function

I could not figure out what was the default when I ran hclust() without specifying the method.
For example:
I just have a code like:
hclust(dist(data))
Any input would be appreciated:)
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2000 Nov 01

5

Performance note: Preallocating helps? and two questions

hi-
in r 1.1 on windows 2000
with length(AU) of 35833
AUcap30<-0
for(i in 1:length(AU))AUcap30[i]<-min(30,AU[i])
took over an hour on pentium II 300 mhertz (I esc'ed before it finished)
but
AUcap30<-AU
for(i in 1:length(AU))AUcap30[i]<-min(30,AU[i])
is very quick (a few seconds)
Is this performance difference common in r (ie is linux the same way)?
Are there other tricks

2000 Nov 01

5

Performance note: Preallocating helps? and two questions

hi-
in r 1.1 on windows 2000
with length(AU) of 35833
AUcap30<-0
for(i in 1:length(AU))AUcap30[i]<-min(30,AU[i])
took over an hour on pentium II 300 mhertz (I esc'ed before it finished)
but
AUcap30<-AU
for(i in 1:length(AU))AUcap30[i]<-min(30,AU[i])
is very quick (a few seconds)
Is this performance difference common in r (ie is linux the same way)?
Are there other tricks

2004 May 19

7

Help with hclust() and plot()

Hi
When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a
hierarchial cluster analysis, I end up with a vertical tree. What do I
need to do to get a horizontal tree?
Also, my users are used to seeing trees who's leaves all "end" at the
same place (eg. Like in minitab). Is this possible in R?
Thanks
Mick
Michael Watson
Head of Informatics
Institute for Animal

2003 Nov 04

1

hclust doesn't return merge details [Solved]

Thanks to Andy and Thomas,
Reading help(hclust) more carefully would have done it but sometimes you do not
see the wood for the trees...
So hc$merge does exactly what I want.
I have never been aware of the command str to get the structure of an R-object. It
seems pretty useful to me.
Thanks,
Arne
> -----Original Message-----
> From: Liaw, Andy [mailto:andy_liaw at merck.com]
>

2013 Dec 17

1

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

Dear R-help,
We are conducting a distance-based redundancy analysis using capscale and
then testing for statistical significance for six terms in the model for the
constrained ordination using anova.cca in the vegan package. The
significance test is sequential, i.e., testing for significance of a term
only after accounting for all preceding terms. Could someone please provide
us with either the

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 =

2000 Aug 31

2

Multiv / hierclust / plclust

I use hierclust (hierarchical clustering) in multiv package. In the
documentation it is said that plclust (plotting a dendrogram) is
available in S-plus. Can I find it anywhere (I have searched through
http://lib.stat.cmu.edu/S and found only quotations of plclust in
multiv) or is it only part of the S package (which I don't have)?
Thanks
---------------
Charles RAUX,

2017 Jun 21

1

getting error while trying to make dendogram based on gene expression

I am trying to make dendogram based on gene expression matrix , but getting
some error:
I
countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F)
colnames(countMatrix)
count_matrix <- countMatrix[,-1] # remove first column
(gene names)
rownames(count_matrix) <- countMatrix[,1] #added first column gene
names as rownames)
>

2000 Feb 25

2

partial correlation coefficients in R?

Hello,
after thorough searching of the R help files as well as S+-help, I'm coming
to the list: Is there a possibility to compute partial correlation
coefficients between multiple variables (correlation between two paired
samples with the "effects of all other variables partialled out")? All I
seem to find are the standard Pearson correlation coefficients (with cor())
and no clue

2006 Apr 03

2

about arguments in "bclust"

Hi All,
Just want to make sure, in function "bclust", do the following argument
only have one option?
argument "dist.method" has one option "Euclidian";
argument "hclust.method" has one option "average";
argument "base.method" has one option "kmeans".
Thank you!
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