Displaying 20 results from an estimated 2000 matches similar to: "outlier identification: is there a redundancy-invariant substitution for mahalanobis distances?"
2011 Sep 26
2
Mahalanobis Distance
Hello R helpers,
I'm trying to use Mahalanobis distance to calculate distance of two time
series, to make some comparations with euclidean distance, DTW, etc, but I'm
having some dificults.
I have, for example, two objects:
s.1 <- c( 5.6324702, 1.3994353, -3.2572327, -3.8311846, -1.2248719,
0.9894694, -2.2835332, -5.1969285, -5.2823988, -3.1499400, -1.7307950,
2.8221209,
2010 Jun 22
1
Mahalanobis distance
I am a new R user. i have a question about Mahalanobis distance.actually i have 300 rows and 7 columns. columns are different measurements, 300 rows are genes. since genes can
classify into 4 categories. i used dist() with euclidean distance and cmdscale to do MDS plot. but find out Mahalanobis distance may be
better. how do i use Mahalanobis() to generate similar dist object which i can use
2005 Dec 14
1
About help on 'mahalanobis'
Hi,
help on 'mahalanobis' (in the stats package in Rv2.2.0) now says:
"Description:
Returns the Mahalanobis distance of all rows in 'x' and the vector
mu='center' with respect to Sigma='cov'. This is (for vector 'x')
defined as
D^2 = (x - mu)' Sigma^{-1} (x - mu)"
It does return D^2 as written. However,
2004 Sep 12
2
mahalanobis distance
Is there a function that calculate the mahalanobis distance in R .
The dist function calculates "euclidean"', '"maximum"', '"manhattan"',
'"canberra"',
'"binary"' or '"minkowski"'.
Thanks ../Murli
2010 Mar 03
1
cluster with mahalanobis distance
How can I perform cluster analysis using the mahalanobis distance instead of
the euclidean distance?
thank you
Naama Wolf
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2005 Aug 04
1
some thoughts on outlier detection, need help!
Dear listers:
I have an idea to do the outlier detection and I need to use R to
implement it first. Here I hope I can get some input from all the
guru's here.
I select distance-based approach---
step 1:
calculate the distance of any two rows for a dataframe. considering
the scaling among different variables, I choose mahalanobis, using
variance as scaler.
step 2:
Let k be the number of
2012 May 30
1
cluster with mahalanobis distance
How can I perform cluster analysis using the mahalanobis distance instead of
the euclidean distance?
Thank you
Maria Froes
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2005 Jun 24
1
Mahalanobis distances
Dear R community
Have just recently got back into R after a long break and have been amazed at
how much it has grown, and how active the list is! Thank you so much to all
those who contribute to this amazing project.
My question:
I am trying to calculate Mahalanobis distances for a matrix called "fgmatrix"
>dim(fgmatrix)
[1] 76 15
>fg.cov <- cov.wt(fgmatrix)
2005 Jul 06
1
Help: Mahalanobis distances between 'Species' from iris
Dear R list,
I'm trying to calculate Mahalanobis distances for 'Species' of 'iris' data
as obtained below:
Squared Distance to Species From Species:
Setosa Versicolor Virginica
Setosa 0 89.86419 179.38471
Versicolor 89.86419 0 17.20107
Virginica 179.38471 17.20107 0
This distances above were obtained with proc
2009 Jul 20
2
mahalanobis distance
http://www.nabble.com/file/p24569511/mahalanobis.txt mahalanobis.txt
http://www.nabble.com/file/p24569511/concentrations.txt concentrations.txt
Dear Forum members,
I have a problem calculating mahalanobis distances. My data file
mahalanobis.txt and categories file concentrations.txt are attached. I do
the following steps:
x <- as.matrix(read.table("mahalanobis.txt", header=TRUE))
2004 Mar 26
1
Mahalanobis
Dear all
Why isn'it possible to calculate Mahalanobis distances with R for a matrix
with 1 row (observations) more than the number of columns (variables)?
> mydata <- matrix(runif(12,-5,5), 4, 3)
> mahalanobis(x=mydata, center=apply(mydata,2,mean), cov=var(mydata))
[1] 2.25 2.25 2.25 2.25
> mydata <- matrix(runif(420,-5,5), 21, 20)
> mahalanobis(x=mydata,
2010 Jan 30
2
Questions on Mahalanobis Distance
Hello,
I am a new R user and trying to learn how to implement the mahalanobis
function to measure the distance between to 2 population centroids. I
have used STATISTICA to calculate these differences, but was hoping to learn
to do the analysis in R. I have implemented the code as below, but my
results are very different from that of STATISTICA, and I believe I may not
have interpreted the help
2011 Mar 20
1
Using the Mahalanobis Function
Hello all,
I am a 2 month newbie to R and am stumped. I have a data set that I've run multivariate stats on using the manova function (I included the data set). Now it comes time for a table of effect sizes with significance. The univariate tests are easy. Where I run into trouble filling in the table of effect sizes is the Mahalanobis D as an effect size. I've included the table so
2007 Feb 20
1
Mahalanobis distance and probability of group membership using Hotelling's T2 distribution
I want to calculate the probability that a group will include a particular
point using the squared Mahalanobis distance to the centroid. I understand
that the squared Mahalanobis distance is distributed as chi-squared but that
for a small number of random samples from a multivariate normal population
the Hotellings T2 (T squared) distribution should be used.
I cannot find a function for
2011 Mar 22
1
Using the mahalanobis( ) function
Hello all,
I am a 2 month newbie to R and am stumped. I have a data set that I've run multivariate stats on using the manova function (I included the data set). Now it comes time for a table of effect sizes with significance. The univariate tests are easy. Where I run into trouble filling in the table of effect sizes is the Mahalanobis D as an effect size. I've included the table so
2008 Dec 08
1
Clustering with Mahalanobis Distance
Dear R ExpeRts,
I'm having memory difficulties using mahalanobis distance to trying to cluster in R. I was wondering if anyone has done it with a matrix of 6525x17 (or something similar to that size). I have a matrix of 6525 genes and 17 samples. I have my R memory increased to the max and am still getting "cannot allocate vector of size" errors. My matrix "x" is
2005 Jul 08
5
Help with Mahalanobis
Dear R list,
I'm trying to calculate Mahalanobis distances for 'Species' of 'iris' data
as obtained below:
Squared Distance to Species From Species:
Setosa Versicolor Virginica
Setosa 0 89.86419 179.38471
Versicolor 89.86419 0 17.20107
Virginica 179.38471 17.20107 0
These distances were obtained with proc 'CANDISC'
2009 Oct 23
1
reference for mahalanobis {stats}
The help on mahalanobis {stats} does not include any reference. I'm
interested in understand why Mahalanobis is defined in its current way
and how to use it. Could somebody point me a good book on this? I have
looked through a few books, but they all give very light explanation
on it.
2007 Apr 11
1
Random Forest Imputations
Dear All,
I am not able to run the random forest with my dataset..
X<- 280 records with satellite data(28 columns) - B1min, b1max, b1std etc..
y<- 280 records with 3 columns - TotBasal Area, Stem density and Volume
yref <- y[1:230,] #Keeping 1st 230 records as reference records
want to set 0 to y values for records 231 to 280..
yimp <- y[231:280,] #records for which we want
2011 Nov 16
2
outlier identify in qqplot
Dear Community,
I want to identify outliers in my data. I don't know how to use identify
command in the plots obtained.
I've gone through help files and use mahalanobis example for my purpose:
NormalMultivarianteComparefunc <- function(x) {
Sx <- cov(x)
D2 <- mahalanobis(x, colMeans(x), Sx)
plot(density(D2, bw=.5), main="Squared Mahalanobis distances, n=nrow(x),