Displaying 20 results from an estimated 1000 matches similar to: "Questions on Mahalanobis Distance"
2002 Dec 04
1
Mixture of Multivariate Gaussian Sample Data
Hey, I am confused about how to generate the sample data from a mixture of
Multivariate Gaussian ditribution.
For example, there are 2 component Gaussian with prior
probability of 0.4 and 0.6,
the means and variances are
u1=[1 1]', Cov1=[1 0;0 1]
and
u2=[-1 -1]', Cov2=[1 0;0 1]
repectively.
So how can I generate a sample of 500 data from the above mixture
distribution?
Thanks.
Fred
2012 Oct 14
1
Problems with coxph and survfit in a stratified model, with interactions
First, here is your message as it appears on R-help.
On 10/14/2012 05:00 AM, r-help-request@r-project.org wrote:
> I?m trying to set up proportional hazard model that is stratified with
> respect to covariate 1 and has an interaction between covariate 1 and
> another variable, covariate 2. Both variables are categorical. In the
> following, I try to illustrate the two problems that
2003 Apr 28
2
stepAIC/lme problem (1.7.0 only)
I can use stepAIC on an lme object in 1.6.2, but
I get the following error if I try to do the same
in 1.7.0:
Error in lme(fixed = resp ~ cov1 + cov2, data = a, random = structure(list( :
unused argument(s) (formula ...)
Does anybody know why?
Here's an example:
library(nlme)
library(MASS)
a <- data.frame( resp=rnorm(250), cov1=rnorm(250),
cov2=rnorm(250),
2012 Jul 06
2
Anova Type II and Contrasts
the study design of the data I have to analyse is simple. There is 1 control group (CTRL) and 2 different treatment groups (TREAT_1 and TREAT_2).
The data also includes 2 covariates COV1 and COV2. I have been asked to check if there is a linear or quadratic treatment effect in the data.
I created a dummy data set to explain my situation:
df1 <- data.frame(
Observation =
2008 Aug 18
1
lmer syntax, matrix of (grouped) covariates?
I have a fairly large model:
> length(Y)
[1] 3051
> dim(covariates)
[1] 3051 211
All of these 211 covariates need to be nested hierarchically within a
grouping "class", of which there are 8. I have an accessory vector, "
cov2class" that specifies the mapping between covariates and the 8 classes.
Now, I understand I can break all this information up into individual
2009 May 22
0
EM algorithm mixture of multivariate
Hi, i would to know, if someone have ever write the code to estimate the
parameter (mixing proportion, mean, a var/cov matrix) of a mixture of two
multivariate normal distribution. I wrote it and it works (it could find
mean and mixing proportion, if I fix the var/cov matrix), while if I fix
anything, it doesn't work. My suspect is that when the algorithm iterates
the var/cov matrix, something
2009 May 22
0
EM algorithm mixture of multivariate gaussian
Hi, i would to know, if someone have ever write the code to estimate the
parameter (mixing proportion, mean, a var/cov matrix) of a mixture of two
multivariate normal distribution. I wrote it and it works (it could find
mean and mixing proportion, if I fix the var/cov matrix), while if I fix
anything, it doesn't work. My suspect is that when the algorithm iterates
the var/cov matrix, something
2006 Jul 11
2
Multiple tests on 2 way-ANOVA
Dear r-helpers,
I have a question about multiple testing.
Here an example that puzzles me:
All matrixes and contrast vectors are presented in treatment contrasts.
1. example:
library(multcomp)
n<-60; sigma<-20
# n = sample size per group
# sigma standard deviation of the residuals
cov1 <- matrix(c(3/4,-1/2,-1/2,-1/2,1,0,-1/2,0,1), nrow = 3, ncol=3, byrow=TRUE,
dimnames =
2009 Aug 02
1
Competing Risks Regression with qualitative predictor with more than 2 categories
Hello,
I have a question regarding competing risk regression using cmprsk package (function crr()). I am using R2.9.1. How can I do to assess the effect of qualitative predictor (gg) with more than two categories (a,b,c) categorie c is the reference category. See above results, gg is considered like a ordered predictor !
Thank you for your help
Jan
> # simulated data to test
> set.seed(10)
2012 Oct 13
4
Problems with coxph and survfit in a stratified model with interactions
I?m trying to set up proportional hazard model that is stratified with
respect to covariate 1 and has an interaction between covariate 1 and
another variable, covariate 2. Both variables are categorical. In the
following, I try to illustrate the two problems that I?ve encountered, using
the lung dataset.
The first problem is the warning:
To me, it seems that there are too many dummies
2013 Oct 18
1
crr question in library(cmprsk)
Hi all
I do not understand why I am getting the following error message. Can
anybody help me with this? Thanks in advance.
install.packages("cmprsk")
library(cmprsk)
result1 <-crr(ftime, fstatus, cov1, failcode=1, cencode=0 )
one.pout1 = predict(result1,cov1,X=cbind(1,one.z1,one.z2))
predict.crr(result1,cov1,X=cbind(1,one.z1,one.z2))
Error: could not find function
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,
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))
2012 Oct 05
2
problem with convergence in mle2/optim function
Hello R Help,
I am trying solve an MLE convergence problem: I would like to estimate
four parameters, p1, p2, mu1, mu2, which relate to the probabilities,
P1, P2, P3, of a multinomial (trinomial) distribution. I am using the
mle2() function and feeding it a time series dataset composed of four
columns: time point, number of successes in category 1, number of
successes in category 2, and
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
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
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
2007 Oct 23
1
How to avoid the NaN errors in dnbinom?
Hi, The code below is giving me this error message:
Error in while (err > eps) { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In dnbinom(x, size, prob, log) : NaNs produced
2: In dnbinom(x, size, prob, log) : NaNs produced
I know from the help files that for dnbinom "Invalid size or prob will
result in return value NaN, with a warning", but I am not able
2006 May 21
2
nls & fitting
Dear All,
I may look ridiculous, but I am puzzled at the behavior of the nls with
a fitting I am currently dealing with.
My data are:
x N
1 346.4102 145.428256
2 447.2136 169.530634
3 570.0877 144.081627
4 721.1103 106.363316
5 894.4272 130.390552
6 1264.9111 36.727069
7 1788.8544 52.848587
8 2449.4897 25.128742
9 3464.1016 7.531766
10 4472.1360 8.827367
11
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