Displaying 20 results from an estimated 30000 matches similar to: "Calculate missing value using a correlation metric"
2010 May 05
2
custom metric for dist for use with hclust/kmeans
Hi guys,
I've been using the kmeans and hclust functions for some time now and
was wondering if I could specify a custom metric when passing my data
frame into hclust as a distance matrix. Actually, kmeans doesn't even
take a distance matrix; it takes the data frame directly. I was
wondering if there's a way or if there's a package that lets you
create distance matrices from
2004 Feb 07
1
knn using custom distance metric
Hi,
There are two packages providing knn classification: class and knnTree.
However, it seems both uses Eucleadian distances only. How can I uses a
custom distance function with either package?
Thanks,
Xiao-Jun
2003 Sep 14
1
title for plot contain 4 subplots
Hi,
I'm plotting 4 graphs on one page (2x2 matrix) but I cant seem to get
the title for the whole page right.
I'm doing:
op <- par(mfrow = c(2,2), pty="s")
hist(var$V2, breaks="FD",main="Euclidean Metric", xlab="Sum of 3NN ...
hist(var$V2, breaks="FD",main="Manhattan Metric", xlab="Sum of 3NN ...
hist(var$V2,
2010 May 06
1
nnclust: nnfind() distance metric?
Hello,
pardon my ingorance, but what distance metric is used in this function
in the nnclust package?
The manual only says:
"Find the nearest neighbours of points in one data set from another
data set. Useful for Mallows-type
distance metrics."
BR,
Jay
2006 Aug 16
1
help about agnes
Hello.
I have the following distance matrix between 8 points:
[1,] 0.000000 3.162278 7.280110 8.544004 7.071068 9.899495 6.403124 8.062258
[2,] 3.162278 0.000000 5.000000 6.403124 4.472136 8.944272 6.082763 8.062258
[3,] 7.280110 5.000000 0.000000 1.414214 1.000000 5.000000 4.242641 5.830952
[4,] 8.544004 6.403124 1.414214 0.000000 2.236068 4.123106 4.472136 5.656854
[5,] 7.071068 4.472136
2002 Oct 21
1
dist() {"mva" package} bug: treats +/- Inf as NA
Vince Carey found this (thank you!).
Since the fix to the problem is not entirely obvious, I post
this to R-devel as RFC:
help(dist) says:
>> Missing values are allowed, and are excluded from all computations
>> involving the rows within which they occur. If some columns are
>> excluded in calculating a Euclidean, Manhattan or Canberra
>> distance, the sum is
2012 Oct 01
6
nlme: spatial autocorrelation on a sphere
I have spatial data on a sphere (the Earth) for which I would like to run an gls model assuming that the errors are autcorrelated, i.e. including a corSpatial correlation in the model specification.
In this case the distance metric should be calculated on the sphere, therefore metric = "euclidean" in (for example) corSpher would be incorrect.
I would be grateful for help on how to
2002 Jul 26
2
estimating missing data
Hello R group
Do you know if an EM algorithm exits for R to estimate missing data in a
sample?
I just found knn algorithm in to the package emv but it doesn't look to be
the usual EM algorithm.
Thanks
Xavier
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Send "info",
2011 Jun 27
3
New to R, trying to use agnes, but can't load my ditance matrix
Hi,
I'm mighty new to R. I'm using it on Windows. I'm trying to cluster using a
distance matrix I created from the data on my own and called it D10.dist. I
loaded the cluster package. Then tried the following command...
> agnes("E:D10.dist", diss = TRUE, metric = "euclidean", stand = FALSE,
> method = "average", par.method, keep.diss = n < 1000,
2009 Aug 30
1
about isoMDS method
Hi,
For example:
I built a half matrix "w" using a daisy(x, metric = c("euclidean"))
http://www.nabble.com/file/p25211016/1.jpg
And next I transformed this matrix "w" using isoMDS function, for example
isoMDS(w, k=2) and as result I got:
http://www.nabble.com/file/p25211016/2.jpg
And now I have two questions:
1. If number in matrix w[2, 1] (= 0.41538462) match
2017 Jun 13
0
Mean correlation within cluster
Hello all,
I'd like to calculate the mean correlation within a cluster and understand if it's significantly >0. I'm using packages 'geomorph' and 'paleomorph'.
#Simulate an array A <- array ( rep ( 1 : 36 , by = 4 ), dim = c ( 12 , 3 , 4 )) #Load 'geomorph' package and superimpose coordinates test.gpa <- gpagen ( A , print.progress = FALSE ) #Load
2005 Jun 07
1
Specifying medoids in PAM?
I am using the PAM algorithm in the CLUSTER library.
When I allow PAM to seed the medoids using the default __build__
algorithm things work
well:
> pam(stats.table, metric="euclidean", stand=TRUE, k=5)
But I have some clusters from a Hierarchical analysis that I would
like to use as seeds for the PAM algorithm. I can't figure what the
mediod argument wants. When I put in the
2011 Mar 16
1
Specify feature weights in model prediction (CARET)
Using the 'CARET' package, is it possible to specify weights for features
used in model prediction? And for the 'knn' implementation, is there a way
to choose a distance metric (i.e. Mahalanobis distance)?
Thanks,
~Kendric
[[alternative HTML version deleted]]
2008 Aug 01
2
correlation between rows of data.frame
Dear R users,
I need to come up with an efficient method to compute the correlation (or at
least, the euclidean distance if that's easier) between specific rows in a data
frame (46,232 rows, 29 columns). The pairs of rows between which I want to
find the correlation share a common value in one of the columns. So for
example,
in the following
2008 Feb 19
1
Calculating the distance samples using distance metics method
***********reading in data**********
data<-read.table("microarray.txt",header=T, sep="\t")
head(data)
dim(data)
attach(data)
***********creating matrix and calculating variance across probesets********
x<-1:20000
y<-2:141
data.matrix<-data.matrix(data[,y])
variableprobe<-apply(data.matrix[x,],1,var)
hist(variableprobe)
**************filter out low
2018 Mar 15
3
stats 'dist' euclidean distance calculation
Hello,
I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated:
3x3 subset used
2003 Nov 13
0
Help: Strange MDS behavior
Hi!
I have a dissimilarity matrix X and try to compare it with X' =
dist(cmdscsale(X,k)).
If I increase k, I should expect that the error (or fit) should
monotonically decrease, right.
Here is a sample code;
library(mva)
set.seed(12345)
x <- as.matrix(dist(matrix(rnorm(100),ncol=10,byrow=T)))
# x[1,2]<-x[2,1]<-1000 ## <<--** 1
# x[5,6]<-x[6,5]<-1000 ##
2009 Nov 05
3
Bhattacharyya distance metric
I need to use the Bhattacharyya distance metric to determine population
separation. Has anyone written a Bhattacharyya distance metric function in
R?
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2013 Dec 07
1
How to perform clustering without removing rows where NA is present in R
I have a data which contain some NA value in their elements.
What I want to do is to **perform clustering without removing rows**
where the NA is present.
I understand that `gower` distance measure in `daisy` allow such situation.
But why my code below doesn't work?
__BEGIN__
# plot heat map with dendogram together.
library("gplots")
library("cluster")
2013 Feb 10
1
Training with very few positives
I have a binary classification problem where the fraction of positives is
very low, e.g. 20 positives in 10,000 examples (0.2%)
What is an appropriate cross validation scheme for training a classifier
with very few positives?
I currently have the following setup:
========================================
library(caret)
tmp <- createDataPartition(Y, p = 9/10, times = 3, list = TRUE)