search for: manhattan

Dear R users, When I run the following code, R crashes: require(cclust) x <- matrix(c(0,0,0,1.5,1,-1), ncol=2, byrow=TRUE) cclust(x, centers=x[2:3,], dist="manhattan", method="kmeans") While this works: cclust(x, centers=x[2:3,], dist="euclidean", method="kmeans") I'm posting this here because I am not sure if it is a bug. I've been searching for a manhattan kmeans method and I found a solution by using the package...

To whom it may concern: My name is Jillian Weinfeld. I am currently and undergraduate student at New York University and working at Mount Sinai School of Medicine doing research with epilepsy patients. At the moment I am creating a manhattan plot with my data set. After reading many forums and such, I have appropriately plotted my data, however, I wanted to see how I can change the colors of the data points for my plot. The normal function that I use for color is not working. I have tried many different arguments, but none seem to work...

Hello, I am trying to create a simple Manhattan plot for a small list of 200 SNPs spread out in the genome in different genes. I have tried different functions (using ggplot2 and a function created by Stephen Turner, mhtplot etc.)-none of them work smoothly. Does anyone have a simple way to create the plot (not for all 22 chromosomes)- with the...

Hi, Tenfei, I have two group of data composed of gene mutation and deletion on specific sites. Will it be possible for me to use the Manhattan Plot for comparison? Thank you for you attention! Li-Wu Guo, Ph.D. Sent from Windows Mail [[alternative HTML version deleted]]

Hello Martin Maechler and All, A simple question (I hope): How can I compute the "sum of the dissimilarities" that appears in the pam command (from the cluster package) ? Is it the "manhattan" distance (such as the one implemented by "dist") ? I am asking since I am running clustering on a dataset. I found 7 medoids with the pam command, and from it I have the medoid to which each observation belongs to. But when I check it, I find only (about) 90% of observations has t...

Dear All, I'm dealing with a case, where 'manhattan' distance of each of 100 vectors is calculated from 10000 other vectors. For achieving this, following 4 scenarios are tested: 1) scenario 1: > x<-read.table("query.vec") > v<-read.table("query.vec2") > d<-matrix(nrow=nrow(v),ncol=nrow(x)) > for (i in...

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Hi I've successfully installed Duke Nukem Manhattan Project, but when I try to start it, it prompts for the CD, although the CD is in the drive and the drive is set up properly in Wine settings. It seems people have run the game successfully on wine, so perhaps someone's got a clue about this issue. Thanks for any help!

Hello all. I wish to run k-means with "manhattan" distance. Since this is not supported by the function "kmeans", I turned to the "pam" function in the "fpc" package. Yet, when I tried to have the algorithm run with different starting points, I found that pam ignores and keep on starting the algorithm from the s...

...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$V2, breaks="FD",main="Euclidean Metric", xlab="Sum of 3NN ... hist(var$V2, breaks="FD",main="Manhattan Metric", xlab="Sum of 3NN ... At this point I would like to place a title at the head of the pag...

Dear All, I have a data, suppose it is an N*M matrix data. All I want is to classify it into, let see, 3 classes. Which method(s) do you think is(are) appropriate for this purpose? Any reference will be welcome! Thanks! Best, Baoqiang Cao

I'm working on a project related to document clustering. I know that R has clustering algorithms such as clara, but only supports two distance metrics: euclidian and manhattan, which are not very useful for clustering documents. I was wondering how easy it would be to extend the clustering package in R to support other distance metrics, such as cosine distance, or if there was an API for custom distance metrics. Best regards, Raymond Pon pon3 at llnl.gov x43062

Is there a function that calculate the mahalanobis distance in R . The dist function calculates "euclidean"', '"maximum"', '"manhattan"', '"canberra"', '"binary"' or '"minkowski"'. Thanks ../Murli

...> repeatedly until some ceratain conditions > for a cluster are met. Unfortunately, > the system crashes on the second call (after debugging). > > # kmeans res1 is a well defined matrix > cl <- cclust(res1, as.numeric(ncntrs), iter.max = 20, verbose = FALSE, > dist="manhattan", method="kmeans") > > > RGui has generated errors and will be closed by Windows. ... > > What might be the problem? There is a section in the rw-FAQ on how to find out. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics...

Hello all! I am performingsome clustering analysis on microarray data using agnes{cluster} and I have created my own dissimilarity matrix according to a distance measure different from "euclidean" or "manhattan" etc. My question is, if I choose for example method="complete", how are the distances between the elements calculated? Are they taken form the dissimilarity matrix I have provided as the first argument? clust.complete.agnes<-agnes(as.dist(D),diss="TRUE",method="co...

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This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---559023410-162216788-916833047=:29339 Content-Type: TEXT/PLAIN; charset=US-ASCII On my R installation (0.62.4) there is no dist() function, so I attach one possibility. It provides

Hi, I would like to use xyplot to create a figure. Unfortunately, I cannot find documentation in xyplot to specify alternating the x-axis tick labels with the x-axis tick marks. I can do this with the regular R plot function as follows. #A small version of my data looks like this data<-data.frame(matrix(ncol=3,nrow=12)) data[,1]<-rep(c(1,2,3),c(4,4,4)) data[,2]<-rep(c(1,2,3,4),3)

...he 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 scaled up proportionally to the number of >> columns used. If all pairs are excluded when calculating a >> particular distance, the value is `NA'. but the C code in ....../src/library/mva/src/distance.c, has, e.g. for the Euclidean d...

...cclust function in cclust package repeatedly until some ceratain conditions for a cluster are met. Unfortunately, the system crashes on the second call (after debugging). # kmeans res1 is a well defined matrix cl <- cclust(res1, as.numeric(ncntrs), iter.max = 20, verbose = FALSE, dist="manhattan", method="kmeans") RGui has generated errors and will be closed by Windows. ... What might be the problem? Thank you, Igor.