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I have a matrix of similarity scores that I want to convert into a matrix of dissimilarity scores so that I can apply some clustering methods to the data. That is, high values in my matrix signify similarity and low values (zero being the lowest) signify no similarity. What functions/options in R or its packages are av...

Hi I am doing this sort of thing: POLY: > > obj = best.tune(svm, similarity ~., data = training, kernel = "polynomial") > summary(obj) Call: best.tune(svm, similarity ~ ., data = training, kernel = "polynomial") Parameters: SVM-Type: eps-regression SVM-Kernel: polynomial cost: 1 degree: 3 gamma: 0.04545455...

Hello, I’m Andrew Litteken, and I am working on a framework for defining, detecting, and deduplicating similar code sections at the IR level. Programmers can introduce sections of code that perform nearly the same operation. By copying and pasting code throughout a code base, or using a piece of code as a reference to create a new piece of code that has nearly the same structure redundancies are inadverte...

Dear List: I have a question regarding an MDS procedure that I am accustomed to using. I have searched around the archives a bit and the help doc and still need a little assistance. The package isoMDS is what I need to perform the non-metric scaling, but I am working with similarity matrices, not dissimilarities. The question may end up being resolved simply. Here is a bit of substantive background. I am working on a technique where individuals organize items based on how similar they perceive the items to be. For example, assume there are 10 items. Person 1 might group it...

I frequently use hclust on a similarity matrix. In R only a distance matrix is allowed. Is there a simple reliable transformation of a similarity matrix that will result in a distance matrix making hclust work the same as S-Plus with a similarity matrix? Venables & Ripley 3rd edition implies that a simple reversal of values wil...

I checked the R procedure HCLUST (hierarchical clustering) but it looks like it requires a full triangular n x n similarity matrix as input, where n = number of observations. The number of variables is 200. My data set has n = 50,000 observations (keywords), and I use ad-hoc similarity measures, not available in R, to measure keyword similarity. Here, the vast majority of the n x n similarities are equal to zero. S...

Hi all, Suppose I have 2 matrices A and B. And I want to measure how good each of this matrix is. So I intend to compare A and B with another "gold standard" matrix X. Meaning the more similar a matrix to X the better it is. What is the common way in R to measure matrix similarity (ie. A vs X, and B vs X) ? - Gundala Viswanath Jakarta - Indonesia

...ow if there's a way of summarizing the overall distance by some kind of metrics. If anyone know a proper way of doing so and/or a package I would greatly appreciate your suggestions. Thanks very much! Kel -- View this message in context: http://r.789695.n4.nabble.com/How-to-measure-level-of-similarity-of-two-data-frames-tp4631466.html Sent from the R help mailing list archive at Nabble.com.

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 [[alternative HTML version

Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a similarity matrix which tells me how many times each individual occurs with another. My eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 1 0 1 2 2 3 0 1 3 1 1 1 And I...

my major is bioinformatics, and i'm trying to cluster ( agglomerate the closest pari of observations ) in R. i have already got my own similarities metric, but do not know how to clust it based on similarities instead of dissimilarities. since the help document of hierclust mentions the parameter "sim", which seems good to me, but it doesn't appear in the code of hierclust() function again? and no sample about it. so coul...

Dear all, I would like to use the apply or a similar function belonging to this family, but applying for each column (or row) but let say for each q columns. For example I would like to apply a function FUN for the first q columns of matrix X then for q+1:2*q and so on. If I do apply (X, 2, FUN) it applies for each column and not for every q columns....

Dear listers, a little off-topic: I am looking for and compare algorithms which can calculate "distance" or "similarity" between two gene lists with different lengths. Any paper, any implementation in R and any suggestion is welcome! Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML...

I am doing hierarchical clustering with cluster package.  I couldnot find similarity measures like matching coefficient, Jaccard coefficient and sokal and sneath. Could anyone please tell package with similarity measures for binary data? kind regards, Ms.Karunambigai M PhD Scholar Dept. of Biostatistics NIMHANS Bangalore India From cricket scores to your friends. Try th...

Dear All, I am analyzing the miRNA data set in which I have 817 unique probes for each they have 20 features each . I have to group the similar features and take the median across them so that I have a data with no repeats to perform invariant analysis . My data looks something similar format probename sample1 sample2 sample3 A 2.3 2.4 2.5 A 8.9 3.6 7.9 A 4...

Hello, how can I get the similarity value (i.e., the inner cluster similarity) that was used to cut a hierarchical tree at a specific height? I would appreciate your help! Best regards, Madeleine

Hi, i'm wondering is there a possibility to do like ABCSok do (http://nyheter.abcsok.no/), to make "Main article" and "Same articles" collapsed to it. Like on http://news.google.com/?hl=en the same thing. "Parent" and "same article on other sites" (they do differ from each other a little bit). Maybe somebody know how to do that thing or where to read

Hi All, I see that llvm-readobj displays information similar to GNU readelf does except DWARF data. I also see llvm-dwarfdump dumps all DWARF data in user readable format. Is there a plan for readobj to incorporate similar options? This will make readobj more feature complete for reading objects similar to readelf. If this is not the plan, will llvm-dwar...

Hi Has anyone used OpenRico''s "on-demand listbox" LiveGrid or something similar in a Rails app already? How well does it behave? I''m asking this because I need a scrollable list but the number of records in the table could be well above 5000. In the past I''ve used similar "on-demand fetchings" in desktop apps and it was a real blessing (the d...

...://lists.samba.org/archive/rsync/2007-January/017033.html I have a related but different observation to share: with files in the multi-gigabyte-range, I've noticed that rsync's runtime also depends on how much the source/destination diverge, i.e., synchronization is faster if the files are similar. However, this is not just because less data must be transferred. For example, on an 8 GiB file with 10% updates, rsync takes 390 seconds. With 50% updates, it takes about 1400 seconds, and at 90% updates about 2400 seconds. My current explanation, and it would be awesome if someone more knowledg...