Re: [R] statdataml question

Bryan: > > Hi, > > I was wondering if Statdataml is currently the preferred way to > represent statistical data in XML in R. This is hard to tell. We think it is a _possible_ way doing that. Do you have some alternatives in mind? And also if the Statdataml api > provides ways to load the XML

Re: [R] nnet 10-fold cross-validation

Hi all, there is tune() in the e1071 package for doing this in general, and, among others, a tune.nnet() wrapper (see ?tune): > tmodel = tune.nnet(Species ~ ., data = iris, size = 1:5) > summary(tmodel) Parameter tuning of `nnet': - sampling method: 10-fold cross validation - best paramete

[R] [R-pkgs] package "relations" updated

ness from a specified property (e.g., symmetry, transitivity, etc.). David and Kurt. -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Tel: +43-1-313 36 4393 Fax: +43

[R] Problems with e1071 and SparseM

Chris: yes, this is indeed a bug (in predict.svm) - will be fixed in the next release of e1071. Thanks for pointing this out, David -- Hello all, I am trying to use the "svm" method provided by e1071 (Version: 1.5-16) together with a matrix provided by the Sparse

[R] [R-pkgs] New package "proxy" for distances and similiarities

Dear useRs, a new package for computing distance and similarity matrices made it to CRAN, and will propagate to the mirrors soon. It includes an enhanced version of "dist()" with support for more than 40 popular similarity and distance measures, both for auto- and cross-distances. Some importa

Re: [R] Question for svm function in e1071

Adschai: The function is written in C++, so debugging the source code of the R svm() function will not really help. What you can do to make the C-code more verbose is the following: - get the sources of e1071 - in the src/ directory, look up the svm.cpp file - In line 37, there is: #if 0 void

Re: [R] Question about framework to weighting different classes in SVM

Adschai: here is an example for class.weights (isn't it on the help page?): data(iris) i2 <- iris levels(i2$Species)[3] <- "versicolor" summary(i2$Species) wts <- 100 / table(i2$Species) wts m <- svm(Species ~ ., data = i2, class.weights = wts) Cheers, D

[R] [R-pkgs] New package: relations

Dear useRs, it is our great pleasure to announce the new package "relations" to appear on all CRAN-mirrors soon. This package provides data structures and methods for creating and manipulating relations, relation ensembles, sets, and tuples. The feature list includes: * creation of relations by

[R] string edit distance

It's in package cba (sdists()). David -- I have a column of words, for example "DOG" "DOOG" "GOD" "GOOD" "DOOR" ... and I am interested in creating a matrix that contains the string edit distances between each pair of words. I am this close -> ' ' <- to writing the algorit

Re: [R] training svm

Oldrich: > > The columns in data passed to svm need to contain only numeral values. This is not correct, svm() of course also accepts factors and then builds a model matrix similar to lm(). But it won't accept, e.g., character vectors. > I simply assigned a number to each category of each fea

[R] distance metrics

> Hello: > > > > > > Does anyone know if there exists a package that handles methods for [ > for > > > dist objects? > > > > > > I would like to access a dist object using matrix notation > > > > > > e.g. > > > > > > dMat = dist(x) > > > dMat[i,j] You can use the [[ operator defined f

Re: [R] PROC TABULATE with R

ea is to create a package for that, since XMLA and JOLAP > specifications > > > should able us to do so ! > > > > > > -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wi

[R] training svm

Hello (whoever you are), your data looks problematic. What does head(ne_span_data) reveal? BTW, svm() will not handle NA values. Best David - Hello. I'm new to R and I'm trying to solve a classification problem. I have a training dataset of about 40,000 rows and 50 column

[R] "contingency table" for several variables

David: >I ‘m trying to draw ONE table that summarize SEVERAL categorical >variables >according to one classification variable, say “sex”. The result would >look >like several contingency tables appended one to the other. All the >variables >belong to a data frame. >The summary.formula

[R] naiveBayes question

Aimin: The problem is that the columns you choose for training (only 4 variables) do not match the ones used for prediction (all except y). David I try to use naiveBayes > p.nb.90<-naiveBayes(y~aa_three+bas+bcu+aa_ss,data=training) > pr.nb.90<-table(predict(p.nb.90,training[,-13],ty

Re: [R] svm plot question

e my code. it doesn't work. > It is pity not saving my original code. > > Now the question is the plot I get using your code is different from > what I got before. > Moreover I did remember I use plot(m.svm,p5.new,As~Cur) > > Do you know why? > > Thanks, > >

Re: [R] svm plot question

.new$Y) <- list(Out=c(1), In=c(0)) >> attach(p5.new) >> m.svm<-svm(Y~P+Aa+As+Cur,data=p5.new) >> summary(m.svm) > > Call: > svm(formula = Y ~ P + Aa + As + Cur, data = p5.new) > > > Parameters: >SVM-Type: C-classification > SVM-Kernel: radial >

Re: [R] vcd package, assoc()

t;null"), mar[2], legend_width) : >>>> It is invalid to combine unit objects with other types >>> Works for me. Which version of R is this? R-2.4.0, R-patched or >>> R-devel? >>> >> > > > -- Dr. David Meyer Department of Information

[R] package e1071 - class probabilities

Vince: the implementations for both are different, so this might happen (although undesirably). Can you provide me an example with data (off-list)? David __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do r

[R] comparing 2 odds ratios

testing whether the 2 odds ratios are the same? -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Tel: +43-1-313 36 4393 Fax: +43-1-313 36 90 4393 HP: http://wi.wu-wien.ac.at

[R] Getting SVM minimized function value

model (svm from the package e1071) but I have not succeed. Does anyone knows a way to get that value? Pau -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Tel: +43-1-313 36 4393

[R] Predict function for 'newdata' of different dimension in svm

;TOF" "EXT" "Acode" > dim(new.dat) [1] 175 3 Now try to predict: > predict(cd1.svm,newdata=new.dat) Error in "names<-.default"(`*tmp*`, value = c("1", "2", "3", "4", "5", : '

[R] Fixed legend in vcd/mosaicplot

Dieter, there is no way of fixing the range of the residuals yet, we will add sth. like a ylim argument to legend_foo(). Thanks for pointing this out, David PS: there is no mosaicplot() function in vcd, but a mosaic() ... -- Dr. David Meyer Department of Information Systems and Operations

Re: [R] getting probabilities from SVM

TRUE when training the model, but doesn't show an > example. Then I try to predict with probabilities, I still only get > classifications back. Anyone get this to work and can help me out? -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economi

[R] Help with plot.svm from e1071

r plot.svm, which has a simple example (that works) ## a simple example library(MASS) data(cats) m <- svm(Sex~., data = cats) plot(m, cats) I don't see what the difference between their example and mine. -- Dr. David Meyer Department of Information Systems and Operat

[R] e1071::SVM calculate distance to separating hyperplane

t;repetitive: >How can one (elegantly) calculate the distance between data points (in the >transformed space, I suppose) and the hyperplane that separates the 2 >categories when using svm() from the e1071 library? >thanks a lot, >Hans -- Dr. David Meyer Department of Informa

Re: [R] str and structable error

rror on some objects but I just was not so lucky to > > meet one?. > > > > W2000, R2.2.0, vcd package Built: R 2.2.0; ; 2005-11- > > 22 14:23:44; windows, > > > > Best regards. > > > > Petr > > > > Petr Pikal > > [EMAIL PROTECTED] &

[R] [R-pkgs] vcd package 0.9-5 released

table(), etc. are available * New panel function pairs_diagonal_text() for pairs() * The alternative legend function legend_fixed() now looks more similar to the legend of mosaicplot() in base R Comments are more then welcome! David, Achim, Kurt. PS: If you like modern art, try out demo(mondrian

[R] how to use tune.knn() for dataset with missing values

Well, since knn() can't handle incomplete data as it says, you can choose to either omit incomplete observations (e.g., using na.omit()), or to impute the data if the conditions are met (missingness at random, ...); see, e.g., packages cat, mix, norm, and e1071 for that. HTH, David

Re: [R] How to insert a certain model in SVM regarding to fixed kernels

l yet for time series. Cheers, David > Its possible that what works already is enough for Amir. For example, > > library(e1071) > library(dyn) > set.seed(1) > y <- ts(rnorm(100)) > y.svm <- dyn$svm(y ~ lag(y)) > yp <- predict(y.svm) > ts.plot(y, yp, col = 1:

Re: [R] How to insert a certain model in SVM regarding to fixed kernels

Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313 36x7

Re: [R] setting weights for such a two-class problem in nnet and svm

intend to set 1 for class one, 49 for class 2. How do I do that? Just weights=49? Meanwhile I'd like to try svm(e1071), again, how do I setup "class.weights"? Thanks. -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business

[R] [R-pkgs] New version of "vcd" package

y table. Happy drawing! David, Achim, Kurt -- Dr. David Meyer Department of Information Systems and Operations Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313 36x746 Tel: +43-1-313 36x4393 HP: http://wi.wu-wien.ac.at/~meyer/

Re: [R] Running SVM {e1071}

> > Dear David, Dear Friends, > > After any running svm I receive different results of Error estimation > of 'svm' using 10-fold cross validation. using tune.svm(), or the `cross' parameter of svm()? > What is the reason ? It is caused by the algorithm, libsvm , e1071 or > something els?

Re: [R] svm and scaling input

ith the math behind svms, so my assumtions maybe > completely wrong ... or obvious. Will the svm automatically expand the > factors into a binary matrix? yes. > If I add numeric variables outside the range of 0 to 1 do I have to > scale them to have 0 to 1 range? svm() will scale your data

[R] SVM parameters...

Vivek, I certainly would agree that every help page, including the one of svm(), could be improved, but I think it is not _that_ deficient. In particular, it tells you which parameters are used in the various kernels available. Have you read the corresponding article in R News (basically contain

Re: [R] best.svm

Stephen: you need to supply the parameter ranges, your call did not tune anything at all. best.svm() is really just a wrapper for tune.svm(...)$best.model. The help page for 'tune()' will tell you more on the available options. HTH, David [...] > svm.model = best.svm(data[1:3000,1:23],data[1:

[R] tune.svm in {e1071}

Support >Vectors , gamma, cost , nu , >epsilon , after model<- tune.svm( ) ? >these are not possible? I receive only "Error estimation of 'svm' " >with model and summary(model) functions. Clear from the above, I think. HTH, David >Best Wishes and so man

[R] SVM linear kernel and SV

> Thank you for your answer, > but my problem concerns the support vectors. Indeed the two classes > are well separated and the hyperplane is linear but the support > vectors aren't aligned in parallel to the hyperplane. And according to > me, the support vectors (for each class) should be aligned

[R] SVM linear kernel and SV

w and threshold b ? On the data set, and therefore also on w and b. Best, David -- Dr. David Meyer Department of Information Systems and Process Management Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax:

[R] Status

ALERT! This e-mail, in its original form, contained one or more attached files that were infected with a virus, worm, or other type of security threat. This e-mail was sent from a Road Runner IP address. As part of our continuing initiative to stop the spread of malicious viruses, Road Runner s

Re: [R] Error using e1071 svm: NA/NaN/Inf in foreign function call

Joao: 1) The error message you get when setting nu=0 is due to the fact that no support vectors can be found with that extreme restriction, and this confuses the predict function (try svm(, fitted = false): the model returned is empty). In fact, the C++ code interfaced by svm() clearly allows

[R] read.matrix.csr bug (e1071)?

This is a bug, thanks for pointing this out. Fixed for the next release of e1071. David - Hello, I would like to read and write sparse matrices using the functions write.matrix.csr() and read.matrix.csr() of the package e1071. Writing is OK but reading back the matrix fails:

Re: [R] probabilty calculation in SVM

Raj: The references given on the help page will tell you. Best, David - Hi All, In package e1071 for SVM based classification, one can get a probability measure for each prediction. I like to know what is method that is used for calculating this probability. Is it calculated using logi

[R] Rgui.exe - Error while tuning svm

ssage: "Die Anweisung in 0x6c48174d verweist auf Speicher > 0x. Der Vorgang "read" konnte nicht auf dem Speicher > ausgef_hrt werden. ." Which version of e1071 are you using? There has been a memory leak problem until 1.5-1 which could very well cause this

Re: [R] How to interpret and modify "plot.svm"?

> I updated the e1071 package but still can't find > the other three arguments for plot.svm. It's in e1071 since version 1.5-3. (current version: 1.5-4). > In addition, I can plot a > gray-colored contour region by adding the argument "col = c(gray(0.2), > gray(0.8))". But I failed to change th

Re: [R] erro in SVM (packsge "e1071")

ds) for > training. The error is in the svm function. May be because SVM uses > other functions, but it happens when I run svm. > > Thanks a lot for the help > > Joao > ___ > FEUP - Engineering Faculty, Porto University > Engineering and Industri

Re: [R] erro in SVM (packsge "e1071")

)? Thanks for any help Joao -- Dr. David Meyer Department of Information Systems Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313 36x746 Tel: +43-1-313 36x4393 HP: http://wi.wu-wien.ac.at/~meyer/ ___

[R] How to interpret and modify "plot.svm"?

? see filled.contour(). The input is determined by a grid of predicted values. Best, -d > Thank you very much, > Frank -- Dr. David Meyer Department of Information Systems Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313

[R] Problem with SVM and scaling

round this? -- Dr. David Meyer Department of Information Systems Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313 36x746 Tel: +43-1-313 36x4393 HP: http://wi.wu-wien.ac.at/~meyer/ __ [EMAIL

[R] svm- class.weights

Uwe: [the language of the list is English!] Try using a *factor* for classification. The described behavior (segfault when using class.weights with a *numeric* dependent variable) should be fixed in the current version of e1071 (1.5-2), so please check if you are using the latest version of e107

[R] tuning SVM's

d <= .5] = 0 > table(testing$similarity, pred) pred 0 1 0 8 30 1 26 107 > and then taking out the kappa statistic to see if I am getting anything significant. I get kappas of 15 - 17% - I don't think that is very good. I know kappa is really for comparing the

[R] Re: What is nu-regression for svm?

> Content-Type: text/plain; charset=ISO-8859-1 > > > Does anyone knows what is the nu-regression option for the type > parameter in svm (from package e1071)? I cannot find any explanation > on that and I have a reasonable understanding on svm fundamentals. > > Thanks > >

[R] Re: R library(e1071) question: definition of performance in tune.* functions

gested, you might want to check if your target variable is indeed a factor. In case it is and you still get values greater than 1, drop me a mail with a piece of code (and data) enabling me to reproduce the phenomenon. Best, David -- Dr. David Meyer Department of Information Systems Vienna Univers

Re: [R] reading a "sparse" matrix into R

Have you considered the read.matrix.csr() function in pkg. e1071? It uses another sparse input format, but perhaps you can easily transform your data in the supported one. Also, in my experience, data frames are not the best basis for a sparse format since they might turn out to be very memory cons

[R] SVM question

cation results per >cross >validation out the svm? I mean e.g. numbers about the true >positives ,fp,fn,tf ? No, because the accuracies are not computed using a confusion matrix. The computation is internally done in C. >How do I get a list of the classified examples ? -- Dr. David M

[R] Re: R-help Digest, Vol 13, Issue 14

You could look at @Article{ e1071-papers:meyer+leisch+hornik:2003, author= {David Meyer and Friedrich Leisch and Kurt Hornik}, title = {The Support Vector Machine under Test}, journal = {Neurocomputing}, year = 2003, month = {September

[R] SVM unbalanced classes

You might consider using the `weight' argument of svm(). Best, David. Hi! I am using R 1.8.1 and the svm of the e1071 package for classification. The problem is that I have unbalanced classes e.g. the first one is much bigger than the second one and therfore the svm is biased to the first clas

Re: [R] svm in e1071 package: polynomial vs linear kernel

On Mon, 3 Nov 2003 [EMAIL PROTECTED] wrote: > I am trying to understand what is the difference between linear and > polynomial kernel: > > linear: u'*v > > polynomial: (gamma*u'*v + coef0)^degree > > It would seem that polynomial kernel with gamma = 1; coef0 = 0 and degre

Re: [R] problem with tune.svm

On Fri, 31 Oct 2003 [EMAIL PROTECTED] wrote: > > rng <- list(gamma = 2^(-1:1), cost = 2^(2:4)) > > rng > $gamma > [1] 0.5 1.0 2.0 > > $cost > [1] 4 8 16 > > > obj <- tune.svm(pIC50 ~ ., data = data, ranges = rng) > Error in tune(svm, train.x = x, data = data, ranges = ranges, ...) : >

Re: [R] svm from e1071 package

> This suggests to me that data are scrambled each time - the last time I > looked at libsvm python interface > this is what was done. Is this the same here (I hope) ? yes. g., David __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mail

Re: [R] Logit reality check

> > If I try the model below, R seems to grumble with a complaint. > > > > glm(cbind(Y,1-Y) ~ X, family = binomial) > > > > non-integer counts in a binomial glm! in: eval(expr, envir, enclos) > > For binomial models (as described in the help page), the response must be either a factor or a n x 2 m

Re: [R] How to detect which function is used for e.g. printing an object of a given class

> Is there an alternative way of "dispatching" the printing, such that > the usual print method for loglm is used after doing what is special > for hllm? You might want to have a look at `NextMethod()' Best, David __ [EMAIL PROTECTED] mailing list https:

Re: [R] problem with HoltWinters

rt. I will change the code to give a better error message in such cases. Best, David. On 2003.09.03 18:32, Luis Miguel Almeida da Silva wrote: The data goes in attachment. I used ts to create data.ts data.ts<-ts(data=data,start=c(2001,1),frequency=12) -Original Message- From: Dav

Re: [R] problem with HoltWinters

How did you construct `data.ts'? Can you send me the file? best, David On 2003.09.03 15:57, Luis Miguel Almeida da Silva wrote: Dear helpers I'm having a problem with function HoltWinters from package ts. I have a time series that I want to fit an Holt-Winters model and make predictions for the n

Re: [R] R, geochemistry, ternary diagrams

And in package vcd function ternaryplot(). g., -d On 2003.07.15 09:33, Tobias Verbeke wrote: > Are there enough geochemists using R already that he'd find > like-minded people to discuss technical issues with if he _did_ > switch to R? Is there a package somewhere already that does ternary > and o

Re: [R] Can't load e1071

Andrew, 1) The current R version is 1.7.1 2) Which version of `e1071' are you using? 3) Does the `e1071.so' file exist (in e1071/libs)? best, David. On 2003.06.24 21:43, Andrew Perrin wrote: After upgrading to 1.7.0 under debian linux, I can't get e1071 working properly. The first problem I had wa

Re: [R] formula (joint, conditional independence, etc.) - mosaicplots

On 2003.06.13 02:11, g wrote: Hi, Can someone set me straight as to how to write formulas in R to indicate: complete independence [A][B][C] Freq ~ A + B + C joint independence [AB][C] Freq ~ A * B + C conditional independence [AC][BC] Freq ~ A * C + B * C nway interaction [AB][AC][BC

Re: [R] Code for Support Vector Clustering Algorithm

Support Vector Machines Description: `svm' is used to train a support vector machine. It can be used to carry out general regression and classification (of nu and epsilon-type), as well as density-estimation. A formula interface is provided. David Meyer <[EMAIL PROTECTED]>

Re: [R] Code for Support Vector Clustering Algorithm

On 2003.06.12 09:15, Uwe Ligges wrote: Iouri Tipenko wrote: Dear R-Users, I'm a master student in Mathematics and Statistics at Carleton University, Ottawa, Canada. I'm studying Clustering methods including different related algorithms. One of them is Support Vector Clustering algorithm. I was w

Re: [R] Error Compiling e1071

> > I am trying to compile the package e1071 (version 1.3-11) with R CMD > INSTALL. I tried with R 1.7.0 on Redhat Linux 2.4.7-10 and R 1.6.2 on > Linux 2.4.9-34smp but keep getting the same error message during > configure : > > WARNING: g++ 2.96 cannot reliably be used with this package. Please

Re: [R] Goodness of fit tests

Try `goodfit' in package `vcd'. g., -d Mag. David MeyerWiedner Hauptstrasse 8-10 Vienna University of Technology A-1040 Vienna/AUSTRIA Department of Tel.: (+431) 58801/10772 Statistics and Probability Theory Fax.: (+431) 58801/10798

Re: [R] RODBC and Excel in Widows

xcel problem or an sql problem.? I did not find anything in > >> the r-help archives relative to this problem. > >> Thanks for any help > >> > >> __ > >> [EMAIL PROTECTED] mailing list > >> https:

Re: [R] where is kurtosis??

E.g., in package e1071. best, -d Mag. David MeyerWiedner Hauptstrasse 8-10 Vienna University of Technology A-1040 Vienna/AUSTRIA Department of Tel.: (+431) 58801/10772 Statistics and Probability Theory Fax.: (+431) 58801/10798 On Sat, 8 Mar

Re: [R] svm

tp://stat.ethz.ch/~hennig/ > [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ > ### > ich empfehle www.boag.de > > __ > [EMAIL PROTECTED] mailing list > http://www.stat.math.ethz.ch/

Re: [R] svm regression in R

-8013, fax -8007 > :: [EMAIL PROTECTED] > :: http://www.informatik.uni-freiburg.de/~helma/ > > __ > [EMAIL PROTECTED] mailing list > http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- Mag. David MeyerWiedner Hauptstrasse 8-10 Vienna University of Techn