similar to: listing components of an object

Hi!! I am trying to figure out how to use the string kernel "stringdot" in kernlab. k <- function(x,y) { (sum(x*y) +1)*exp(-0.001*sum((x-y)^2)) } class(k) <- "kernel" data(promotergene) ## train svm using custom kernel gene.k <- ksvm(Class~.,data=promotergene,kernel=k,C=10,cross=5) # works fine in this case gene.rbf <-

If I have two vectors X<-1:10 Y<-1:5 When I combine them using cbind, the shorter one is repeated and both are made of the same length. Is there a methods that does this without duplicating the shorter one. I want to use this to store the data back to a file. Thanks ../Murli [[alternative HTML version deleted]]

If my sample size is small is there a particular switch option that I need to use with t.test so that it calculates the t ratio correctly? Here is a dummy example? á =0.05 Mean pain reduction for A =27; B =31 and SD are SDA=9 SDB=12 drgA.p<-rnorm(5,27,9); drgB.p<-rnorm(5,31,12) t.test(drgA.p,drgB.p) # what do I need to give as additional parameter here? I can do it manually but

If I have a calculated t can I get the probability associated with it using an R function by giving it the df and t? I know I can do the whole calculation using t.test() or get the t-distribution using qt(). If t=1.11 and df =9 can I get the probability? Thanks../Murli [[alternative HTML version deleted]]

Hi !! Is there a good tutorial for the R language ? I really find it hard to find methods in R. Thanks and Cheers ../Murli

Is there a function that calculates the inter-rater agreement index (kappa) in R? Thanks ../Murli [[alternative HTML version deleted]]

I am trying to calculate coordinate transformations and in the process of debugging my code using debug I found the following Browse[1]> direction[i] [1] -1.570796 Browse[1]> cos(direction[i]) [1] 6.123032e-17 Browse[1]> cos(-1.570796) [1] 3.267949e-07 Browse[1]> direction[i] [1] -1.570796 Browse[1]> cos(direction[i]) [1] 6.123032e-17 Browse[1]> cos(-1.570796) [1] 3.267949e-07

I am trying to sample a subset from a matrix using sample. The size of the matrix is 20X 1532. It works fine with this, but when I transpose the matrix and try to sample it, it returns null. pick.set<-sample(tissue.exp.t,5,replace=FALSE,prob=NULL) Is there something that I am missing here ? Thanks ../Murli

I am running a recursive feature selection wrapper on svm for a large data set. The routine gets progressively slower. I am deleting the objects not required. Is there anything else you advise me look for? I tried running it from the command line but it does not print anything on the screen. I did not specify any output file and was expecting the screen to be the default. Can any one help me

Hi I am trying to fit an svm to predict speech recognition errors. I am using best.svm like this: svm.model = best.svm(data[1:3000,1:23],data[1:3000,24],tunecontrol = tune.control()) I got this: > print(svm.model) Call: best.svm(x = data[1:3000, 1:23], tunecontrol = tune.control(), data[1:3000, 24]) Parameters: SVM-Type: eps-regression SVM-Kernel: radial cost: 1

Is there an option to draw concentration ellipses in biplots ? It seems really nice to summarize large number of points of each group. Cheers../ Murli

Here it is again, hope this is more clear I am using the following data (only a small subset is given): Habitat Fungus.yield Birch 20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049

Which is the parameter that is used to decrease the size of ylabs plotted in biplot? I tried playing with cex and cex.lab I am not getting it right pc <- princomp(USArrests) biplot(pc, xlabs = rep("", nrow(USArrests)),ylabs=(colnames(USArrests))) Thanks../Murli [[alternative HTML version deleted]]

I used the multcomp package sometime back for doing multiple comparisons. I see that it has been updated and the methods like simint are no longer supported. When I run the program it prompts to me to use glht. How do I get the lower and upper conf int and the pValues using glht? Does anyone have an example? Thanks ../Murli [[alternative HTML version deleted]]

Can I insert an element in an array at a particular position without destroying the already existing element? X<-c(1,2,3,4,5) I want to insert an element between 1 and 2. Thanks ../Murli [[alternative HTML version deleted]]

Hi!! I am interesting in computing the radius of an arc that best approximates a curve. Is there an R function that I can use to draw an arc? Nothing useful came up when I searched help.search. Does anyone have any suggestion to do this? Thanks ../Murli

I am trying split a string and use one part of it to label graphs. I am using strsplit for that. While I am able to split it, how do I access the separated parts. > filName<-"chrI_2223" >part<- strsplit(filName,"\\_") > part [[1]] [1] "chrI" "2223" > part[1] [[1]] [1] "chrI" "2223" I looked up the help archive but did

Hi !! I am trying to analyze some of my data using linear discriminant analysis. I worked out the following example code in Venables and Ripley It does not seem to be happy with it. ============================ library(MASS) library(stats) data(iris3) ir<-rbind(iris3[,,1],iris3[,,2],iris3[,,3]) ir.species<-factor(c(rep("s",50),rep("c",50),rep("v",50)))

Can I run jobs in the background and the check the status of it from time to time in Windows version of R? Thanks ../Murli [[alternative HTML version deleted]]

I am interested in plotting histograms for the following data Isoform Tumor_65_198 Tumor_50_192 Tumor_80_167 Tumor_80_204 Tumor_95_197 Tumor_70_189 Tumor_90_202 Tumor_40_177 Tumor_60_21 Tumor_70_174 Tumor_70_147 Tumor_50_5 ABCC4-2007 1 1 1 6 1 9 10 1 2 0 10 1 ABCC4-2008 5 8 7 5 3 10 5 5 7 3 10 3 ABCC4-2009 0 0 0 0 0 0 0 0 0 0 0 0 ABCC4-2010