similar to: tune.svm

I run the following code, all other is ok, but plot(m.svm,p5.new,As~Cur) is not ok Anyone know why? install.packages("e1071") library(e1071) library(MASS) p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv") p5.new<-subset(p5,select=-Ms) p5.new$Y<-factor(p5.new$Y) levels(p5.new$Y) <- list(Out=c(1), In=c(0)) attach(p5.new)

Dear list I've a generic question about how to tune an SVM I'm trying to classify with caret package some population data from a case-control study . In each column of my matrix there are the SNP genotypes , in each row there are the individuals. I correctly splitted my total dataset in training(132 individuals) and test (50 individuals) (respecting the total observed genotypic

Hi all, I'm having this error, since I'm working with a data matrix I don't understand what's happening; I've tried several ways to solve this, even working with sparse matrix, but nothing seems to solve it, I've also tried svm (with a simple matrix 3*3 and still got the same error. > dados<-read.table("b.txt",sep="",nrows=30000) >

I run the following code, all other is ok, but plot(m.svm,p5.new,As~Cur) is not ok Anyone know why? install.packages("e1071") library(e1071) library(MASS) p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv") p5.new<-subset(p5,select=-Ms) p5.new$Y<-factor(p5.new$Y) levels(p5.new$Y) <- list(Out=c(1), In=c(0)) attach(p5.new)

I am trying to fit a logistic regression model for this data set. Firstly, I want to plot P(Y=1) vs As and P(Y=1) vs Aa. Does any body know how to do these in R. Thanks, Aimin > p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv") > str(p5) 'data.frame': 1030 obs. of 6 variables: $ P : Factor w/ 5 levels "821p","8ABP",..: 1

I have a dataset like this: p aa index x y z sdx sdy sdz delta as ms cur sc 1 821p MET 1 -5.09688 32.8830 -5.857620 1.478200 1.73998 0.825778 13.7883 126.91 92.37 -0.1320180 111.0990 2 821p THR 2 -4.07357 28.6881 -4.838430 0.597674 1.37860 1.165780 13.7207 64.09 50.72 -0.0977129 98.5319 3 821p GLU 3 -5.86733 30.4759

I have a data set with about 30,000 training cases and 103 variable. I've trained an SVM (using the e1071 package) for a binary classifier {0,1}. The accuracy isn't great. I used a grid search over the C and G parameters with an RBF kernel to find the best settings. I remember that for least squares, R has a nice stepwise function that will try combining subsets of variables to find

Dear all, I am exploring the possibilities for automated classification of my data. I have successfully used KNN, but was thinking about looking at SVM (which I did nto use before). I have a pairwise distance matrix of training observations which are classified in set classes, and a distance matrix of new observations to the training ones. Is it possible to use distance matrices for SVM, and

Hello, I use nnet to do prediction for a continuous variable. after that, I calculate correlation coefficient between predicted value and real observation. I run my code(see following) several time, but I get different correlation coefficient each time. Anyone know why? In addition, How to calculate prediction accuracy for prediction of continuous variable? Aimin thanks, > m.nn.omega

I have a data(ABC) like this: x y A 3 4 A 1 3 B 2 6 B 4 8 C 5 4 C 6 7 I want to split this data into A: x y A 3 4 A 1 3 B B 2 6 B 4 8 C C 5 4 C 6 7 anyone knows how to do that? thanks, Aimin Yan

I have a set data={A,B,C,D,E,F,G} I want to choose 2 letter from 8 letters, i.e. generate the combination set for choose 2 letters from 8 letters. I want to get the liking: combination set={AB,AC,AD,....} Does anyone konw how to do in R. thanks, Aimin

I have a question in R. In directory H:/Delta_angle I have 19 files like this: ALA.delta ASN.delta ASP.delta CYS.delta GLN.delta GLU.delta HIS.delta ILE.delta LEU.delta LYS.delta MET.delta PHE.delta PRO.delta SER.delta THR.delta TRP.delta TYR.delta VAL.delta I want to read these files to 19 data sets in R. All these data sets have "P","AA",index","delta"

I try Sweave and get Sweave-test-1.tex but hot to run LaTeX on 'Sweave-test-1.tex'? I am using WinEdt. thanks, Aimin > Sweave(testfile) Writing to file Sweave-test-1.tex Processing code chunks ... 1 : print term verbatim 2 : term hide 3 : echo print term verbatim 4 : term verbatim 5 : echo term verbatim 6 : echo term verbatim eps pdf 7 : echo term verbatim eps pdf

I have a data set like this I want to assign "outward" to Y if sc <90 and assign "inward" to Y if sc>=90. then cbind(p1982,Y) to get like these p aa as ms cur sc Y 1 154l_aa ARG 152.04 108.83 -0.1020140 92.10410 inward 2 154l_aa THR 15.86 28.32 0.2563560 103.67100 inward 3 154l_aa ASP 65.13 59.16 0.0312137 7.27311 outward 4 154l_aa CYS 57.20 49.85

Dear R list, I have a question in R, it could be very simple, but I don't know how to do it? for example: I assign 6 to x in beginning of of my R script code > x<-6 ...... After many line code, I forget using x variable before, I use x again, and do assignment like this > x<-45 > x [1] 45 then value 6 of previous x is replaced by 45. I am wondering if there are some way R

How to add mean,sd, number of observation in each panel for lattice histogram? Aimin

Does anyone know how to solve this question about R.matlab? I am in windowsXP, my matlab is matlab 7.0.0 19920(R14) thanks, Aimin > matlab <- Matlab(host="localhost", port=9998) > if (!open(matlab)) throw("Matlab server is not running: waited 30 seconds.") Error in list("throw("Matlab server is not running: waited 30 seconds.")" =

I try to type this in my R-winEdt. but I got these. Do you know? Aimin > install.packages('http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip') Warning in download.packages(pkgs, destdir = tmpd, available = available, : no package 'http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip' at the

I draw dotplot using the following code: sd.dotplot<-dotplot(data.47.nmr$om_sd ~ as.factor(data.47.nmr$position) |as.factor(data.47.nmr$pr), data = data.47.nmr,layout=c(1,1), xlab="Position", xlim=range(data.47.nmr$position),ylab="Sd", main="Changes of omega angle in different positions", scales = list(x = list(rot = 45))) However I get same xlim for each

if I want to put fig1plot to the left, figYPplot to the right figYAaplot on the bottom. How to modify the following cod to do these? \begin{figure}[H] \centering \begin{minipage}[t]{0.5\textwidth} \centering <<label=fig1plot,fig=TRUE,echo=FALSE>>= <<fig1plot>> @ %\caption{Caption 1} \end{minipage} \begin{minipage}[t]{0.5\textwidth} \centering