similar to: question about svm(e1071)

Hello, I want to perform an lme on a database with this structure: ID Sequence Temperature Tumour Error 1 5 0 1 8.721872e-08 1 5 0 2 8.695348e-08 1 5 0 3 2.019604e-13 1 5 37 1

Hi friends, I need suggestions/directions on how to producing a waterfall plot for present extend of change in tumour size for a set of respondents in a study.  Example of use of waterfall plot is in the following slides presented at ASCO 2007 by Axel Grothey. Link is

Dear all, I have a couple of questions regarding the survival:::cch function. 1) I notice that Prentice and Self-Prentice functions are giving identical standard errors (not by chance but by programming design) while their estimates are different. My guess is they are both using the standard error form from Self and Prentice (1986). I see that standard errors for both methods are

Dear All. I have the following table that I want to analyze using multinom function freq segments sample 4271 Seg1 tumour 4311 Seg2 tumour 3515 Seg1 normal 3561 Seg2 normal I want to compare model with both factors to the one where only sample is present. model1=multinom(freq~segments+sample,data=table) model2=multinom(freq~ sample,data=table)

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Hola. Como te dijo Carlos, el problema está en los nombres de las columnas y en los nombres de las filas. Cuando hice la importación (con dd<-read.csv('mortality.csv'), tuve problemas con las filas de nombre: - Malignant tumour of the larynx trachea bronchus and lungs - Malignant tumour of the lip pharynx and mouth - Other endocrinological metabolic and nutritional conditions

Hello, I have the next function call: lme(fixed=Error ~ Temperature * Tumour ,random = ~1|ID, data=error_DB) which returns an lme object. I am interested on carrying out some kind of lsmeans on the data returned, but I cannot find any function to do this in R. I'have seen the effect() function, but it does not work with lme objects. Any idea? Best, Dani -- Daniel Valverde Saub? Grup

Hi, The following code, from Angelo Canty article on line "Resampling Methods in R: the boot Package, 2002", works fine for Angelo Canty using R 2.6.0 on Windows XP. It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after installing the S-PLUS bootstrap library, with slight differences in my outputs. > library(boot) > library(survival) >

Hello all, I posted a question to this list last week and received no response. I am unsure if this means no-one knows the answer or if I posed the question badly. I'm going to assume I posed the question badly and try again. I am new to R so it is quite likely it's a very naive question, however if there is something blindingly obvious that I am missing or if there is another resource I

I have what I *think* should be a simple problem in R, and hope someone might be able to help me. I'm working with cancer survival data, and would like to calculate adjusted survival figures based on the age of the patient and the tumour classification. A friendly statistician told me I should use Cox proportional hazards to do this, and I've made some progress with using the

Hi, I am currently using the aCGH package in R version 2.1.0 Windows with some supporting packages (eg. cluster) built under R 2.1.1.Using aCGH package, I am able to identify regions of genomic aberrations in my cell lines using the HMM model. However, when I tried to use aCGH for my paraffin embeded tumour sample, I got the following warning. Warning: MAD could not ben computed for one of

Dear all, I got a code for e1071 package in R for SVM regression. I have used *m$coefs* for extracting the coefficients but I am getting only 72 . How can I extract coefficients of the predictors set? Does it mean that I will get only 72 as *Number of Support Vectors: 72. * ** Thanks in advance Code: -------------- library(e1071) > # create data > x <- seq(0.1, 5,

Dear R users, I'm running a SVR in package e1071 but I did not able to calculate the parameters w and b of the regression. I don't know how to do that and if it is possible to do it with this package. Someone have some idea. Any help would be much appreciated. Marlene [[alternative HTML version deleted]]

Greetings everyone, I have the following problem (illustrating R-code at bottom of mail): Given a training sample with binary outcomes (-1/+1), I train a linear Support Vector Machine to separate them. Afterwards, I compute the weight vector w in the usual way, and obtain the fitted values as w'x + b > 0 ==> yfitted = 1, otherwise -1. However, upon verifying with the

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Hi all, I'm new to R and I'm struggling to decipher an error message. Briefly, I am trying to use the pvclust package to do hierarchical clustering of some CGH data. The data is from the Progenetix CGH database. It is arranged as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change,

How can I define environments within a function so that they are visible to calls to a sub-function? I have defined an objective function, ProfileErr = function(params,...) which I would like to optimize using standard routines (optim, nlminb,....) but which contains auxiliary variables which need to be updated along with params. No optimization routine in R that I have found has facilities

Hi, The following code, from Angelo Canty article on line "Resampling Methods in R: the boot Package, 2002", works fine for Angelo Canty using R 2.6.0 on Windows XP. It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after installing the S-PLUS bootstrap library, with slight differences in my outputs. > library(boot) > library(survival) >

Hi all I want to assign a constant to a different column for each row eg: m[1,2] <- 0; m[2,3] <- 0; m[3,1] <- 0; m[4,2] <- 0; m[5,1] <- 0; ... etc... i've tried apply/tapply with no luck and also the following coefs <- rtt.abs[,5:8]; coefs.i <- coefs[] == 1; coefs[coefs.i] <- 0; wich results in "matrix subscripts not allowed in replacement"

Hi, The following code, from Angelo Canty article on line "Resampling Methods in R: the boot Package, 2002", works fine for Angelo Canty using R 2.6.0 on Windows XP. It also works for me using R 1.2.1 and S-PLUS 2000 on Windows XP after installing the S-PLUS bootstrap library, with slight differences in my outputs. > library(boot) > library(survival)