similar to: question

Hello, I analyse some free-sorting data so I use hierarchical clustering. I want to compare my proximity matrix with the tree representation to evalute the fitting. (stress, cophenetic correlation (pearson's correlation)...) "The cophenetic similarity of two objects a and b is defined as the similarity level at wich objects a and b become members of the same cluster during the course of

I am trying to write a wrapper for the last example in help(cv.glm) that deals with leave-one-out-cross-validation (LOOCV) for a logistic model. This wrapper will be used as part of a bigger program. Here is my wrapper funtion : logistic.LOOCV.err <- function( formu=NULL, data=NULL ){ cost.fn <- function(cl, pred) mean( abs(cl-pred) > 0.5 ) glmfit <- glm(

In the package lasso2, there is a Prostate Data. To find coefficients in the prostate cancer example we could impose L1 constraint on the parameters. code is: data(Prostate) p.mean <- apply(Prostate, 5,mean) pros <- sweep(Prostate, 5, p.mean, "-") p.std <- apply(pros, 5, var) pros <- sweep(pros, 5, sqrt(p.std),"/") pros[, "lpsa"] <-

All, For my understanding, I wanted to see if I can get glmnet predictions using both the predict function and also by multiplying coefficients by the variable matrix. This is not worked out. Could anyone suggest where I am going wrong? I understand that I may not have the mean/intercept correct, but the scaling is also off, which suggests a bigger mistake. Thanks for your help. Juliet Hannah

Describe fails for me with a message similar to what was an issue in 2008 and got fixed according to posts. R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-pc-mingw32/i386 (32-bit) # output truncated > options(chmhelp = FALSE, help_type = "text") > .help.ESS <- help >

Hi Everyone, I have a question regarding the construction of 3D graphs in 'R', BUT these graphs also need to illustrate movement (with time) of the prostate gland (using radiological techniques). I am not sure how to do this in 'R' although I'm sure there is some way of doing it. Below, I have copied and pasted some of the data with which I'm working on. The data

Hi List, I have the following time series and i want to be able to plot it while having the x-axis running from 1998 to 2006 but in a bi-annual format So here is my example: x<-sample (10:100, 17) x<-ts(x, start=c(1998,1), frequency=2) plot(x) When I plot the ts it goes from 1998 to 2006 by 2years, when in fact i want it to go from 1998 to 2006 with the following form:1998 may, 1998

In an .Rd example for a package, I want to use data from another package, but avoid loading the entire package and avoid errors/warnings if that other package is not available. If I don't care about loading the other package, I can just do: if (require("ElemStatLearn", quietly=TRUE)) { data(prostate) # rest of example } I'd rather just be able to do something like:

Dear Asterisk Community, Does your company provide inbound 800# origination? If so, please read this message and e-mail us a quote for monthly co-lo hosting of our asterisk server and per-minute inbound 800# origination. The Prostate Cancer Research and Education Foundation (PC-REF) is a non-profit organization dedicated to helping prostate cancer sufferers and their loved ones. We have

Hi, First, when I try the example Prostate with bound 0.44 (as in the manual), I got a different result: > l1c.P <- l1ce(lpsa ~ ., Prostate, bound=0.44) > l1c.P .... Coefficients: (Intercept) lcavol lweight age lbph svi 1.0435803 0.4740831 0.1953156 0.0000000 0.0000000 0.3758199 lcp gleason pgg45 0.0000000 0.0000000

Hi, I need to build ROC curve in R, can you please provide data steps / code or guide me through it. Thanks and Regards Rithesh M Mohan [[alternative HTML version deleted]]

Brokers Move On ERMX! EntreMetrix Inc. (ERMX) $0.18 Heavy trading today as ERMX announced its launch of digital support tools for its portfolio companies. Brokers are getting ahead of this steady climb as they grab up large blocks of shares for there clients. Look at the numbers and get on ERMX Friday morning! KNEEguru: Are there any contraindications for the procedure? if the laws of physics

Brokers Move On ERMX! EntreMetrix Inc. (ERMX) $0.18 Heavy trading today as ERMX announced its launch of digital support tools for its portfolio companies. Brokers are getting ahead of this steady climb as they grab up large blocks of shares for there clients. Look at the numbers and get on ERMX Friday morning! KNEEguru: Are there any contraindications for the procedure? if the laws of physics

Dear all, I did post this more or less identical mail in a follow up to another question I posted, but under another heading. I try again, but now under the correct header. upon running this code (from the Hmisc library-latex function) I believe the call to summary.formula is allright and produces wonderful tables, but the latex command results in a correct formatted table but where all the

I have the following files list: > list.files() [1] "Prostate-Cancer_cvs_Dir" [2] "Prostate_Cancer-miRNAs&Genes.Pathway.xml" [3] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir" [4] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir.zip" [5] "Prostate-miRNAs.OrganTargets.txt"

Full_Name: Kem Phillips Version: 2.7.1 (2008-06-23) OS: Windows Xp professional Submission from: (NULL) (98.221.200.108) The Hmisc function describe fails, giving the error message: Error in formatDateTime(dd, atx, !timeUsed) : could not find function "format.dates" Loading the chron package, where function dates apparently resides, does not fix the problem. Note

Hi everybody, this is a real dummy thing. I sorted a matrix based on a given column, and what I get is right, until it comes to columns of negative and positive values; than, "order" orders everything from max to min in the negative values, and then AGAIN from max to min in the positive values!!! Why isn't everything order from max to min, and that's it? Thank you!!! Attached

Dear All, I'm reading Frank Harrell's wonderful Regression Modeling Strategies book and ran into a problem following the example in Chapter 8. I'm working on platform: Ubuntu 8.04 (i486-pc-linux-gnu) R version: 2.7.2 (2008-08-25) and my command sequence was: library(chron) library(Hmisc) load("prostate.sav") describe(prostate) The last command returned the error

Hi, everyone: I ask for help about translating a stata program into R. The program perform cross validation as it stated. #1. Randomly divide the data set into 10 sets of equal size, ensuring equal numbers of events in each set #2. Fit the model leaving out the 1st set #3. Apply the fitted model in (2) to the 1st set to obtain the predicted probability of a prostate cancer diagnosis. #4. Repeat

Hi, I am interested in using the cast function in R to perform some aggregation. I did once manage to get it working, but have now forgotten how I did this. So here is my dilemma. I have several thousands of probes (about 180,000) corresponding to each gene; what I'd like to do is obtain is a frequency count of the various occurrences of each probes for each gene. The data would look