similar to: confidence interval and cross validation

Dear all, can anybody help me with the program below? The function predict.lda seems to be defined but cannot be used by errortest. The R version is 1.7.1 Thanks in advance, Stefan ---------------- library("MASS"); library("ipred"); data(iris3); tr <- sample(1:50, 25); train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3]); test <- rbind(iris3[-tr,,1],

Hi Cristian, I don't know about a R routine for exact CIs, but I found a function called "ageadjust" using a gamma distribution approximation some time ago -take a look at http://medepi.org/epitools/rfunctions/index.html. That Webpage seems a bit outdated now, but the calculations given in the ageadjust functions should still work, I think. Maybe this helps; regards Heinrich.

Hello, struggling with the very basic needs... :( any help appreciated. #using the package doBY #who drinks how much beer per day and therefor cannot calculate rowise maxvals evaluation=data.frame(date=c(1,2,3,4,5,6,7,8,9), name=c("Michael","Steve","Bob", "Michael","Steve","Bob","Michael","Steve","Bob"),

Dear all, I need to read an ASCII file with diffent length lines. This is what is contained in the file gene.txt: 1st line ID description snp_id genotype 2nd line 10003 Low rs152240 3rd line 10003 Moderate rs189011 TC 4th line 10004 Conservative rs152240 GC 5th line 10004 Bad rs154354 6th line 10013 Bad rs152240 7th line 10019 Conservative rs152240 AC etc... This is what I would like to obtain

Dear All, Is it possible to get confidence intervals for Harrell's concordance index or, equivalently, Somer's D using the rms package or in some other way ? I have survival data it would be the c-index in the Cox model setting Many thanks Dr Bernard North Statistical Consultant Statistical Advisory Service Advice and Courses on Research Design and Methodology Imperial College South

Dear all, I have a surprising problem with the representation of frequencies in a histogram. Consider, for example, the R code: b<-rnorm(2000,3.5,0.3) hist(b,freq=F) When I plotted the histogram, I expected that values in the y-axis (the probability) varied between 0 and 1. Instead, they varied within the range 0-1.3. Have you got any suggestion for obtaining a correct graph with

Hi! How can I fill with colors a portion of a graph (e.g.: I want fill in red the area within two confidence intervals)? Thank you very much Cristian ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Cristian Pattaro ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Unit of Epidemiology & Medical Statistics University of Verona Tel +39 045 8027668 fax +39 045 505357 cristian at biometria.univr.it

Dear all, I'm using the package "Genetics", and I'm interested in the computation of D' statistics for Linkage Disequilibrium, for which the LD() command has been realised. Unfortunately I don't find any reference on "how" the D' is computed by the LD() function. In the package documentation it is generally referred as "MLE" estimation, but

Dear all, is there a automatic method to obtain Odds Ratio estimates and their confidence intervals from a GLM Logistic model? Thanks Cristian ============================================= Cristian Pattaro ============================================= Unit of Epidemiology & Medical Statistics Department of Medicines and Public Health University of Verona cristian@biometria.univr.it

Last week Giovanni Parrinello posted a message asking why various packages were loaded when he loaded an .Rdata file. Brian Ripley replied saying he thought it was because the saved workspace contained a reference to the namespace of ipred. (Correspondence copied below). This begs the question: how did the reference to the namespace of ipred come to be in the .Rdata file? Brian did say it is

Last week Giovanni Parrinello posted a message asking why various packages were loaded when he loaded an .Rdata file. Brian Ripley replied saying he thought it was because the saved workspace contained a reference to the namespace of ipred. (Correspondence copied below). This begs the question: how did the reference to the namespace of ipred come to be in the .Rdata file? Brian did say it is

Dear List, I have a question regarding "ipred" package. Under 10-fold cv, for different knn ( = 1,3,...25), I am getting same misclassification errors: ############################################# library(ipred) data(iris) cv.k = 10 ## 10-fold cross-validation bwpredict.knn <- function(object, newdata) predict.ipredknn(object, newdata, type="class") for (i in

Apologies - I was not trying to correct you Brian, but to explore how the situation could arise. I'm sure you had a good idea why the namespace (or a reference to it) had been saved, but this was not clear to me and I thought, possibly not to others either. Thanks for putting me right over parent environments vs. enclosures - again I was not trying to correct you with the point I made there,

-- GOOD NEWS! -- As ground transportation and the costs associated therewith are something of an issue. So, in the spirit of making AstriCon available I've contacted the hotel and arranged/discovered some low cost options: -- MARTA -- MARTA, the Atlanta mass-transit system (i.e. train) can get you there. Take MARTA from the airport north to the Brookhaven station. The hotel shuttle will

Hello everyone. This is a question regarding generation of the concordance index (c index) in R using the function rcorr.cens. In particular about interpretation of its direction and form of the 'predictor'. One of the arguments is a "numeric predictor variable" ( presumably this is just a *single* predictor variable). Say this variable takes numeric values.... Am I

Dear All, I am new to R and am trying to learn how to create functions using R. Below is code which calculates Lin's Concordance Coefficient. After I calculate the coefficient I want to create a scatter plot which annotates the coefficient along with preceding text onto the plot. The below code doesn't seem to work. If I use only the object 'lincc' on the text command it works

Hi! After installing R 2.0.0, I have problem with the "help.search" as below: > help.search("table") Error in help.search("table") : could not find package 'file23525' > help.search("mean") Error in help.search("mean") : could not find package 'file23525' I have had the same problem with other request... What is

Hi, I'm trying to calculate 95% confidence interval of C statistic of logistic regression model using rcorr.cens in rms package. I wrote a brief function for this purpose as the followings; CstatisticCI <- function(x) # x is object of rcorr.cens. { se <- x["S.D."]/sqrt(x["n"]) Low95 <- x["C Index"] - 1.96*se Upper95 <- x["C

Dear R users, I have been using the rpart procedure to predict the occurrence of depression in a large data file. Since the prevalence is very low (5%), I have been using classification trees with a loss matrix that penalized false negatives more than false positives. I have become interesested in bagging these (successful!) classification trees, and have been using the ipred package for

Carlos, mi intencion es entender el codigo: https://github.com/woobe/blenditbayes/blob/master/2013-06-street-level-crime/analysis.R Para luego hacer mi trabajo, algo similar a esto, pero adaptado a mi región. Si te fijas en las lineas 141-161, esta esto: ## Convert the base map into a ggplot object ## All added Cartesian coordinates to enable more geom options later on map.ggmap <-