search for: lung

Dear R users, Please can you help me with a relatively straightforward problem that I am struggling with? I am simply trying to plot a baseline survivor and hazard function for a simple data set of lung cancer survival where `futime' is follow up time in months and status is 1=dead and 0=alive. Using the survival package: lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung, dist='weibull') plot (lung.wbs) Returns the error msg: Error in xy.coords(x, y, xlabel, ylabel,...

I?m trying to set up proportional hazard model that is stratified with respect to covariate 1 and has an interaction between covariate 1 and another variable, covariate 2. Both variables are categorical. In the following, I try to illustrate the two problems that I?ve encountered, using the lung dataset. The first problem is the warning: To me, it seems that there are too many dummies generated. The second problem is the error: -- View this message in context: http://r.789695.n4.nabble.com/Problems-with-coxph-and-survfit-in-a-stratified-model-with-interactions-tp4646095.html S...

Dear all - I have followed the thread the reply to which was lead by Thomas Lumley about using pweibull to generate fitted survival curves for survreg models. http://tolstoy.newcastle.edu.au/R/help/04/11/7766.html Using the lung data set, data(lung) lung.wbs <- survreg( Surv(time, status)~ 1, data=lung, dist='weibull') curve(pweibull(x, scale=exp(coef(lung.wbs)), shape=1/lung.wbs $scale,lower.tail=FALSE),from=0, to=max(lung$time)) lines(survfit(Surv(time,status)~1, data=lung), col="red") Assuming th...

...y of them together, i.e., the file data/cancer.rda contains 19 data sets, many of them small. The resulting file (using xz compression) is quite a bit smaller than the individual ones.? (I still get a warning note about size from R CMD check, but I'm no longer 2x the limit.) 2. Consider the lung data set.? All of these fail: ?? data(lung) ?? data("lung") ?? data(lung, package="survival") ?a. The lung.Rd file had \usage{data(lung)}; that error was not caught by R CMD check.? (Several other .Rd files as well.) ?b. In broader examples for teaching, I sometimes load...

...o set up proportional hazard model that is stratified with > respect to covariate 1 and has an interaction between covariate 1 and > another variable, covariate 2. Both variables are categorical. In the > following, I try to illustrate the two problems that I?ve encountered, using > the lung dataset. > > > > The first problem is the warning: > > > > To me, it seems that there are too many dummies generated. > > The second problem is the error: > Please try to fix this in the future (Nabble issue?) As to the problems: handling strata by covariate intera...

...2 ME:M14 -0.73942 -0.73904 Melanoma 40 LE:SR -0.93541 2.95346 Leukemia 25 CO:SW_620 -1.53265 -1.35446 Colon 63 RE:CAKI_1 -2.48443 0.43245 Renal 39 LE:RPMI_8226 -2.59561 -1.9448 Leukemia 26 LC:A549 -2.66221 0.71215 Lung 61 RE:A498 -2.89402 0.93287 Renal 9 BR:HS578T -2.94118 1.1217 Breast 34 LC:NCI_H522 -2.94381 0.3859 Lung 66 RE:TK_10 -2.95281 1.26245 Renal 52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian 57 OV:SK_OV_3 -3.04477 2.15405 O...

Hi, I'm sure this should be simple but I can't figure it out! I want to get the median survival calculated by the survfit function and use the value rather than just be able to print it. Something like this: library(survival) data(lung) lung.byPS = survfit(Surv (time, status) ~ ph.ecog, data=lung) # lung.byPS Call: survfit(formula = Surv(time, status) ~ ph.ecog, data = lung) 1 observation deleted due to missingness n events median 0.95LCL 0.95UCL ph.ecog=0 63 37 394 348 574 ph.ecog=1 113...

...t; i.e., the file data/cancer.rda contains 19 data sets, many of them small. The resulting > file (using xz compression) is quite a bit smaller than the individual ones.? (I still get > a warning note about size from R CMD check, but I'm no longer 2x the limit.) > > 2. Consider the lung data set.? All of these fail: > ?? data(lung) > ?? data("lung") > ?? data(lung, package="survival") > > ?a. The lung.Rd file had \usage{data(lung)}; that error was not caught by R CMD check. > (Several other .Rd files as well.) > > ?b. In broa...

...he gave. Following is not so much a question, but rather an answer from Morgan that might be useful to others. Here is the edited part of an email conversation with him: On Thursday, August 26, 2010 1:36 PM, Martin Morgan wrote: Fun! I think the problem is > x = new("censored", lung$time, event=lung$status) > x[1:5] [1] 306 455 1010 210 883 which splom does (subsetting) as part of it's parsing of the general case. So setMethod("[", "censored", function(x, i, j, ..., drop=TRUE) { initialize(x, x at .Data[i], event=x at event[i]) }...

...8.150 10.966 14 Colon 1 7.329 11.309 15 Colon 1 2.512 10.493 16 Colon 3 6.797 9.829 17 Colon 3 8.657 11.766 18 Leukemia 1 2.603 9.421 19 Leukemia 1 2.353 9.283 20 Leukemia 1 2.360 9.413 21 Leukemia 1 2.322 7.200 22 Leukemia 1 2.330 7.880 23 Lung 1 6.607 12.805 24 Lung 1 6.945 11.144 25 Lung 3 8.055 12.421 26 Lung 3 9.407 12.531 27 Lung 3 8.781 12.473 28 Lung 3 10.076 11.881 29 Lung 3 4.073 11.569 30 Melanoma 1 5.829 11.183 31 Melanoma 1 2.533 10.812 32 Melanoma 1 3.253 11.278 3...

...n calculations (which I do in loops), I only need a certain group of sub-lists/dataframes, which I want to specify with a name vector and paste together the object name and pass it on to a function. Here an (hopefully) instructive example #Data Example gnuff<-list() gnuff$IHD$LE<-66 gnuff$LUNG$LE <-55 #This is the list, where I collect data for different diseases at the second level of the list #Now I want to do calcualtions just for these two diseases and the sub-list "LE" within these diseases nam <- c("LUNG","IHD") for(i in 1:2) x[i] <- paste...

...stistics with S" and trying the corresponding examples both in the book and in ../lib/R/library/MASS/script, I'm now trying chapter 4 plotting bars with the following code on a linux box with R 1.8.1: ---------------------- library(MASS) library(lattice) options(echo=T, width=65, digits=5) lung.deaths <- aggregate(ts.union(mdeaths, fdeaths), 1) barplot(t(lung.deaths), names = dimnames(lung.deaths)[[1]], main = "UK deaths from lung disease") if(interactive()) legend(locator(1), c("Males", "Females"), fill = c(2, 3)) ----------------------- The...

I have a sample of lung capacities from a population measured against height. I need to know the 95% CI of the lung capacity of a person of average height. I have fitted a regression line. How do I get a minimum and maximum values of the 95% CI? My thinking was that this has something to do with covariance, but how?...

...oxph, which is why I went that route, but never noted the difference till now (preparing for my course in Nashville). Could someone shed light on the rationale for non-preservation? Terry T. Simple example > library(survival) > lfit <- lm(time ~ factor(ph.ecog) + ns(age, 3), data=lung) > ltemp <- model.frame(lfit, data=lung[1:2,]) > ltemp time factor(ph.ecog) ns(age, 3).1 ns(age, 3).2 ns(age, 3).3 1 306 1 -0.1428571 0.4285714 0.7142857 2 455 0 0.0000000 0.0000000 0.0000000 > lfit$model[1:2,] time factor(ph.ecog...

...he necessary changes to the smb.conf file but don't want to restart samba in the middle of the day since it is a high traffic server and don't want to break connections. Is there a way to just have samba load all these printers without restarting the service???? Thanks for help. Matt Lung

...w if that has something to do with it or not. I do have kernel oplocks turned on. Hopefully someone else having similar problems or had similar problems can lend a helping hand. This is really starting to get annoying since it is so random. Any advice would be appreciated. Thanks -- Matt Lung Midwest Tool & Die, Corp.

...fails miserably. I looked at some old posts but could not figure out the solution. Here's what I did where for one single patient, the answer is "NULL". Could anyone help me with the problem? R.app GUI 1.34 (5589 Leopard build 32-bit) > library(glmpath) *> dataall <- list(x=lung.data$x[1:130,], time=lung.data$time[1:130], status=lung.data$status[1:130])* * > fit.a <- coxpath(dataall) > testall <- list(x=lung.data$x[131:137,], time=lung.data$time[131:137], status=lung.data$status[131:137]) > testpred <- predict(fit.a, testall, s=0.99, type='coxph...

...fails miserably. I looked at some old posts but could not figure out the solution. Here's what I did where for one single patient, the answer is "NULL". Could anyone help me with the problem? R.app GUI 1.34 (5589 Leopard build 32-bit) > library(glmpath) *> dataall <- list(x=lung.data$x[1:130,], time=lung.data$time[1:130], status=lung.data$status[1:130])* * > fit.a <- coxpath(dataall) > testall <- list(x=lung.data$x[131:137,], time=lung.data$time[131:137], status=lung.data$status[131:137]) > testpred <- predict(fit.a, testall, s=0.99, type='coxph...

http://wiki.rubyonrails.com/rails/show/HomePage Now sure if anyone has noticed yet, but the above page has been hacked.

...I became aware of the coxpath() in R package glmpath does lasso on Cox model. I have tried the sample script on the help page of coxpath(), but I have difficult time understanding the output. Therefore, I would greatly appreciate if anyone can help me understand how to use the function. > data(lung.data) > attach(lung.data) > fit.a <- coxpath(lung.data) > print(fit.a) Call: coxpath(data = lung.data) Step 1 : karno Step 2 : celltype Step 5 : trt Step 6 : prior Step 7 : age Step 8 : diagtime > summary(fit.a) Call: coxpath(data = lung.data) Df Log.p.lik AIC...