search for: cuminc

Hello everyone, (This is my second question posted today on the R list). I am carrying out a competing risks analysis using the cuminc function...this takes the form: cuminc(ftime,fstatus,group) In my study, fstatus has 3 different causes of failure (1,2,3) there are also censored cases (0). "group" has two levels (0 and 1). I therefore have 6 different cumulative incidence curves: cause 1, group=0; cause 1 group=1...

Dear R-help list members, I am trying to create my own axes when plotting a cumulative incidence curve using the plot.cuminc function in the CMPRSK library. The default x-axis places tick marks and labels at 0, 20, 40, 60, and 80 (my data has an upper limit of 96), whereas I want them at my own specified locations. Here is my example code: library(cmprsk) attach(MYDATA) MYCUMINC <- cuminc(ftime=TIME,fstatus=STA...

Dear friends: I'm interested to make a stacked plot of cumulative incidence. that's, the cuminc model is fitted [fit=cuminc(time, relapse)] and cumulative incidence is in place. I'd like to stack the cuminc plots (relapse of luekemia and death free from leukemia, for example) , then the constituent ratio of leukemia relapse and treatment related mortality is very clear. Can you give me s...

Hi, I am trying to figure out how to put tick marks for censored observations using plot.cuminc for my competing risk analysis (survfit does this automatically). I've searched online for resources but found nothing. Does anybody know how to do this? Thank you in advance for your input. KC [[alternative HTML version deleted]]

Hi, To use cuminc() from cmprsk package, if a subject has 2 events (both the event of interest and the event of competing risk), should I create 2 observations for this subject in the dataset, one for each event with different fstatus (1 and 2), or just 1 observation with whatever event that happened first? My a...

Hello everyone,   I am a very new user of R and I have a query about the cuminc function in the package cmprsk. In particular I would like to verify that I am interpreting the output correctly when we have a stratification variable.   Hypothetical example:   group : fair hair, dark hair fstatus: 1=Relapse, 2=TRM, 0=censored strata: sex (M or F)   Our data would be split into:...

Dear R-community, I would like to plot the numbers at risk for the different causes of failure at specific timepoints below a cumulative incidence function plot (plot.cuminc-function, cmprsk-package). For a Kaplan-Meier plot I know this is possible with the n.risk-argument in the survplot-function (rms-package), but to my knowledge no such readily-available functions are available for competing risks approaches. I am not very experienced with programming, so any advice...

Hi All, I'm trying to figure out the cumulative incidence curve in R in some limited time. I found in package "cmprsk", the command "plot.cuminc" can get this curve. But I noticed that there is no mark for the censored time there, comparing with the KM curve by "plot.survfit". Here are my codes (attached is the data): ---------------- dat<-read.table("F://wendy/BMT data analysis/final data.txt",header=TRUE,s...

Dear Prof Gray and everyone, As our package developers discussed about incompatibility between Design and survival packages, I faced another problem with cmprsk- a survival dependent packacge. The problem is exactly similar to what happened to the Design package that when I just started running cuminc function, R was suddenly closed. These incidents suggest that maybe many other survival dependent packages being involved the problem Could you please consider the matter My R version: 2.8.1 Window XP Service pack 3 Regards Nguyen D Nguyen Garvan Institute, Australia [[alternative HTML version...

Dear R-users Has anybody implemented a function/package that will compute an individual's risk of an event in the presence of competing risks, adjusted for the individual's covariates? The only thing that seems to come close is the cuminc function from cmprsk package, but I would like to adjust for more than one covariate (it allows you to stratify by a single grouping vector). Any help/tips will be extremely appreciated. Eleni Rapsomaniki Research Associate Cambridge [[alternative HTML version deleted]]

Hello everyone, This is just a quick double check. It concerns the 'scatterplot function' in R. I have 6 curves and I wish to represent each of them by a different kind of line (their colour must be black). The curves are derived from the cuminc function...the coordinates of which are in 'xx'. Upon reading the documentation in R, it looks like I can use the 'on/off' command for lty and I can merely run: plot(xx,color="black",lty=c("11","13","1343","73","2262",&qu...

...require(Epi) data(lungDK) fit <- glm(D/Y ~ as.factor(A5)+as.factor(A5):P5-1, data=lungDK, subset=(P5>=1970), weight=Y, family=poisson("identity")) # (Hakulinen and Dyba) ## calculate some summary statistics (e.g. cumulative incidence to 85 years) require(plyr) cuminc <- function(object,year=P5,newdata=NULL) ddply(newdata,deparse(substitute(year)),function(data) sum(5*predict(object,newdata=data)))[,-1,drop=TRUE] ## Now: get summary statistics and SEs using the delta method predictnl(fit,cuminc,newdata=subset(lungDK,A5<85 & P5>=1970)) My...

Hi, I am wondering if anyone can explain to me if cumulative incidence (CI) is just "1 minus kaplan-Meier survival"? Under what circumstance, you should use cumulative incidence vs KM survival? If the relationship is just CI = 1-survival, then what difference it makes to use one vs. the other? And in R how I can draw a cumulative incidence plot. I know I can make a Kaplan-Meier

...er and more classical approach would be to implement the Kalbfleisch & Prentice method (1980, p 169), where one fits cause specific cox models for the event of interest and each type of competing risk, and then calculates incidence based on the overall survival. I believe that this is what the cuminc function in the aforementioned package does, but it does not allow to adjust for a vector of covariates. My question is, is there an R package that implements the Kalbfleisch & Prentice method for competing risks with covariates? for example, if k1 is the cause of interest among k compe...

...tc[i]>=1) stype[i] <- 3 if(data$all.otc[i]>=1) stype[i] <- 4 if(data$all.o[i]>=1) stype[i] <- 4 } return(stype) } fita <- survdiff(Surv(rem.Remtime,rem.Rcens)~stypea(nmarma)+strata(nmrpa),data=nmarma) fita lrpvalue=1-pchisq(fita$chisq,3) xx <- cuminc(nmarma$rem.Remtime/365,nmarma$rem.Rcens,stypea(nmarma),strata=nmrpa) plot(xx,curvlab=c("Simple/Complex","SC+2gentc or 2gentc","TC or My/Ab or My/Ab+gentc","Other"),lty=1,color=c(2:5),xlab="Time from randomisation (years)",ylab="Probability of 1...

Hello everyone, I am a very new user of R and I have a query about the cuminc function in the package cmprsk. In particular I would like to verify that I am interpreting the output correctly when we have a stratification variable. Hypothetical example: group : fair hair, dark hair fstatus: 1=Relapse, 2=TRM, 0=censored strata: sex (M or F) Our data would be split into:...

Dear everyone, My question involves the use of the survival object. We can have Surv(time,time2,event, type=, origin = 0) (1) As detailed on p.65 of: http://cran.r-project.org/web/packages/survival/survival.pdf My data (used in my study) is 'right censored' i.e. my variable corresponding to 'event' indicates whether a person is alive (0) or dead (1) at date last seen

Dear R-help, I'm very sorry to ask 2 questions in a week. I am using the package 'crr' and it does exactly what I need it to when I use the dataset a. However, when I use dataset b I get the following error message: Error in drop(.Call("La_dgesv", a, as.matrix(b), tol, PACKAGE = "base")) : system is computationally singular: reciprocal condition number =

Hi All, I am running a scatter plot and trying to add a best fit line. I use an abline function, but get no line drawn over the points. I also get no error. I arm using V 2.10.0 on Windows 7. Here is my code, including the SAS transport file import: require (foreign) require (chron) require (Hmisc) require (lattice) clin <- sasxport.get("y:\\temp\\subset.xpt") attach(clin)

...charset=us-ascii > As our package developers discussed about incompatibility between Design and survival packages,  I faced another problem with cmprsk- a survival dependent packacge. > The problem is exactly similar to what happened to the Design package that when I just started running cuminc function, R was suddenly closed. > These incidents suggest that maybe many other survival dependent packages being involved the problem   I don't see how this is related to survival.  I just checked the source code to the cmprsk function, and it has no dependencies on my library.  As I wou...