similar to: Calculating Cumulative Incidence Function

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: Fair, male,

Dear R users, I d like to assess the effect of "treatment" covariate on a disease relapse risk with the package cmprsk. However, the effect of this covariate on survival is time-dependent (assessed with cox.zph): no significant effect during the first year of follow-up, then after 1 year a favorable effect is observed on survival (step function might be the correct way to say that ?).

I posted several months about the problem with adding tick marks to curves using lines.survfit. This occurs when lines.survfit is used to add a curve to survival curves plotted with plot.survfit. The help for this function implies that mark.time=TRUE thus: plot(pfsfit,conf.int=FALSE,xscale=365.25,yscale=100,xlab="Years",ylab="% surviving",lty=2,mark=3)

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

I am sorry to trouble the list with this, but I'm hoping that someone will be able to help me track down this reference. I am looking for a good reference on repeated measures, and many of the relevant functions in R refer in their "help" to: Hand, D. J. and Taylor, C. C. (1987) _Multivariate Analysis of Variance and Repeated Measures._ Chapman and Hall. This sounds

I have a longitudinal competing risk data of the form: ID COMPL SEX HEREDITY 1 0 1 2 1 0 1 2 1 3 1 2 2 0 0 1 2 1 0 1 2 2 0 1 2 2 0 1 3 0 0 1 3 0 0 1 3 0 0 1 3 0 0 1 3 2 0 1 4 0 1 2 4 0 1

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

Hello R-community, It's been a week now that I am struggling with the implementation of a cox model in R. I have 80 cancer patients, so 80 time measurements and 80 relapse or no measurements (respective to censor, 1 if relapsed over the examined period, 0 if not). My microarray data contain around 18000 genes. So I have the expressions of 18000 genes in each of the 80 tumors (matrix

Hello again, I m trying to use timereg package as you suggested (R2.7.1 on XP Pro). here is my script based on the example from timereg for a fine & gray model in which relt = time to event, rels = status 0/1/2 2=competing, 1=event of interest, 0=censored random = covariate I want to test library(timereg) rel<-read.csv("relapse2.csv", header = TRUE, sep = ",",

Dear list, I am not familiar with survival analysis and I would need your help to understand a result I have obtained. I have used the following command line to look at number of events and probability of survival at the first 5 years: > su = summary(survfit(Surv(a[, Date], a[, Event]) ~ strata(a[,Prediction]), data = a), times=c(0,1,2,3,4,5)) I have studied two kind of events (disease-free

Hi Bert, I am sorry to bother you on weekend. I am still struggling on defining a correct function. I first defined the function RFS (see below), then run it by provide the two argument. m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 ) I do not get error message, but no figure displays on screen. I do not know what is going on. Can you help me a little more on this issue? Thank you,

FAQ 7.22 You must print a ggplot object, for example with print(m52.2cluster) For the FAQ, run the line system.file("../../doc/FAQ") in R on your computer. Open up the resulting filepath in your favorite editor and scroll down to 7.22 On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <ycding at coh.org> wrote: > Hi Bert, > > I am sorry to bother you on weekend. >

Dear list, I am trying to build a cox model and then perform ROC analysis in order to retrieve some genes that are correlated with breast cancer. When I calculate the hazard score taking into account different numbers of genes and their coefficients ( I am trying to find the pest predictor number of genes), I retrieve from around 1 values (for few genes included ) to size of e+80 values (for many

Hi Richard, Thank you so much!! I understand the problem now, I assign a name to the "ggsurvplot" object and then add print(fig) at bottom of function definition, now figure gets printed on screen. Ding # function to generate RFS curves RFS <- function( inputfile, N ) { cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters, data =

Dear R users: Analysis of the impact of a time-dependent covariate (GVHD or use of steroid after bone marrow transplantation) on two competing endpoints (invasive fungal infection and death) is frequently encountered in the setting of BMT data. Coxph package can be used as the following: for the analysis of GVHD: > gvhd -> coxph(Surv(start,stop,status = =1) ~ GVHD, data=bmt.data)

Dear R users: Analysis of the impact of a time-dependent covariate (GVHD or use of steroid after bone marrow transplantation) on two competing endpoints (invasive fungal infection and death) is frequently encountered in the setting of BMT data. Coxph package can be used as the following: for the analysis of GVHD: > gvhd -> coxph(Surv(start,stop,status = =1) ~ GVHD, data=bmt.data)

That is certainly OK, but you can also just use print(ggsurvplot(...)) as your final statement. out <- RFS( ...) would then return the ggsurvplot object *and* graph it. Any good R tutorial or a web search will provide more details on function returns, which you might find useful. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and

Thank you, your suggestion is simpler and logically better. I had impression that the last object in a function gets returned, so I did not add the print function at the bottom line of the function definition. Returning an object and graph the object are different process, I am a beginner for writing R function and need to find a good guide source about writing R functions. If you know a good

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:   Fair, male,

On Thu, 29 Jan 2009 20:55:19 +0100 r-help-request at r-project.org wrote: > Welcome to the R-help at r-project.org mailing list! > > To post to this list, send your email to: > > r-help at r-project.org > > General information about the mailing list is at: > > https://stat.ethz.ch/mailman/listinfo/r-help > > If you ever want to unsubscribe or change your