search for: aalen

Hi, I am taking a survival class. Recently I need to do the Nelson-Aalen estimtor in R. I searched through the R help manual and internet, but could not find such a R function. I tried another way by calculating the Kaplan-Meier estimator and take -log(S). However, the function only provides the summary of KM estimator but no estimated values. Could you please help...

Dear R-helpers: I am trying to use aalen{timereg} to run a model and found that it generates the following message. the data set I used is > dim(indf) [1] 13743 10 #R code: fit_aalen <- aalen(Surv(durdxdeathp, die) ~ 1+factor(gender), indf) #start of error message below Non unique survival times: break ties ! Break ties yourself...

...<- 5 * runif(n) h <- 0.02 * exp(0.04 * (age-50) + 0.8 * (sex=='Female')) dt <- -log(runif(n))/h e <- ifelse(dt <= cens, 1, 0) dt <- pmin(dt, cens) Srv <- Surv(dt, e) f <- coxph(Srv ~ age + sex, x=TRUE, y=TRUE) system.time(ans <- survfit(f, type="aalen", se.fit=FALSE, newdata=f$x)) When I run the above code with sample sizes, n, taking on values of 500, 1000, 2000, and 4000, the time it takes for survfit to run are as follows: # n <- 500 > system.time(ans <- survfit(f, type="aalen", se.fit=FALSE, newdata=f$x)) user...

Hi, I am computing the Nelson-Aalen (NA) estimate of baseline cumulative hazard in two different ways using the "survival" package. I am expecting that they should be identical. However, they are not. Their difference is a monotonically increasing with time. This difference is probably not large to make any impact in the...

...windows when I need to do some statistical work. And here is my first question. I'm actually trying to model a survival curve using a cox model. But I need the baseline cumulative hazard. I've been looking around on the web and the archives, and I found that it as to do with the nelson-aalen estimation. But I must not understand all the doc very well, because I can't get the baseline hazard. Could you help me, please. Best regards. PS : I hope you'll forgive my poor english writing. -- Blaise TRAMIER aka Meles. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-...

Dear all, Currently, I am doing a research project about serum sodium levels and falling. I am doing my analysis in R. I am performing the multiple imputation right now. I want to perform a survival analysis later, but therefore I need to specify the Nelson-Aalen estimator. My dataset is called DF1, the event indicator is Falls and the time variable is Time. The code that I use is as follows: NAE <- nelsonaalen(data = DF1, statusvar = Falls, timevar = Time) However, I get this error: Error in Surv(time, status) : Time variable is not numeric If I do t...

...musmc.nl> wrote: > > Dear all, > > Currently, I am doing a research project about serum sodium levels and falling. I am doing my analysis in R. I am performing the multiple imputation right now. I want to perform a survival analysis later, but therefore I need to specify the Nelson-Aalen estimator. My dataset is called DF1, the event indicator is Falls and the time variable is Time. The code that I use is as follows: > > NAE <- nelsonaalen(data = DF1, statusvar = Falls, timevar = Time) > > However, I get this error: Error in Surv(time, status) : Time variable is no...

Dear useRs, I'm trying to estimate the proportion of individuals with a without a certain recurring ailment at several times points. The data are of the survival type, with "start"-"stop" dates and whether the individual had the ailment in that interval. Some cases are observed until database closure and some died or are lost to followup. The interest is not on death. I

...Pinfectionandbronchitis) ss<-survfit(fit) plot(ss,fun="cumhaz") My question is on whether the cumulative hazard given by the above command is actually a breslow estimator for baseline cumulative hazard ,i.e, estimator=sum( number of death/ (sum(risk score in risk set)) or a nelson-Aalen estimator. if the above command does not give me breslow estimator, please advise on how I can get it. Thanks for any help given. kind regards, sing yee [[alternative HTML version deleted]]

...nd dyn.load an .so file, which makes things a bit easier. > > Running with R -d "valgrind --tool=memcheck --leak-check=full" one of > my test files > crashes in simple R code a dozen lines after the likely culprit has been > called, i.e, the > survfit function for an Aalen-Johansen, containing a .Call to the new C > code. The > valgrind approach had already allowed me to find a few other (mostly dumb) > errors that led > to an out of bounds access, e.g., the wrong endpoint variable in a for( ) > loop. What > would others advise as a next step...

Hi everyone, I am using the package cmprsk in R to estimate the cumulative incidence function and its variance. In the manual it is mentioned that the variance is calculated based on Dr. Aalen's paper (1978, Nonparametric estimation of partial transition probabilities in multiple decrement models). I would appreciate if someone could provide me with a source where the variance is expressed in a more readable way, for example as a sum. I appreciate your help. Thank you. Melan...

Is there an implementation of the Cox-Snell residuals / Nelson-Aalen plot for goodness of fit? Or otherwise is there an appropriate Goodness of Fit diagnostic? Thanks Murray -- Murray Pung Statistician, Datapharm Australia Pty Ltd 0404 273 283 [[alternative HTML version deleted]]

...source all the .R files and dyn.load an .so file, which makes things a bit easier. ? Running with R -d "valgrind --tool=memcheck --leak-check=full" one of my test files crashes in simple R code a dozen lines after the? likely culprit has been called, i.e, the survfit function for an Aalen-Johansen, containing a .Call to the new C code.???? The valgrind approach had already allowed me to find a few other (mostly dumb) errors that led to an out of bounds access, e.g., the wrong endpoint variable in a for( ) loop.??? What would others advise as a next step? Here is the last part of...

I installed the RApril with all the warnings of a pre-beta version, but had it quickly produce some beautiful graphs etc. Then, since I'm interested in regression, I downloaded the S-plus package for Aalen's additive regression model, and I got a fixed version for Windows/R already by the next day, but when I tried library(addreg) I got the error below. Error in system(call, intern) : "system" is only available on Unix> Well, all beginning is difficult, but what now ? R really looks...

Dear all, I was wondering if anyone can help? I am an R user but recently I have resorted to SAS to calculate the probability of the event (and the associated confidence interval) for the Cox model with combinations of risk factors. For example, suppose I have a Cox model with two binary variables, one for gender and one for treatment, I wish to calculate the probability of survival for the

...09"), person("Atkinson", "Elizabeth", role="ctb"), person("Crowson", "Cynthia", role="ctb")) Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. License: LGPL (>=2) URL: https://github.com/therneau/survival [[alternative HTML version deleted]]

Hi, I am attempting to evaluate the prediction error of a coxph model that was built after feature selection with glmnet. In the preprocessing stage I used na.omit (dataset) to remove NAs. I reconstructed all my factor variables into binary variables with dummies (using model.matrix) I then used glmnet lasso to fit a cox model and select the best performing features. Then I fit a coxph model

Is it possible to calculate Kaplan-Meier for left-truncated, right-censored data using survival5? -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at

...-batch hangs Product: rsync Version: 3.0.9 Platform: x64 OS/Version: Linux Status: NEW Severity: normal Priority: P5 Component: core AssignedTo: wayned at samba.org ReportedBy: christian.heinlein at htw-aalen.de QAContact: rsync-qa at samba.org The following command hangs: mkdir 1 touch 1/a ln 1/a 1/b rsync -aH --only-write-batch=1-2 1/ 2 Adding --no-inc-recursive solves the problem. -- Configure bugmail: https://bugzilla.samba.org/userprefs.cgi?tab=email ------- You are receiving this mai...

Hello , I am hoping for some advice regarding obtaining the values for the hazard function in a cox regression that I have undertaken. I have a model in the following form, analysed with the package survival (v. 2.34-1) and a log-log plot obtained using Design (v. 2.1-2). For two variables, the lines in the survival curves crossed. The statistician I been obtaining advice from (who does not