similar to: Cox model with time-dependent coefficients

Dear All, I got a warning message "X matrix deemed to be singular" in Cox model with a time dependent coefficient. In my analysis, the variable "SEX" is a categorical variable which violate the PH assumption in Cox. I first used the survSplit() function to break the data set into different time intervals, and then fit the model. The procedures can be described as follows:

Dear R users, I am doing Cox regression using coxph(Survival) or cph(Design). I have time varying effects (diagnosed with schoenfeld residuals Chi2 test and graph) so I first want to split time into 2 separate intervals : t<6months and t>=6months, to estimate one hazard ratio (hr) for each interval. I am analysing Overall survival according to 3 prognostic factors (age,deep,ldh).

Dear All, I would like to use R function 'selectFGR' of fine gray model in competing risks model. I used the 'Melanoma' data in 'riskRegression' package. Some of the variables are factor. I get solution for full model but not in variable selection model. Any advice how to use factor variable in 'selectFGR' function. The following R code is produced below

To Danardonos concern of splitting time for records with delayed entry: This can fairly easily be accomodated, by simply splitting time in small intervals of time since entry into the study, and then compute the value of the other timescales for each of these e.g.: current.age <- time.from.entry + age.at.entry but the cut on the other timescales will not be exactly where you may want them

Dear all, I would like to obtain the Brier score prediction error at different times t for an extended Cox model. Previously I have used the 'pec' function (pec{pec}) to obtain prediction error curves for standard Cox PH models but now I have data in the counting process format (I have a covariate with a time-varying effect) and it seems that the pec function does not support the counting

Dear Raja, A Fine and Gray model can be fitted using the standard coxph function with weights that correct for right censoring and left truncation. Hence I guess any function that allows to perform stepwise regression with coxph should work. See e.g. my article in Biometrics https://doi.org/10.1111/j.1541-0420.2010.01420.x, or the vignette "Multi-state models and competing risks" in the

Dear All, since years I am struggling with Surv objects in data.frames. The following seems to have to do with it. See below the modified example from the help page of survSplit. The original works, as expected. If, however, a Surv object is added to the data.frame, each record gets doubled. Is there some solution other than avoiding Surv objects in data.frames? Thanks, Heinz

Dear Geskus, I want to develop a prediction model. I followed your paper and analysed thro' weighted coxph approach. I can develop nomogram based on the final model also. But I do not know how to do internal validation of the model and subsequently obtain calibration plot. Is it possible to use Wolbers et al Epid 2009 approach 9 (R code for internal validation and calibration) . It is

I am trying to find methods for testing and visualizing calibration to Cox models with time-depended coefficients. I have read this nice article <http://journals.sagepub.com/doi/10.1177/0962280213497434>. In this paper, we can fit three models: fit0 <- coxph(Surv(futime, status) ~ x1 + x2 + x3, data = data0) p <- log(predict(fit0, newdata = data1, type = "expected")) lp

Hi All, I am in the annoying position of having to present some data to someone who seems to be somewhat less than numerate. I need to label the y-axes of a multhist with the y-axis labeled not as counts but as percentage of a population. Plotting the standard histogram is in a way fine, all I need is to: -- have a left-handside y-axis labels for pop 1 and a right-handside y-axis labels for pop2

Hi, I am new to time-dependent Cox model to estimate time dependent hazard ratios. Let me use aml dataset from survival package: > aml3<-survSplit(aml2,cut=c(5,10,20),end="time",start="start", event="status",episode="i") If I want to esimate hazard ratio for each of the time intervals 0-5, 5-10, 10-20 and >=20, would the following calculate

Hi- I would like to assign distance classes (lags) to the moran''s I test in R. I don¹t have equally spaced points since I was mapping shrubs across a landscape (vs. an experiment or survey in a grid). I somehow need to select points based on the distances in the distance matrix (i.e., I need to select all pairs of points that occur 0-25 m from each other, 25-50 m, etc...). Does

UNCLASSIFIED//// I am seeing the following errors occasionally when doing an rsync between servers (Solaris 9) at the local and remote site. Has anyone seen these errors before or know what they are? rsync error: error in rsync protocol data stream (code 12) at io.c(1122) [sender=2.6.9] rsync error: protocol incompatibility (code 2) at io.c(954) [sender=2.6.9] rsync error: protocol

Suppose I have a dataset contain three variants, looks like > head(dta) Sex tumorsize Histology time status 0 1.5 2 12.1000 0 1 1.8 1 38.4000 0 ..................... Sex: 1 for male; 0 for female., two levels Histology: 1 for SqCC; 2 for High risk AC; 3 for low risk AC,

Dear R-users, I use the survsplit function in the survival package to change my data into counting-process format and the transformed format is as follow: (a) start stop event DP age .... 0 5 0 1 20 5 10 0 1 20 10 25 1 1 20 looking at the above three entries that belong to the same person, if an event happen at

I'm trying to convert a dataset from the time-independent analysis form > head(addicts) id clinic status survtime prison meth clinic01 1 1 1 1 428 0 50 1 2 2 1 1 275 1 55 1 3 3 1 1 262 0 55 1 into the "counting data format" necessary to perform extended Cox regression. I got

First, as others have said please obey the mailing list rules and turn of First, as others have said please obey the mailing list rules and turn off html, not everyone uses an html email client. Here is your code, formatted and with line numbers added. I also fixed one error: "y" should be "status". 1. fit0 <- coxph(Surv(futime, status) ~ x1 + x2 + x3, data = data0) 2. p

> Well that didn't work....I now get this error > > > Jan 12 16:56:21 NOTICE[4989]: app_dial.c:746 dial_exec: Unable to > create > channel of type 'SIP' > == Everyone is busy/congested at this time > -- Executing VoiceMail("IAX2/iaxfwd@65.39.205.121:4569/5", "b") in > new > stackJan 12 16:56:21 WARNING[4989]:

I am a test engineer, testing SSH server implementation of SSH into one of our switches. How can I automate the login and logout of an SSH client from the command line? I have in a script file the following, but I get prompted for the password. How can I automate the password and the exit. ssh2 -l $1 $2 (ssh2 -l <username> <host ip>) Theresa C. Karpowicz Software

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