similar to: Time-dependent coefficients in a Cox model with categorical variants

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

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,

Hello, I want to have the x-axis title of my plot in 2 lines, centered: experiment 1: log2(Ratio H/L) I know that in principle that works with '\n'. However, I am also using the 'substitute' command for my axis title. However, it does not make a new line. What I have so far: logbase <- 2 test <- "bait" cellline <- "cellline" plot(

Dear List, After including cluster() option the coxreg (from eha package) produces results slightly different than that of coxph (from survival) in the following time-dependent treatment effect calculation (example is used just to make the point). Will appreciate any explaination / comment. cheers, Ehsan ############################ require(survival) require(eha) data(heart) # create weights

Dear R Helpers, I have noticed that when I use lmer to analyse data, the summary function gives different values for the AIC, BIC and log-likelihood compared with the anova function. Here is a sample program #make some data set.seed(1); datx=data.frame(array(runif(720),c(240,3),dimnames=list(NULL,c('x1','x2','y' )))) id=rep(1:120,2); datx=cbind(id,datx) #give x1 a

Hi guys, we have a rebalance running on eight bricks since July and this is what the status looks like right now: ===Tue Oct 18 13:45:01 CST 2011 ==== rebalance step 1: layout fix in progress: fixed layout 223623 There are roughly 8T photos in the storage,so how long should this rebalance take? What does the number (in this case) 22362 represent? Our gluster infomation: Repository

Hello dear R help members. I am trying to understand the anova.rq, and I am finding something which I can not explain (is it a bug?!): The example is for when we have 3 nested models. I run the anova once on the two models, and again on the three models. I expect that the p.value for the comparison of model 1 and model 2 would remain the same, whether or not I add a third model to be compared

Dear R developers, I noticed a bug in the stats4 package, specifically in the confint method applied to ?mle? objects. In particular, when some ?fixed? parameters define the log likelihood, these parameters are stored within the mle object but they are not used by the ?confint" method, which retrieves their value from the global environment (whenever they still exist). Sample code: >

Hello, I would like to use the parfm package: https://cran.r-project.org/web/packages/parfm/parfm.pdfhttps://cran.r-project.org/web/packages/parfm/parfm.pdf in my work. This package fits parametric frailty models to survival data. To ensure I was using it properly, I started by running some small simulations to generate some survival data (without any random effects), and analyse the data using

Hi , I want to apply the following code fo my data with 400 predictors. I was wondering if there ia an alternative way instead of typing 400 predictors for the following code. I really appreciate your help. fit0<-lm(Y~1, data= mydata) fit.final<- lm(Y~X1+X2+X3+.....+X400, data=mydata) ??? step(fit0, scope=list(lower=fit0, upper=fit.final), data=mydata, direction="forward")

I'm trying to manually garbage data on bricks (when the volume is stopped) and then check whether healing is possible. For example: Start: # glusterd --debug Bricks (on EXT4 mounted with 'rw,realtime'): # mkdir /root/data0 # mkdir /root/data1 # mkdir /root/data2 Volume: # gluster volume create gv0 replica 3 [local-ip]:/root/data0 [local-ip]:/root/data1 [local-ip]:/root/data2

Hi, I have the following test case: define void @foo(<2 x float>* noalias nocapture %out, <2 x float>* noalias nocapture %data0) nounwind { entry: %val1 = load <2 x float>* %data0, align 8 store <2 x float> %val1, <2 x float>* %out, align 8 fence acq_rel %val2 = load <2 x float>* %data0, align 8 store <2 x float> %val2, <2 x float>*

windows xp R 2.8.1 I am trying to plot the -log(log(survival)) to visually test the proportional hazards assumption of a Cox regression. The plot, which should give two lines (one for each treatment) gives only one line and a warning message. I would appreciate help getting two lines, and an explanation of the warning message. My problem may the that I have very few events in one of my strata,

I'm running a samba pdc on my gentoo box in a mixed environment with a couple of Windows XP clients and only a few MacOSX clients. The users told me, the file locking across the platforms does not work properly sometimes. I tried to google my problem, but without luck. I switched all the flags related the lock mechanism of samba on and off, but the problem seems to be solved yet. The only

R 2.8.1 Windows XP I am trying to plot the results of a coxph using plot(survfit()). The plot should, I believe, show two lines one for survival in each of two treatment (Drug) groups, however my plot shows only one line. What am I doing wrong? My code is reproduced below, my figure is attached to this EMail message. John > #Create simple survival object >

Here is an example, modified from the help page to use test="Cp": -------------------------------------------------------------------------------- > fit0 <- lm(sr ~ 1, data = LifeCycleSavings) > fit1 <- update(fit0, . ~ . + pop15) > fit2 <- update(fit1, . ~ . + pop75) > anova(fit0, fit1, fit2, test="Cp") Error in `[.data.frame`(table, , "Resid.

Dear all, I have a couple of questions regarding the survival:::cch function. 1) I notice that Prentice and Self-Prentice functions are giving identical standard errors (not by chance but by programming design) while their estimates are different. My guess is they are both using the standard error form from Self and Prentice (1986). I see that standard errors for both methods are

On Wed, Jun 12, 2013 at 6:17 PM, Guo, Xiaoyi <Xiaoyi.Guo at amd.com> wrote: > Hi, > > I have the following test case: > > define void @foo(<2 x float>* noalias nocapture %out, <2 x float>* > noalias nocapture %data0) nounwind { > entry: > %val1 = load <2 x float>* %data0, align 8 > store <2 x float> %val1, <2 x float>* %out,

I am new to the R language. I am trying to plot multiple figures on one page through a loop, but the code just produce one graph on one page. Can someone show some light on what's wrong? Here is my code: library("quantreg") tcdata<-read.table("mydata.txt",header=TRUE) postscript("myfigure.ps") basins<-

Hello, All: ????? The default "simulate" method for lm and glm seems to ignore the sampling variance of the parameter estimates;? see the trivial lm and glm examples below.? Both these examples estimate a mean with formula = x~1.? In both cases, the variance of the estimated mean is 1. ??? ??????? * In the lm example with x0 = c(-1, 1), var(x0) = 2, and