search for: cox

...1)/50)*(i-1)} lambda1=rep(lambda, each=2) dummy=rep(c(exp(beta),1),51) elf=lambda1*dummy r=70 #the number of bootstrap replicates #mymodels=function(dataset.number){ #seed=2006*dataset.number time=rexp(102, rate=elf) data=cbind(pat,trt,status,site,time) data1=data.frame(data) #### Cox proportional hazard model stratified on site model1.cox=coxph(Surv(time,status) ~ trt + strata(site), data=data1, iter.max=500) model1.surv=survfit(model1.cox) #### Cox proportional hazard model with dummy covariates for site model2.cox=coxph(Surv(time,status) ~ trt + factor(site), data...

Dear R-people: I tried to create a shared library in Windows XP. However I got error messages which attached below: C:\lasso>Rcmd SHLIB all.f cox.f gcc all.o libR makeMakedeps all.dll -o all gcc.exe: libR: No such file or directory gcc.exe: makeMakedeps: No such file or directory make: *** [all] Error 1 I have created shard libraries successfully before. Also for the same fortran files: all.f cox.f, I can create the object all.so succe...

...hat I *know* works - simply cut and paste into R on either Windows and Linux and it works perfectly, no errors or warnings, nothing, nyet. However, when I run "R CMD check" on the library, I get an error. I am running R CMD check on linux, and the offending piece of code appears to be: cox[cox$group %in% onc,] "cox" is a data frame, one of the columns of which is group, which contains numbers. "onc" is a vector of numbers. The output on Linux from R CMD check is this: > # lots of code > # lots of code >cox[cox$group + + + # the rest of my code Error:...

Dear All: I have a question on using coxph for multiple genes: I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data. However, I don't know how to work with the result for each gene: survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. 3.cox[,'...

Dear experts, I tried to learn about Box-Cox-transformation but found the following thing: When I had to add a constant to make all values of the original variable positive, I found that the lambda estimates (box.cox.powers-function) differed dramatically depending on the specific constant chosen. In addition, the correlation between the t...

This works ok: > cox = coxph(surv ~ bucket*(today + accor + both) + activity, data = data) > fit = survfit(cox, newdata=data[1:100,]) but using strata leads to problems: > cox.s = coxph(surv ~ bucket*(today + accor + both) + strata(activity), > data = data) > fit.s = survfit(cox.s, newdata=data[1:100,])...

Dear all R users, I am building a Cox PH model on a small dataset. I am wondering how to measure the predictive power of my cox model? Normally the ROC curve or Gini value are used in logistic regression model. Is there any similar measurement suitable for Cox model? Also if I use C-index statistic to measure the predictive power, is...

The following works, you need to include x=TRUE in the call to coxph. Passing the time and status variables as additional arguments is a matter of personal preference. f.coxph.zph<-function(x, timeVar, statusVar) { cox.fit <- coxph(Surv(timeVar, statusVar) ~ x, na.action = na.exclude, method = "breslow", x=TRUE) fit.zph<-cox.zph(cox.fit) fit...

Hi: Recently, I want to perform a transformation on my data to make it more normal, meanwhile the order statistics is unchanged. So I decided to use a box-cox transformation. below is the qq-plot of the original data http://n4.nabble.com/file/n1011015/start%2Bvalue%2Bproblem%2B02.jpeg Note that the min of my data is -1099, so I add a fix value 1200 to the original sample. I choose the "box.cox.powers" function in package 'car'. Here i...

Hi, It seems there is a problem regarding ControlMaster and scp'ing a file depending on the current working directory: $ cd ~/Personnel $ scp -o ControlMaster=yes cox.jpg host.local: muxserver_listen bind(): No such file or directory lost connection $ scp -o ControlMaster=no cox.jpg host.local: cox.jpg 100% 222KB 222.1KB/s 00:00 $ cd $ scp -o ControlMaster=yes Personnel/cox.jpg host.local: cox.jpg...

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...

Good morning, Sorry to trouble the list. I have a problem I hope to seek your advice on. Essentially, I am trying to 'validate' a multivariate Cox proportional hazards model built in a training set, by testing it on an external test set. I have performed a survfit using the Cox model to predict survival for the test set, and obtained individual predictions for survival time, with standard error for each test sample. Each of these cases has an...

...vnc=1 vncunused=1 --- sudo xm create build/jim.cfg Using config file "./build/jim.cfg". Error: Device 51728 (tap) could not be connected. /home/fred/local/jim/build/foo_swap.img does not exist. The symlink is local which points to /var/local local -> /var/local/ Regards, -- Bobby Cox _______________________________________________ Xen-users mailing list Xen-users@lists.xensource.com http://lists.xensource.com/xen-users

Hello, I'm an MD working in an eye clinic. I'm learning by myself to use R for use in my research works and for implementation in a software project. There are some authors who recomends the use of Cox regression as a substitute for Logistic regression (<a href="http://www.biomedcentral.com/1471-2288/3/21.pdf"> Barros AJD, Hirakata VN. BMCMedical Research Methodology, 2003; 3:21 </a>. The use of Cox regression permit the estimation of the prevalence rates rather than Odds ra...

This is a question about the use of the Cox proportional hazards model to analyze event histories. I am looking at the responses of sympathetic nervous system activity to a stimulus. The activity I observe is a burst that can only occur once per heart beat cycle (e.g., a binary count). Typically bursts occur in 60-80% of the heart cycles...

Hi, When I run the following Cox proportional hazards model on the Mayo clinic's PBC data set (given in the "survival" package), the regression coefficients do not agree with the results presented in Table 4.6.3 (p. 195) of Fleming & Harrington's book. library(survival) data(pbc) ans.cox <- coxph(Sur...

Hi, I wrote a function that worked well in R, but not in S-Plus, can anyone suggest a solution? > f.coxph.zph<-function(x) { cox.fit <- coxph(Surv(time.cox, status.cox) ~ x, na.action = na.exclude, method = "breslow") fit.zph<-cox.zph(cox.fit,transform='log') fit.zph$table[,3] } yyy is my data frame that contains survial time, censor status and predictor variables. &gt...

Hello I am using box.cox() and I get this error message: Warning message: 'box.cox' is deprecated. Use 'bcPower' instead. See help("Deprecated") and help("car-deprecated"). I went to help but I did not understand the explanation, I am still wondering what is really happening. Thanks...

Dear Rlist, Using an example in box.cox.powers() help, I have the following warning message. example: library(car) >attach(Prestige) > box.cox.powers(income) Box-Cox Transformation to Normality Est.Power Std.Err. Wald(Power=0) Wald(Power=1) 0.1793 0.1108 1.6179 -7.4062 L.R. test, power = 0: 2.7103 df = 1...

I have been working on fitting Cox model for prediction by using rms package. I want to measure model's calibartion and discrimination. Discrimination was measured by using validate() in rms, Dxy can be transferred to Harrell's c index. But in this way, I cannot get 95%CI of c index. How can I do this in R? And by the way, w...