search for: pbc

...albumin" argument (I only chose albumin because it had no missing values, not because of any real relevance). Below are my code with the resulting error messages. Thanks in advance! > pfit <- coxph(Surv(time,status>0) ~ trt + log(bili) + log(protime) + age + + + platelet, data=pbc + ) > > pfit Call: coxph(formula = Surv(time, status > 0) ~ trt + log(bili) + log(protime) + age + +platelet, data = pbc) coef exp(coef) se(coef) z p trt -0.000624 0.999 0.17304 -0.00360 1.0000 log(bili) 0.985497 2.679 0.08949...

...quot; codes in it. (Note, Tom Fleming originally got the data from me, so I'm fairly confident in calling my Mayo version the authoritative one). I'll make sure this gets fixed. You can grab a correct data set from our department web page. Code is below. Terry Therneau pbcurl <- "http://mayoresearch.mayo.edu/mayo/research/biostat/upload/therneau_upload/pbc.d at" pbc <- read.table(pbcurl, header=F, col.names=c('id', 'time', 'status', 'trt', 'age', 'sex',...

thunderbird just crashed, and I've never seen this before. Any idea what happened? this was in the dovecot log: 2010-12-02 13:06:40 imap-login: Info: Maximum number of connections from user+IP exceeded (mail_max_userip_connections): user=<pbc>, method=PLAIN, rip=127.0.0.1, lip=127.0.0.1, secured 2010-12-02 13:06:40 imap-login: Info: Maximum number of connections from user+IP exceeded (mail_max_userip_connections): user=<pbc>, method=PLAIN, rip=127.0.0.1, lip=127.0.0.1, secured 2010-12-02 13:06:40 imap-login: Info: Maximum numbe...

Dear R-users: I can not reproduce figure 4 of *Statistical Tables and Plots using S and LATEX* by Prof. Frank Harrell with the following code: rm(list=ls()) library(Hmisc) getHdata(pbc) attach(pbc) age.groups <- cut2(age, c(45,60)) g <- function(y) apply(y, 2, quantile, c(.25,.5,.75)) y <- with(pbc, cbind(Chol=chol,Bili=bili)) # You can give new column names that are not legal S names # by enclosing them in quotes, e.g. 'Chol (mg/dl)'=chol vars <- with(pbc, c(...

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(Surv(time, status) ~ log(bili) + log(alb) + age + log(proti...

Hi there, Can anyone please help me because I am going to get crazy with the pbc data set. I just want to apply simple cox regression in the data set. I am a beginner in R but I don't think I am doing anything wrong. I have the book of Fleming and Harrington 1990. I perform cox regression by typing: out<- coxph(Surv(times/365,status)~log(bili)+log(proth)+edema+log(alb...

...(The documentation talks about "Tukey pairwise-comparisons"). Is it possible to carry out a "pairwise" logrank test? Am I totally misguided? Thank you very much for help. ################################### R code ################################################# > data(pbc) > pbc$stage <- factor(pbc$stage) > (fit <- coxph(Surv(time,status==2)~stage,data=pbc)) Call: coxph(formula = Surv(time, status == 2) ~ stage, data = pbc) coef exp(coef) se(coef) z p stage2 1.10 3.01 0.737 1.50 0.13000 stage3 1.53 4.63 0.722 2.12 0.0340...

...( I have no trouble writing my own simple latex code and converting it to pdf using pdftex in miktex). Thanks, Mike Babyak Department of Psychiatry and Behavioral Science Duke University Medical Center ************************** Here's the code: library(Hmisc) library(survival) getHdata(pbc) pbc<-upData(pbc, moveUnits=TRUE, labels=c(stage='Histologic Stage\nLudwig Criteria')) kmsurv <- function(S, times) { f <- survfit.km(factor(rep(1,nrow(S))), S) tt <- c(0, f$time) ss <- c(1, f$surv) # add first point to survival curve approx(tt, ss, xout=times, method='c...

Hello, I'm attempting to use the ratetable argument to survexp in the survival package. I use the example from the ?survexp help page below, and then slightly modify it to produce an error. library(survival) data(pbc) #fit a model without any factors pfit1 <- coxph(Surv(time, status > 0) ~ trt + log(bili) + log(protime) + age + platelet, data=pbc) #this works as expected survexp(~ trt, ratetable = pfit1, data = pbc) #now I fit a similar model, simply adding the 'sex' term #note sex...

Hello, I wonder when I do coxph in R: coxph( Surv(start, stop, event) ~ x, data=test) If x is a categorical varible (1,2,3,4,5), should I creat four dummy varibles for it? if yes, how can I get the overall p value on x other than for each dummy variable? Thanks Lisa Wang Princess Margaret Hospital Phone 416 946 4501

I would like to determine the probability of an event at a specific timepoint given the linear predictor of a given Cox model. For instance, assume that I fit the following model: data(pbc) fit <- coxph(Surv(time, status)~ age, data=pbc) To extract the value of the linear predictor for each patient in the dataset: prd <- predict(fit, newdata=pbc, type="lp") However, what I am really interested in is the predicted probability from the Cox model that an ind...

...ative risk (or log r.r.) versus the predictors). When there is only 1 predictor in the model, termplot returns a "?". In this case, I have not been able to figure out how to create the desired plot. Otherwise,termplot is easy to use. Example: library(survival) library(splines) data(pbc) fit1<-coxph(Surv(time,status)~ns(bili,4)+ns(age,4), data=pbc) fit2<-coxph(Surv(time,status)~ns(bili,4), data=pbc) par(mfrow=c(2,2)) termplot(fit1) # returns two plots (one for bili and one for age) termplot(fit2) # returns a "?" prompt Does anyone have any suggestions for obtain...

...ve superimposed upon an overall survival curve, but I will illustrate my problem using the example given in the help for lines.survfit. I would like to have tick marks for censored data points on both curves, so I would like to do something like: > fit <- survfit(Surv(time, status) ~ sex, pbc,subset=1:312) > plot(fit[2], mark.time=TRUE, xscale=365.24, + xlab='Years', ylab='Survival') > lines(fit[1], lwd=2, xscale=365.24, mark.time=TRUE) but when I do this, no tick marks appear on the second curve. Can anyone see what I am doing wrong here? Rachel [[alternative...

Dear Prof Harrell and everyone, My PC: Window XP service pack 3 and service pack 2 R version 2.8.1 and 2.9 alpha For the last 3 days, after updating R, my two computers have been facing problems when running existing and runable R commands that involves with Design package I attempt to use 'survest', but I failed all the times with R (both 2.8.1 and 2.9 alpha) being shut down

...analyses) oldClass(object) <- c("mira", "coxph") return(object) } ------------ The problem that I encounter occurs when I try to use the "pool" function to pool the fitted models into one general model. Here is some code that reproduces the error using the pbc dataset. ------------ d <- pbc[,c('time','status','age','sex','hepmeg','platelet', 'trt', 'trig')] d[d==-9] <- NA d[,c(4,5,7)] <- lapply(d[,c(4,5,7)], FUN=as.factor) str(d) imp <- mice(d, m=10, maxit=10, diagnostics=T,...

...-helpers: I am using R 2.5 on Windows XP, packages all up to date. I have run into an issue with the MIcombine function of the mitools package that I hoped some of you might be able to help with. I will work through a reproducible example to demonstrate the issue. First, make a dataset from the pbc dataset in the survival package --------------- # Make a dataset library(survival) d <- pbc[,c('time','status','age','sex','hepmeg','platelet', 'trt', 'trig')] d[d==-9] <- NA d[,c(4,5,7)] <- lapply(d[,c(4,5,7)], FUN=as.fac...

Hello, I am trying to find an R function to compute 'direct adjusted survival' with standard errors. A SAS-macro to do this is presented in Zhang X, Loberiza FR, Klein JP, Zhang MJ. A SAS macro for estimation of direct adjusted survival curves based on a stratified Cox regression model. Comput Methods Programs Biomed 2007;88:95-101. It appears that this method is not implemented in R.

...oup[id<50] <- 1 group[id>=50 & id<100] <- 2 group[id>=100 & id<150] <- 3 group[id>=150 & id<200] <- 4 group[id>=200 & id<250] <- 5 group[id>=250 & id<300] <- 6 group[id>=300] <- 7 I estimate the following model, using the Pbc data (with time-varying covariates) from Therneau and Grambsch's book: fitf <- coxph(Surv(start,stop,event==2) ~ age + log(bili) + log(protime) + log(albumin) + edema + frailty(group), na.action=na.exclude, data=Pbcseq) Then I obtain: &g...

Hi, I'm reading van Belle et al "Biostatistics" and trying to run a cox test using a dataset from: http://faculty.washington.edu/~heagerty/Books/Biostatistics/chapter16.html (Primary Biliary Cirrhosis data link at top of the page), I'm using the following code: --------------- start of code library(survival) liver <-

# Dear list, # I am an R-beginner and # spent the last days looking for a method to insert tables produced # with R into a word document. I thought about SPPS: copy a table from # an SPO-file and paste it into a word document # (if needed do some formatting with that table). # Annother idea was, to produce a TEX-file, # insert it and make it a word-table. # I found the following libraries, which