similar to: numerics from a factor

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,]) Error in model.frame.default(data = data[1:100, ], formula = ~bucket + :

On the local machine the command R11 CMD Rd2pdf survfit.Rd works fine. R12 CMD Rd2pdf survfit.Rd fails with the message below. Converting Rd files to LaTeX ... survfit.Rd Creating pdf output from LaTeX ... Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, : Running 'texi2dvi' on 'Rd2.tex' failed. Messages: sh: texi2dvi: command not

First a statistical issue: The survfit routine will produce predicted survival curves for any requested combination of the covariates in the original model. This is not the same thing as an "adjusted" survival curve. Confusion on this is prevalent, however. True adjustment requires a population average over the confounding factors and is closely related to the standardized

Dear all, I am confused with the output of survfit.coxph. Someone said that the survival given by summary(survfit.coxph) is the baseline survival S_0, but some said that is the survival S=S_0^exp{beta*x}. Which one is correct? By the way, if I use "newdata=" in the survfit, does that mean the survival is estimated by the value of covariates in the new data frame? Thank you very much!

I have a model with quant vars only and the error message does not make sense: (mod1 <- coxph(Surv(time=strt,time2=stp,event=(resp==1))~ +incpost+I(amt/1e5)+rate+strata(termfac), subset=dt<"2010-08-30", data=inc,method="efron")) Call: coxph(formula = Surv(time = strt, time2 = stp, event = (resp == 1)) ~ +incpost + I(amt/1e+05) + rate + strata(termfac),

I cloned therneau/survival and the installation failed since there is no definition for exported function survfit(). A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no survfit.R. Georgi Boshnakov ---------------------------------------------------------------------- Message: 1 Date: Thu, 05 Sep 2019 12:53:11 -0500 From: "Therneau, Terry M.,

While implementing R's new 'altrep' functionality in the TERR engine, I discovered a bug in R's 'deferred_string' altrep object: it is not using the correct value of the 'OutDec' option when it expands a deferred_string. See the following example: R 3.5.1: (same results in R 3.6.0 devel engine built 10/5) > options(scipen=0, OutDec=".") >

i want to make survival plots for a coxph object using survfit function. mod.phm is an object of coxph class which calculated results using columns X and Y from the DataFrame. Both X and Y are categorical. I want survival plots which shows a single line for each of the categories of X i.e. '4' and 'C'. I am getting the following error: > attach(DataFrame) >

Is the phrase "index <- match(x, sort(unique(x)))" reliable, in the sense that it will never return NA? Context: Calculation of survival curves involves the concept of unique death times. I've had reported cases in the past where survfit failed, and it was due to the fact that two "differ by machine precision" values would sometimes match and sometimes not,

In the next version of the survival package I intend to make a non-upwardly compatable change to the survfit object.? With over 600 dependent packages this is not something to take lightly, and I am currently undecided about the best way to go about it.? I'm looking for advice. The change: 20+ years ago I had decided not to include the initial x=0,y=1 data point in the survfit object

Dear everyone, My question involves the use of the survival object. We can have Surv(time,time2,event, type=, origin = 0) (1) As detailed on p.65 of: http://cran.r-project.org/web/packages/survival/survival.pdf My data (used in my study) is 'right censored' i.e. my variable corresponding to 'event' indicates whether a person is alive (0) or dead (1) at date last seen

Hi Dear R-users I have a database with 18000 observations and 20 variables. I am running cox regression on five variables and trying to use survfit to plot the survival based on a specific variable without success. Lets say I have the following coxph: >library(survival) >fit <- coxph(Surv(futime, fustat) ~ age + rx, data = ovarian) >fit what I am trying to do is plot a survival

The combination of survfit, coxph, and factors is getting confused. It is not smart enough to match a new data frame that contains a numeric for sitenew to a fit that contained that variable as a factor. (Perhaps it should be smart enough to at least die gracefully -- but it's not). The simple solution is to not use factors. site1 <- 1*(coxsnps$sitenew==1) site2 <-

> Further I appreciate your new function survmean(). At the moment it > seems to be intended as internal, and not documented in the help. The computations done by print.survfit are now a part of the results returned by summary.survfit. See 'table' in the output list of ?summary.survfit. Both call an internal survmean() function to ensure that any future updates stay in

> On Jun 1, 2019, at 12:59 PM, Peter Langfelder <peter.langfelder at gmail.com> wrote: > > On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R-devel > <r-devel at r-project.org> wrote: >> >> In the next version of the survival package I intend to make a non-upwardly compatable >> change to the survfit object. With over 600 dependent packages

Dear useRs, What is the syntax to obtain survival curves for single strata on many subjects? I have a model based on Surv(time,response) object, so there is a single row per subject and no start,stop and no switching of strata. The newdata has many subjects and each subject has a strata and the survival based on the subject risk and the subject strata is needed. If I do newpred <-

> Dear All, > > I have built a survival cox-model, which includes a covariate * time interaction. (non-proportionality detected) > I am now wondering how could I most easily get survival predictions from my model. > > My model was specified: > coxph(formula = Surv(event_time_mod, event_indicator_mod) ~ Sex + > ageC + HHcat_alt + Main_Branch + Acute_seizure +

I am confused when trying the function survfit. my question is: what does the survival curve given by plot.survfit mean? is it the survival curve with different covariates at different points? or just the baseline survival curve? for example, I run the following code and get the survival curve #### library(survival) fit<-coxph(Surv(futime,fustat)~resid.ds+rx+ecog.ps,data=ovarian)

Dear All, Maybe it is a silly question. But I wasn't able to find it from manual or R site search. I was wondering what is the corresponding time axis for survival function outputs in "survfit". I think it is "survfit(.......)$time", but not 100% sure. If it is, is it possible we could make survival function outputs on the pre-specified time grid with fixed increment and

A bug in the survival routines was reported to me today. The root cause is a difference between table, unique, and sort. > temp <- rep(c(1, sqrt(2)^2, 2), 1:3) > unique(temp) [1] 1 2 2 > table(temp) temp 1 2 1 5 I'm using 2.10 on Linux, the user reported from 2.9 on Windows. 1. Minor issue: I think the root rounding occurs in factor. I didn't see any discussion of