search for: survexp

...urvdiff. Executing it, gives the error "Error in floor(temp) : Non-numeric argument to mathematical function" best regards, Heinz library(survival) ## Example from help page of survdiff ## Expected survival for heart transplant patients based on ## US mortality tables expect <- survexp(futime ~ ratetable(age=(accept.dt - birth.dt), sex=1,year=accept.dt,race="white"), jasa, cohort=FALSE, ratetable=survexp.usr) Error in floor(temp) : Non-numeric argument to mathematical function sessionInfo('survival') R versi...

...0.020590 1.021 0.00805 2.55666 0.0110 platelet -0.001699 0.998 0.00085 -2.00130 0.0450 Likelihood ratio test=164 on 5 df, p=0 n= 308, number of events= 143 (110 observations deleted due to missingness) > > plot(survfit(Surv(time, status>0) ~ trt, data=pbc)) > lines(survexp( ~ trt, ratetable=pfit, data=pbc), col='purple') > > pfit.wtd <- coxph(Surv(time,status>0) ~ trt + log(bili) + log(protime) + age + + + platelet, weights=albumin, data=pbc + ) > > pfit.wtd Call: coxph(formula = Surv(time, status > 0) ~ trt + log(bili) + log(pro...

The survexp function can fail when called from another function. The "why" of this has me baffled, however. Here is a simple test case, using a very stripped down version of survexp: survexp.test <- function(formula, data, weights, subset, na.action, rmap, times, cohort=TRUE,...

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, da...

Dear All, when I try to reproduce an example of survexp, taken from the help page of survdiff, I receive the error message "Error in floor(temp) : Non-numeric argument to mathematical function" . It seems to come from match.ratetable. I think, it has to do with character variables in a ratetable. I would be interested to know, if it works fo...

Hello, and thank you in advance. I would like to capture the expected survival from a coxph model for subjects in an observational study with recurrent events, but the survexp statement is failing due to memory. I am using R version 2.13.1 (2011-07-08) on Windows XP. My objective is to plot the fitted survival with the Kaplan-Meier plot. Below is the code with output and [unfortunately] errors. Is there something wrong in my use of cluster in generating the proportion...

...ay. Let me start with two important clarifications - I think this would be a nice addition, but I've had exactly one use for it in the 15+ years of developing the survival package. - I have a work around for the current case. Prioritize accordingly. The ideal would be to change survexp as follows: fit <- survexp( ~ gender, data=mydata, ratetable=survexp.us, ratevar=list(sex=gender, year=enroll.dt, age=age*365.25)) The model statement says that I want separate curves by gender, and is similar to other model statements. The ratevar option gives the mapping between m...

survexp in survival5 doesn't seem to work for me. see below: > library(survival5) Attaching Package "package:survival5": The following object(s) are masked from package:base : sort.list > library(chron) > data(ratetables) > survexp(~ratetable(year=julian(6,1,1991), + se...

Dear All, Does someone have, or know of survexp ratetables for european contries, especially Austria and Germany? I know only about slopop in the package relsurv. Thanks in advance Heinz T??chler

DeaR list I would like to know if there is a direct method to compute the expected remaining survival time for a subject having survived up to time t. survexp gives me the probabilty for subject S to survive up to day D Thanks -- Anne

...ted numbers of events for a new cohort; then, comparing the expected vs. the observed numbers of events would give us some idea of whether the new cohort differs from the reference one. >From my reading of the documentation and the text by Therneau and Grambsch, it seems that the function "survexp" is what I need. But using it I am not able to obtain expected numbers of events that match reasonably well the observed numbers *even for the same reference population.* So, I think I am misunderstanding something quite badly. Below is an example that illustrates the situation. At the end I...

> Several changes in print.survfit, plot.survfit and seemingly in the structure > of ratetabels effect some of my syntax files. > Is there somewhere a documentation of these changes, besides the code itself? I agree, the Changelog.09 file is not as comprehensive as one would like. Specific comments: 1. The ratetables were recently changed to accomodate a new option. I thought

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.

...'t have individual data, but grouped data that allows to obtain a hazard function. I am wondering if there is an R function that allows to obtain a hazard ratio of the two hazard funtions (under the proportionality assumption) taking into account the censoring of the data? I am aware of survexp and survdiff functions, but I am not sure if that is the best way to do what I need. Any help will be highly appreciated. Montse Rue Department of Basic Medical Sciences University of Lleida (Spain)

..."jasa1" ------- snip ---- data(bladder2) # Warning message: # In data(bladder2) : data set ?bladder2? not found data(mgus1) # Warning message: # In data(mgus1) : data set ?mgus1? not found > data(mgus1) Warning message: In data(mgus1) : data set ?mgus1? not found > data("survexp.mn") Warning message: In data("survexp.mn") : data set ?survexp.mn? not found Hypothesis: datasets in a ..library/data/Rdata.rds file whose listing does not match the name of the dataset from which it is derived will cause the behavior in question. And Terry; After executing `d...

...man/coxph.Rd * man/coxph.detail.Rd * man/date.ddmmmyy.Rd * man/lines.survfit.Rd * man/plot.cox.zph.Rd * man/predict.survreg.Rd * man/pyears.Rd * man/residuals.coxph.Rd * man/stanford2.Rd * man/strata.Rd * man/summary.survfit.Rd * man/survdiff.Rd * man/survexp.Rd * man/survfit.Rd * man/survreg.control.Rd * man/survsum.Rd * man/untangle.specials.Rd 2) missing docs: * checking for undocumented objects ... WARNING [1] "[.Surv" "[.coxph.penalty" [3] "[.ratetable" "[.ra...

A user asked me about this and I can't figure it out. tmt% R R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > library(survival) > data(cgd0) Warning message: In data(cgd0) : data set ?cgd0? not found ---- The data set is present and can be

Dear R users, My apologies for the simple question, as I'm starting to learn the concepts behind the Cox PH model. I was just experimenting with the survival and rms packages for this. I'm simply trying to obtain the expected survival time (as opposed to the probability of survival at a given time t). I can't seem to find an option from the "type" argument in the predict

...at) temp1 <- paste( paste(tname, tname, sep='='), collapse=', ') temp2 <- paste("~1 + cbind(", temp1, ")") model.frame(as.formula(temp2), tdata) This came out of a user report to me. Coxph with a very long formula (which does work) followed by a call to survexp leads to a call like the above but using my "ratetable" function instead of "cbind". My machine's details: R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLL...

...publishing a package on CRAN is that it have to pass R CMD check with no errors, warnings *or* notes. So, in that sense notes are no different from warnings. --------------------------------- Getting rid of these notes would be very hard in the survival package. The population survival routines (survexp, pyears) that have to deal with dates try to be very accommodating wrt the date format the user chose, so have constructions like if (user date looks like a chron object) { calculation using chron functions } else if (is from the date package) { use mdy.date } els...