Re: [R] R on a flash drive

I often run R via a Ceedo virtualisation on a USB drive (http://www.ceedo.com/) with XP. It costs a few dollars to it this way, but is a very low stress installation and has worked flawlessly, albeit a little slower (barely noticeable). Very handy if you are often working on various machines

[R] survsplit and multiple event indicators

Hi all, I have a dataset of censored observations which contains 2 variables which I wish to account for in a time-dependent manner (tumour recurrence and subsequent treatment of that recurrence). Hence I need to convert the data to counting process notation. survSplit and the like do a nice job

[R] data recoding problem

Hi R experts, I have a data recoding problem I cant get my head around - I am not that great at the subsetting syntax. I have a dataset of longitudinal toxicity data (for multistate modelling) for which I want to also want to do a simple Kaplan-Meier curve of the time to first toxic event. The

[R] strange fisher.test result

A simple question - using the following fishers test it appears that the P value is significant, but the CI includes 1. Is this result correct? data.50p10min - matrix(c(16,15, 8, 24),nrow=2) fisher.test(data.50p10min) Fisher's Exact Test for Count Data data: data.50p10min

[R] how to fill between 2 stair plots

Hi all, I want to create a simple plot with 2 type='s' lines on it: plot(a, b, type='s') lines(x, y, type='s') I wish to then fill the area between the curves with a colour to accentuate the differences eg col=gray(0.95). I cant seem to come up with a simple method for this. Any pointers in

[R] bootcov and cph error

Hi all, I am trying to get bootstrap resampled estimates of covariates in a Cox model using cph (Design library). Using the following I get the error: ddist2.abr - datadist(data2.abr) options(datadist='ddist2.abr') cph1.abr - cph(Surv(strt3.abr,loc3.abr)~cov.a.abr+cov.b.abr, data=data2.abr,

[R] frailty in coxph or repeated measures in cph (Design)

I am trying to build a model to aid a clinical decision. Certain patients have a blood marker measured at each visit - a rise of this may indicate recurrence of the cancer after treatment (endpoint is clinical recurrence, censored). In a proportion (up to 30%), this rise is a false positive -

[R] actuarial prevalence plots

Hi all, I am trying to produce a series of plots showing the prevalence of a condition, which is subject to censoring. In most cases the condition is temporary and resolves with time. I would like to use the method of Pepe et al Stat Med 1991; 413-421 - essentially the prevalence is the

[R] strata in crr (cmprsk library)

Hi all, I am aware that crr lacks the friendly command structure of functions such as cph. All is clear to me about including covariates until I want to include a stratification term in the competing risk framework (no nice strat command). I am still a bit of a novice in R - I am looking for an

[R] validation, calibration and Design

Hi R experts, I am trying to do a prognostic model validation study, using cancer survival data. There are 2 data sets - 1500 cases used to develop a nomogram, and another of 800 cases used as an independent validation cohort. I have validated the nomogram in the original data (easy with