Re: [R] retrieve p-value from a cox.obj

: an object of class coxph. See 'coxph.object' for details. and help(coxph.object) gives a description of all the components. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] p-value from survreg

The question was how to get the p-value from the fit below, as an S object sr-survreg(s~groups, dist=gaussian) Coefficients: (Intercept) groups -0.02138485 0.03868351 Scale= 0.01789372 Loglik(model)= 31.1 Loglik(intercept only)= 25.4 Chisq= 11.39 on 1 degrees of freedom, p=

Re: [R] R is not a validated software package..

I've been on vacation and so come late to this interesting discussion. Let me add two minor points. 1. I have run into a lot of statements that x is required when dealing with pharma, and in particular wrt NDAs (new drug application). Almost all were false. But I also understand a bit of

Re: [R] Showing NAs when using table()

different for factors, so I expect to remain in the minority. (I can't think of a time I would ever have wanted the actions of the new version of exclude, which for factors is a means only to exclude more things, rather than the usual use of keeping more in the table). Terry Therneau

[R] Stratified Cox proportional Hazard Model

hazard ratios for x2 --- there are none. That is the point of a strata; you are declaring a variable to NOT be proportional hazards, and thus there is no single hazard ratio that describes it. Terry Therneau __ R-help@stat.math.ethz.ch

Re: [R] log rank test p value

); both the obs and exp objects have one element per group. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html

Re: [R] Predicted Cox survival curves - factor coding problems..

. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] stringsAsFactor global option (was character coerced to a factor)

function, because 9 times out of 10 they did it by accident and dont' want it either. But when a user really does want to do so ...) Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Approaches of Frailty estimation: coxme vs coxph(...frailty(id, dist='gauss'))

. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

[R] Documentation for namespaces

these better. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained

Re: [R] R and clinical studies

. Terry Therneau Biostatistics, Mayo Clinic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self

[R] rpart minimum sample size

Look at rpart.control. Rpart has two advisory parameters that control the tree size at the smallest nodes: minsplit (default 20): a node with less than this many subjects will not be worth splitting minbucket (default 7) : don't create any final nodes with 7

Re: [R] survival analysis using rpart

likelihood ratio tests. I don't know how to say which model is better. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

[R] Coxph and ordered factors

that they were 0 = stage 1 (implicit coef) .1= stage 2 .5 = stage 3 .4 = stage 4 Create a new class variable that combines stages 3 and 4, and return to step 1. Terry Therneau

[R] Problem with factor state when subset()ing a data frame

. Terry Therneau Biostatistics, Mayo Clinic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self

Re: [R] predict.survreg() with frailty term and newdata

It can't be done with the current code. In a nutshell, you are trying to use a feature that I never got around to coding. It's been on my to do list, but may never make it to the top. Terry __ R-help@stat.math.ethz.ch mailing list

Re: [R] Survfit with a coxph object

the weeks to do it. The mid term one is to take Frank Harrell's suggestion. If standard errors are not needed, there is an O(n) algorithm, which he has implemented as part of his additions to the coxph suite. Terry Therneau __ R-help

Re: [R] CV by rpart/mvpart

of the second, etc. I was going to write read the manual page for control.rpart, but it seems I forgot to put this feature into the documentation! Terry Therneau On 12/28/06, Pedro Ramirez [EMAIL PROTECTED] wrote: Dear R-list, I am using the rpart/mvpart-package

Re: [R] newbie estimating survival curve w/ survfit for coxph

there are 2 strata and 3 subjects, and curves[1,2] will return the survival curve for strata 1, subject 2. curves[2,1] will return the survival curve for strata 2, subject 1, etc. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https

Re: [R] Confidence intervals for relative risk

computation that this approach is quite common. The idea of adding a fraction is found in Anscombe(1949), Transformations of Poisson, binomial and negative-binomial data. Biometrika, vol 35, p246-254, but for each single estimate not for the ratio. Terry Therneau Mayo Clinic

Re: [R] fraitly in coxph

For a nested model you want to use the coxme function, which is the much superior successor to frailty(). It is currently found in the kinship library. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] counting process form of a cox model (cluster(id))

sense. If there are multiple events per person then one needs the sandwich variance, but for a somewhat different reason. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] terms.inner

secret handshake that will convince R to let you look at it, although I don't remember the form. This Nixonesque passion with hiding things is one of the reasons I still prefer Splus. Terry Therneau [EMAIL PROTECTED] __ R-help

[R] terms.inner() reprise

it is. getAnywhere() seems to be the most general fix to my frustration. I may come back with another note summarizing some of the philosophical debate. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] Problem with coxme

- Begin Forwarded Message - Date: Wed, 5 Jul 2006 09:09:14 -0500 (CDT) From: Terry Therneau [EMAIL PROTECTED] Subject: RE: Problem with coxme To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED], [EMAIL PROTECTED], [EMAIL PROTECTED] Content-MD5: BXKVsHtW/1I9mIUqrXBU0g

[R] graphlets

, graphlets are an extended java graphics device. The identify function, for instance, allows one to link both a label and a set of html links to each point. I am aware of the Sjava package in Omega, and am exploring that, but would be very interested if there is anything more. Terry

[R] graphlets -- more

, this is not an interactive R session. The graphlets package allows this type of operation with java. Terry Therneau __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R