This arose when working on an addition to coxph, which has the features
that the X matrix never has an intercept column, and we remove strata()
terms before computing an X matrix. The surprise: when a terms object
is subset the intercept attribute is turned back on.
My lines 2 and 3 below were being executed just before a call to
model.frame. The simple solution was of course to do them in the
opposite order so I am not waiting on a "fix".
Not to mention that I am not sure a fix is required, though I was
surprised.
Terry T.
tmt1131% R
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
> test <- terms(Surv(time, status) ~ age + strata(ph.ecog),
+ specials='strata')
> attr(test, 'intercept') <- 0 #turn off intercept
> test <- test[-2] #remove strata
> test
Surv(time, status) ~ age
attr(,"variables")
list(Surv(time, status), age)
attr(,"factors")
age
Surv(time, status) 0
age 1
attr(,"term.labels")
[1] "age"
attr(,"specials")
attr(,"specials")$strata
NULL
attr(,"order")
[1] 1
attr(,"intercept")
[1] 1
attr(,"response")
[1] 1
>From the NEWS for 2.13.0-to-be\item \code{drop.terms} and the \code{[} method for class \code{"terms"} no longer add back an intercept. (Reported by Niels Hansen.) so it has been fixed, just not rolled out yet. On Mon, 21 Feb 2011, Terry Therneau wrote:> This arose when working on an addition to coxph, which has the features > that the X matrix never has an intercept column, and we remove strata() > terms before computing an X matrix. The surprise: when a terms object > is subset the intercept attribute is turned back on. > My lines 2 and 3 below were being executed just before a call to > model.frame. The simple solution was of course to do them in the > opposite order so I am not waiting on a "fix". > Not to mention that I am not sure a fix is required, though I was > surprised. > Terry T. > > > tmt1131% R > > R version 2.12.0 (2010-10-15) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > >> test <- terms(Surv(time, status) ~ age + strata(ph.ecog), > + specials='strata') > >> attr(test, 'intercept') <- 0 #turn off intercept >> test <- test[-2] #remove strata > >> test > Surv(time, status) ~ age > attr(,"variables") > list(Surv(time, status), age) > attr(,"factors") > age > Surv(time, status) 0 > age 1 > attr(,"term.labels") > [1] "age" > attr(,"specials") > attr(,"specials")$strata > NULL > > attr(,"order") > [1] 1 > attr(,"intercept") > [1] 1 > attr(,"response") > [1] 1 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
> -----Original Message----- > From: r-devel-bounces at r-project.org > [mailto:r-devel-bounces at r-project.org] On Behalf Of Terry Therneau > Sent: Monday, February 21, 2011 11:32 AM > To: r-devel at r-project.org > Subject: [Rd] Anomaly in [.terms > > > This arose when working on an addition to coxph, which has > the features > that the X matrix never has an intercept column, and we > remove strata() > terms before computing an X matrix. The surprise: when a terms object > is subset the intercept attribute is turned back on.I've wondered about how to deal with terms objects whose formula and attributes disagreed with each other. In your case the intercept attribute was 0 but there was no -1 in the formula and you (and others) complained that [.terms respected the formula and not the attributes. In another case you can set the response attribute to 0 but leave the response term in the formula. Then [.terms alters the formula to drop the response term. > t <- terms(y ~ x1 + x2) > attr(t, "response") [1] 1 > attr(t, "response") <- 0 > t[1] ~x1 attr(,"variables") list(x1) attr(,"factors") x1 x1 1 attr(,"term.labels") [1] "x1" attr(,"order") [1] 1 attr(,"intercept") [1] 1 attr(,"response") [1] 0 attr(,".Environment") <environment: R_GlobalEnv> > version$version.string [1] "R version 2.12.1 (2010-12-16)" Is altering the formula to match the attributes desirable? I suspect you would be displeased if [.terms added a -1 to the formula if the intercept term were 0. If you have a terms object without a response in the formula and you set the response attribute to 1 then [.terms just gets mixed up. Altering most other attributes of a terms object risks confusing lots of functions. Should R have a function to set the intercept term to a legal value so we could say that directly altering the attributes of a terms object should never be done? Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com> My lines 2 and 3 below were being executed just before a call to > model.frame. The simple solution was of course to do them in the > opposite order so I am not waiting on a "fix". > Not to mention that I am not sure a fix is required, though I was > surprised. > Terry T. > > > tmt1131% R > > R version 2.12.0 (2010-10-15) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > > test <- terms(Surv(time, status) ~ age + strata(ph.ecog), > + specials='strata') > > > attr(test, 'intercept') <- 0 #turn off intercept > > test <- test[-2] #remove strata > > > test > Surv(time, status) ~ age > attr(,"variables") > list(Surv(time, status), age) > attr(,"factors") > age > Surv(time, status) 0 > age 1 > attr(,"term.labels") > [1] "age" > attr(,"specials") > attr(,"specials")$strata > NULL > > attr(,"order") > [1] 1 > attr(,"intercept") > [1] 1 > attr(,"response") > [1] 1 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >