Dieter Menne
2010-Mar-18 11:26 UTC
[R] Using nlme and coxme (both!): Looking for workaround
I am trying to use nlme and coxme in one Sweave document. I have read the
thread in r-devel on the subject,
http://markmail.org/thread/snchg6ynofrzbf2v
and nlme::fixef works, but I did not understand what workaround to use when
I am calling a function in a package that I do not want to change.
Dieter
library(nlme)
library(coxme) # hides fixef, among others
deplynestedforeingpackagefunction = function(x){
# I do not want to change this function in another package
fixef(x)
}
fit <- coxme(Surv(time, status) ~ age + (1|ph.ecog), lung)
fixef(fit)
fm1 <- lme(distance ~ age, data = Orthodont)
nlme::fixef(fm1) # can use nlme::
#
deplynestedforeingpackagefunction(fm1) #error
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] splines stats graphics grDevices datasets utils methods
base
other attached packages:
[1] coxme_2.0 bdsmatrix_1.0 survival_2.35-8 nlme_3.1-96
loaded via a namespace (and not attached):
[1] grid_2.10.1 lattice_0.18-3 tools_2.10.1 >
Douglas Bates
2010-Mar-18 14:31 UTC
[R] Using nlme and coxme (both!): Looking for workaround
On Thu, Mar 18, 2010 at 6:26 AM, Dieter Menne <dieter.menne at menne-biomed.de> wrote:> I am trying to use nlme and coxme in one Sweave document. I have read the > thread in r-devel on the subject, > > http://markmail.org/thread/snchg6ynofrzbf2v > > and nlme::fixef works, but I did not understand what workaround to use when > I am calling a function in a package that I do not want to change.We discussed a fix for that which is to add a line to the NAMESPACE file for any packages that want to define methods for the fixef or ranef generic. The line is simply importFrom(nlme, fixef, ranef) I thought Terry was going to add that in the coxme sources.> > library(nlme) > library(coxme) # hides fixef, among others > > deplynestedforeingpackagefunction = function(x){ > ?# I do not want to change this function in another package > ?fixef(x) > } > > fit <- coxme(Surv(time, status) ~ age + (1|ph.ecog), lung) > fixef(fit) > > fm1 <- lme(distance ~ age, data = Orthodont) > nlme::fixef(fm1) # can use nlme:: > # > deplynestedforeingpackagefunction(fm1) #error > > > > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=German_Germany.1252 ?LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] splines ? stats ? ? graphics ?grDevices datasets ?utils ? ? methods > base > > other attached packages: > [1] coxme_2.0 ? ? ? bdsmatrix_1.0 ? survival_2.35-8 nlme_3.1-96 > > loaded via a namespace (and not attached): > [1] grid_2.10.1 ? ?lattice_0.18-3 tools_2.10.1 >> > > ______________________________________________ > R-help at r-project.org 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. >