Sorry for one more email, but here is a more concise and pertinent "ranef" example:
# Allow S4 methods to find S3 asreml objects setOldClass("asreml") if(!isGeneric("ranef")){ setGeneric("ranef", function(object, ...) standardGeneric("ranef")) } ranef.asreml <- function(obj){ effects <- obj$coefficients$random class(effects) <- c("ranef.asreml",class(effects)) return(effects) } print.ranef.asreml <- function(x, ...){ print.default(x) } Kevin On Fri, Mar 5, 2010 at 10:47 AM, Terry Therneau <thern...@mayo.edu> wrote: > The coxme package has a ranef() method, as does lme4. I'm having > trouble getting them to play together, as shown below. (The particular > model in the example isn't defensible, but uses a standard data set.) > > The problem is that most of the time only one of lme4 or coxme will be > loaded, so each needs to define the basic ranef function as well as a > method for it. But when loaded together the last one wins. The coxme > object is an S3 class BTW. (Suggestions to convert it to S4 will not be > well recieved -- but that's a different and unnecessary thread.) > > Odds are that this has a simple solution which I have missed. > Terry Therneau > > > tmt935% R --vanilla > > R version 2.10.0 (2009-10-26) > Copyright (C) 2009 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > library(coxme) > Loading required package: survival > Loading required package: splines > Loading required package: bdsmatrix > > > fit <- coxme(Surv(time, status) ~ age + (1|ph.ecog), lung) > > ranef(fit) > $ph.ecog > Intercept > 0.1592346 > > > library(lme4) > Loading required package: Matrix > Loading required package: lattice > > Attaching package: 'lme4' > > > The following object(s) are masked from package:coxme : > > fixef, > ranef > > > ranef(fit) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "ranef", for signature > "coxme" > > q() > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Kevin Wright [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel