Defining a method in two packages
Terry, this happens since the ranef in coxme is a S3 generic and the one in lme4 is a S4 generic. Of course, after loading lme4, you can still use the ranef from coxme: coxme::ranef(fit) and get the desired result. If you write your own code, you might want to use that call explicitly (i.e. accessing from the correct namepsace). In your own package, you could simply import the generic from coxme. Best wishes, Uwe
On 05.03.2010 17:47, Terry Therneau 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
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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()
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