[R] Problem with nlme package

[David Winsemius]

On Nov 17, 2010, at 5:22 PM, <Bill.Venables at csiro.au> <Bill.Venables at csiro.au 
 > wrote:

> The function is not exported from the package.  You have to get  
> tough with it, e.g.
>
>> library(nlme)
>> summary.lme
> Error: object 'summary.lme' not found


>
> But if you insist:
>
>> nlme:::summary.lme
> function (object, adjustSigma = TRUE, verbose = FALSE, ...)
> {
>    fixed <- fixef(object)
> ...
>
> You cannot do this with lme4 since there the methods are S4 rather  
> than S3 (which is why it has a 4 in the name, I suspect, like the  
> stats4 package).

Then I must be confused. The usual approach of :

methods(summary.lme)  ---> summary.lme*  (among many others)
getAnywhere(summary.lme)

A single object matching ‘summary.lme’ was found
It was found in the following places
   registered S3 method for summary from namespace nlme
   namespace:nlme

... seems to work just fine.

-- 
David.

>
>
> Also, tucked away in the 'ape' package there is a function varcomp()  
> which extracts variance components from lme objects.  This is all I  
> have ever needed in addition to what is provided in nlme directly.
>
> Bill V.
>
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org 
> ] On Behalf Of Joanna Geller
> Sent: Thursday, 18 November 2010 8:07 AM
> To: David Winsemius
> Cc: r-help at r-project.org
> Subject: Re: [R] Problem with nlme package
>
> Thanks for the suggestions - I tried all of them, including
> require(lme4) and require(nlme) and summary.lme still cannot be found.
> I want to use it to get full output of a multi-level model. Maybe it's
> a Mac thing?
>
> Any other suggestions would be much appreciated! Thanks, again.
>
>
> On Wed, Nov 17, 2010 at 3:51 PM, David Winsemius <dwinsemius at comcast.net 
> > wrote:
>>
>> On Nov 17, 2010, at 4:48 PM, David Winsemius wrote:
>>
>>>
>>> On Nov 17, 2010, at 4:39 PM, Joanna Geller wrote:
>>>
>>>> Hello,
>>>>
>>>> I have installed the nlme package, but every time I try to use the
>>>> function "summary.lme,"
>>>
>>> How did you "try to use it"?
>>>
>>>> I get a message that the function cannot be
>>>> found.
>>>
>>>
>>> If it says it cannot be found, then you quite possibly forgot to  
>>> load the
>>> "lme4" package.
>>
>> (or the nlme package)
>> Try:
>>
>> require(nlme)
>>
>> --
>> David Winsemius, MD
>> West Hartford, CT
>>
>>
>
> ______________________________________________
> 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.

David Winsemius, MD
West Hartford, CT