Re: [R] Loop within nlme

From: Spencer Graves <>
Date: Sat 03 Dec 2005 - 16:57:57 EST

          I have not seen a reply to this, so I will offer a couple of feeble comments, hoping that you might find them useful even though they don't answer your question. It is difficult for me to understand your question, because my SAS experience is so limited.

  1. R is open source, so you can get the source code for nlme, read it, modify it to do something similar but different, etc. You can see the source for any function by typing its name at a command prompt. I did this just now with "lme" and "nlme" and found calls to "UseMethod". When I consult help("UseMethod"), it says, "See Also ... methods", and 'methods("lme")' and 'methods("nlme")' identify, among other things "lme.forumla" and "nlme.formula". When I request those two, a listing of R code fills my screen. If you step through either of those line by line, you will likely find a place where you can modify the code to do what you want. If you do this, calling "debug(lme.forumla)' before "lme" will allow you to walk through the code without being encumbered by features of R that work differently when called from within a function than they do when you run them line by line from a command prompt.
  2. What's the more general problem you are trying to solve? Can you simplify you problem to a few lines of R code that will replicate a specific difficulty you have encountered with R (as suggested in the posting guide! "")? A question with that kind of simple, reproducible example will, I believe, more likely receive a useful response quickly than questions that are more difficult for readers of this listserve to parse.
	  hope this helps.
	  spencer graves

Scott Story wrote:

> I am trying to mimic the SAS code below in R. The trick is that each
> row in the dataset has variable "t" which controls how many times the
> do-loop below will be iterated (that is, the model is fit to the
> response, ifate, 0 to t-1 times for each row of data). Is it possible to
> incorporate a loop like this into nlme by writing a function? Can
> anybody provide some hints to get me on my way? The code below is for a
> very simple model, an intercept only model, but more complex models will
> be evaluated (some potentially including random effects). The code is
> used to model daily nest survival.
> Proc Nlmixed data=Mall tech=quanew method=gauss maxiter=1000;
> parms B0=0;
> p=1;
> do i=0 TO t-1;
> logit=B0;
> p=p*(exp(logit)/(1+exp(logit)));
> end;
> model ifate~binomial(1,p);

Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA <>
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Received on Sat Dec 03 17:05:35 2005

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