R-alpha: Bugs

Jim Lindsey (jlindsey@luc.ac.be)
Mon, 13 May 1996 09:24:11 +0200 (MET DST)


From: Jim Lindsey <jlindsey@luc.ac.be>
Message-Id: <9605130724.AA16656@alpha.luc.ac.be>
Subject: R-alpha: Bugs
To: r-testers@stat.math.ethz.ch
Date: Mon, 13 May 1996 09:24:11 +0200 (MET DST)

I have been working with 0.4 over the weekend and found the following problems.
I have just downloaded 0.5 but have not checked if they are corrected.
I have been working primarily with glm() especially with binomial and poisson.

(1) the workspace does not save options (it did in 0.1) such as contr.treatment
(2) for a saturated model with glm(), I always obtain
    Warning: NAs produced in function "pt"
    Then in the table of coefficients, P(>|t|) is a column of NAs
    This does not happen for unsaturated models.
(3) with contr.treatment, coefficients are labelled from 1 to k-1 as if the
    last category were baseline, but the estimates correspond to categories
    2 to k with the first set to zero i.e. baseline
(4) with saturated models, 10 iterations are always used with the
    Warning: Algorithml did not converge
    whereas GLIM stops after 2-3 cycles. Of course, after 10 iterations,
    the deviance is much closer to zero than in GLIM
(5) For seemingly random combinations of data and covariate codings, binomial
    gives
    Error in if(abs((dev-devold)/sum(dev^2)) < control$epsilon & abs((coef
      -coefold)/sum(   : missing value where logical needed.
    Here is an example:
y1 <- c(23,35)
y2 <- c(34,132)
inf <- cbind(y1,y2)
cont <- c(0,1)
glm(inf~cont,family=binomial)
however, if I define  cont <- c(-1,1), it works!
I also have more complex examples of this problem.
  Cheers, Jim
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