Re: [R] extracting p-values from lmer()

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Tue 06 Dec 2005 - 20:03:31 EST

>>>>> "Renaud" == Renaud Lancelot <renaud.lancelot@gmail.com> >>>>> on Tue, 6 Dec 2005 08:09:35 +0100 writes:

    Renaud> For example:

....

>> vc <- vcov(m1, useScale = FALSE)
>> b <- fixef(m1)
>> se <- sqrt(diag(vc))
>> z <- b / sqrt(diag(vc))
>> P <- 2 * (1 - pnorm(abs(z)))
>>
>> cbind(b, se, z, P)

    Renaud>                   b            se         z  P
    Renaud> (Intercept)  0.3596720 0.007023556  51.20939 0
    Renaud> x1           0.2941068 0.002371353 124.02487 0
    Renaud> x2          -0.9272545 0.010087717 -91.91917 0

I still see much too many uses of "1 - p<dist>(...)" which in cases as the above case leads to complete loss of accuracy (1 - 1 = 0) -- well actually the above case is too extreme to make any difference; but let me explain the general principle: Though the loss is usually no problem for decision making based on P-values, it is unnecessary:

One of the (extra) features of R are the arguments 'lower.tail' and 'log.p' of all the p<dist>() functions -- which (in not yet quite all cases) allow avoid precision loss.

E.g.,

  > 1 - pnorm(c( 6,8,10,20))
  [1] 9.865877e-10 6.661338e-16 0.000000e+00 0.000000e+00   > pnorm(c(6,8, 10,20), lower.tail=FALSE)   [1] 9.865876e-10 6.220961e-16 7.619853e-24 2.753624e-89

BTW, example(pnorm) ends in two plots which show the advantage of using 'log.p' for additional precision gain e.g. for log-likelihood computation.

Martin Maechler, ETH Zurich



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