Extracting p-values from an lme object (any help would be appreciated)

Adam,

I'm sorry, I must jump in here.  See responses to specific points below.

Regards,   Rob Kushler
On Wed, 25 Nov 2009, Ben Bolker wrote:

Ben Zuckerberg wrote:
I know that p-value estimation in mixed models are somewhat
controversial at the moment, but I am simply curious how one extracts
p-values for the fixed factors from an lme object (using nlme)? The
summary() gives the desired p-values; all I want to do is access them.
The names() command shows the returned values (e.g., fitted, residuals)
for many components of the model, but I can't seem to access the
p-values.  Thank you in advance!

library(nlme)
example(lme)
summary(fm1)$tTable[,"p-value"]
Or perhaps more simply,
It's true that calling "pt" is a simple way to *compute* the
     p-values, but the question was how to *extract* them.  In general
     the ability to manipulate objects is a key advantage of R.
pt(t, df, lower.tail)

gives you the p-value associated with a given t-value and its degrees of
freedom. lower.tail is whether you want the p below the t-value (usually 
you want this when p is negative), or above.
I think you mean "when t is negative" - but that's still not correct.
     You want "lower=TRUE" when the alternative hypothesis Ha says "<" and
     "lower=FALSE" when Ha says ">", regardless of the sign of t.
Multiply by 2 for a 2-tailed test.
Actually you need "2*pt(-abs(t), df, lower=TRUE)" to ensure a
     correct two-sided p-value.
summary() is almost certainly just calling pt().

--Adam

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Extracting p-values from an lme object (any help would be appreciated)

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