FAQ
Under the description of the 'type' argument, ?residuals.gls says
'Defaults to ?"pearson"?.'

But residuals.gls starts

residuals.gls <-
function(object, type = c("response", "pearson", "normalized"), ...)
{
type <- match.arg(type)

...

which sure looks to me like it defaults to "response", not "pearson"
(and it behaves that way in tests).

It would seem to make more sense to change the documentation rather than
the code
since anyone who looked at the docs would have been confused already,
whereas someone who had
been happily using the code without looking at the docs would see a
sudden change in the results ...

This is in nlme 3.1-96, from a fresh tools/rsync-recommended. Sending it
to r-devel for comment because r-core is listed as the maintainer.

sincerely
Ben Bolker

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  • Prof Brian Ripley at Sep 22, 2010 at 9:41 am

    On Tue, 14 Sep 2010, Ben Bolker wrote:
    Under the description of the 'type' argument, ?residuals.gls says
    'Defaults to ?"pearson"?.'

    But residuals.gls starts

    residuals.gls <-
    function(object, type = c("response", "pearson", "normalized"), ...)
    {
    type <- match.arg(type)

    ...

    which sure looks to me like it defaults to "response", not "pearson"
    (and it behaves that way in tests).

    It would seem to make more sense to change the documentation rather than
    the code
    since anyone who looked at the docs would have been confused already,
    whereas someone who had
    been happily using the code without looking at the docs would see a
    sudden change in the results ...

    This is in nlme 3.1-96, from a fresh tools/rsync-recommended. Sending it
    to r-devel for comment because r-core is listed as the maintainer.
    Whereas bug reports should be sent to the maintainer or (for packages
    maintained by R-core) R-bugs. The SVN version of nlme has
    BugReports: http://bugs.r-project.org
    since reports here are easily overlooked.

    I've changed the SVN sources, but most likely a new release of nlme
    will be made only when something substantive is changed.

    --
    Brian D. Ripley, ripley at stats.ox.ac.uk
    Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
    University of Oxford, Tel: +44 1865 272861 (self)
    1 South Parks Road, +44 1865 272866 (PA)
    Oxford OX1 3TG, UK Fax: +44 1865 272595

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postedSep 14, '10 at 4:42p
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