[R] Strange error returned or bug in gam in mgcv????

[Corrado]

Dear Gavin, Simon,

this is the result of str:

> str(dist_scot24_vector_with_climate)
'data.frame':   2265025 obs. of  14 variables:
 $ X       : int  1 2 3 4 5 6 7 8 9 10 ...
 $ tetrad_i: Factor w/ 1505 levels "HP61A","HP61I",..: 1505 1504 1503 1502 
1501 1500 1499 1498 1497 1496 ...
 $ tetrad_j: Factor w/ 1505 levels "HP61A","HP61I",..: 1505 1505 1505 1505 
1505 1505 1505 1505 1505 1505 ...
 $ bray    : num  0 0.566 0.251 0.407 0.45 ...
 $ PC1     : num  -3.97 -3.14 -7.27 -5.77 -5.88 ...
 $ PC2     : num  3.26 2.87 3.19 2.96 2.97 ...
 $ PC3     : num  -0.16511 -0.28601 -0.00362 -0.11685 -0.09695 ...
 $ PC4     : num  -0.629 -0.696 -0.6 -0.683 -0.639 ...
 $ PC5     : num  0.2603 0.3818 -0.0148 0.0967 0.094 ...
 $ PC6   : num  -3.97 -3.97 -3.97 -3.97 -3.97 ...
 $ PC7   : num  3.26 3.26 3.26 3.26 3.26 ...
 $ PC8   : num  -0.165 -0.165 -0.165 -0.165 -0.165 ...
 $ PC9   : num  -0.629 -0.629 -0.629 -0.629 -0.629 ...
 $ PC10   : num  0.26 0.26 0.26 0.26 0.26 ...
>

It looks ok to me. What do you think?

On Tuesday 01 September 2009 18:43:24 Gavin Simpson wrote:
> On Tue, 2009-09-01 at 17:55 +0100, Corrado wrote:
> > Dear Simon,
> >
> > I have stored all information at the link:
> >
> > http://scsys.co.uk:8002/33309?hl=on&submit=Format+it!
>
> You could have included that in your mail to the list - it is just plain
> text after all.
>
> > I have the same problem if I do
> > s(PC1)  + ..... + s(PC10) or
> > s(Pc1,PC2,PC3,PC4,PC5)+s(PC6,PC7,PC8,PC9,PC10) or
> > s(PC1,PC2,PC3,PC6,PC7,PC8) .....
> >
> > I have renamed PC1.1,PC2.1,PC3.1,PC4.1,PC5.1 to PC6,PC7,PC8,PC9,PC10 for
> > simplicity.
>
> What does
>
> str(dist_scot24_vector_with_climate)
>
> show? I seem to recall getting similar errors when I'd done something
> silly in a data prep routine and had data in a data frame that wasn't
> numeric but looked like it was - a factor for example.
>
> If you can't do some quite simple things like the first of your three
> alternatives above, that suggests something amiss with the data. That'd
> be the first thing to check.
>
> HTH
>
> G
>
> > Regards
> >
> > On Tuesday 01 September 2009 17:31:04 Simon Wood wrote:
> > > The basic problem is that you have requested a 10 dimensional thin
> > > plate spline, with a basis dimension of 196830. In reality it will not
> > > be possible to compute this, even if you have more than 196830 data. In
> > > any case it would be unlikely to provide a very useful model --- the
> > > "simplest" function that it can theoretically represent will have 3003
> > > degrees of freedom.
> > >
> > > That said the error message is obviously rather unhelpful... Can you
> > > tell me how many data you are actually trying to fit, and I'll try and
> > > track down exactly where it's failing, and put in a more informative
> > > message.
> > >
> > > best,
> > > Simon
> > >
> > > On Tuesday 01 September 2009 14:51, Corrado wrote:
> > > > Dear friends,
> > > >
> > > > what is this error message in gam???? I cannot understand what it
> > > > means .... is it a bug?
> > > >
> > > > gam_bray_scot24_pc_0505<gam(bray~s(PC1,PC2,PC3,PC4,PC5,
> > > > PC1.1,PC2.1,PC3.1,PC4.1,PC5.1),data=dist_scot24_vector_with_climate)
> > > >
> > > > Error in if (length(data) != vl) { :
> > > >   missing value where TRUE/FALSE needed
> > > > Calls: gam ... smooth.construct -> smooth.construct.tp.smooth.spec ->
> > > > array In addition: Warning message:
> > > > In array(0, n * k) : NAs introduced by coercion
> > > > Execution halted
> > > >
> > > > Thanks in advance,
> > > >
> > > > Best regards



-- 
Corrado Topi

Global Climate Change & Biodiversity Indicators
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct529 at york.ac.uk