R help - Nov 2012 - [mgcv][gam] Manually defining my own knots?

Dear List,

I'm using GAMs in a multiple imputation project, and I want to be able 
to combine the parameter estimates and covariance matrices from each 
completed dataset's fitted model in the end.  In order to do this, I 
need the knots to be uniform for each model with partially-imputed 
data.  I want to specify these knots based on the quantiles of the 
unique values of the non-missing original data, ignoring the NA's.  When 
I fit the GAM with the imputed data included, I don't want mgcv to use 
the data that it is supplied to figure out the knots, because this will 
lead to un-comparable results when the many fitted models are combined.

Here is a caricatured example of what I want to do:

#Random data
x = runif(1000,0,1)
y = (log(x^2)+x^3)/sin(x)
example = gam(y~s(x))
plot(example)

#But I want to define my own knots
dumb.knots = c(.7,.8,.9)
dumb.example = gam(y~s(x,k=3),knots=list(dumb.knots))
plot(dumb.example)
dumb.example2 = gam(y~s(x,k=3))
plot(dumb.example2)

Dumb example 1 is the same as dumb example 2, but it shouldn't be.

Once I figure out how to do this, I'll take the fitted coefficients from 
each model and average them, then take the vcv's from each model and 
average them, and add a correction to account for within and between 
imputation variability, then plug them into a gamObject$coeffient and 
gamObject$Vp matrix, plot/summarize, and have my result.  Comments 
welcome on whether or not this would be somehow incorrect would be 
welcome as well.  Still have a lot to learn!

Thanks,
Andrew

	[[alternative HTML version deleted]]

Hi Andrew,

mgcv matches the knots to the smooth arguments by name. If an element of
'knots' has
no name it will be ignored. The following will do what you want...

dumb.example = gam(y~s(x,k=3),knots=list(x=dumb.knots))

best,
Simon

On 29/11/12 23:44, Andrew Crane-Droesch wrote:
> Dear List,
>
> I'm using GAMs in a multiple imputation project, and I want to be able
> to combine the parameter estimates and covariance matrices from each
> completed dataset's fitted model in the end.  In order to do this, I
> need the knots to be uniform for each model with partially-imputed
> data.  I want to specify these knots based on the quantiles of the
> unique values of the non-missing original data, ignoring the NA's. 
When
> I fit the GAM with the imputed data included, I don't want mgcv to use
> the data that it is supplied to figure out the knots, because this will
> lead to un-comparable results when the many fitted models are combined.
>
> Here is a caricatured example of what I want to do:
>
> #Random data
> x = runif(1000,0,1)
> y = (log(x^2)+x^3)/sin(x)
> example = gam(y~s(x))
> plot(example)
>
> #But I want to define my own knots
> dumb.knots = c(.7,.8,.9)
> dumb.example = gam(y~s(x,k=3),knots=list(dumb.knots))
> plot(dumb.example)
> dumb.example2 = gam(y~s(x,k=3))
> plot(dumb.example2)
>
> Dumb example 1 is the same as dumb example 2, but it shouldn't be.
>
> Once I figure out how to do this, I'll take the fitted coefficients
from
> each model and average them, then take the vcv's from each model and
> average them, and add a correction to account for within and between
> imputation variability, then plug them into a gamObject$coeffient and
> gamObject$Vp matrix, plot/summarize, and have my result.  Comments
> welcome on whether or not this would be somehow incorrect would be
> welcome as well.  Still have a lot to learn!
>
> Thanks,
> Andrew
>
> 	[[alternative HTML version deleted]]
>
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