[R] Why are the number of coefficients varying? [mgcv][gam]
Simon Wood
s.wood at bath.ac.uk
Mon Jan 28 08:54:50 CET 2013
Hi Andrew,
Do you know which coefficients are missing (i.e. which terms have
missing coefficients)? This would help to narrow down the possibilities.
Is it certain that all levels of all factors occur in all replicates? If
not then you will get different numbers of coefficients (in the
parametric part of the model).
btw. what is tryCatch catching here?
best,
simon
On 28/01/13 05:36, Andrew Crane-Droesch wrote:
> Dear List,
>
> I'm using gam in a multiple imputation framework -- specifying the knot
> locations, and saving the results of multiple models, each of which is
> fit with slightly different data (because some of it is predicted when
> missing). In MI, coefficients from multiple models are averaged, as are
> variance-covariance matrices. VCV's get an additional correction to
> account for how variable they are between each other.
>
> For this to work in the context of a penalized spline model, the knots
> need to be specified identically for each model (this is assisted by
> context knowledge), and each model needs to have the same number of
> knots. This is what I've done, below. I run that code multiple times
> with slightly different (imputed) datasets, but the number of
> coefficients varies (between 263-265).
>
> What gives? Why don't all of my models have the same number of
> coefficients?
>
> Thanks in advance!
>
> Best,
> Andrew
>
> BCAR.knots = c(2,15,60,120)
> INAR.knots = c(50,100,200,300)
> bcph.knots = c(7.5,8.5,9.5,10.5)
> htt.knots = c(350,450,550,650)
> bc.prc.C.knots = c(.3,.45,.6,.8)
> phi.knots = c(4.5,5.5,6.5,7.5)
> CEC.knots = c(5,12,19,26)
> soc.knots = c(10,20,30,40)
> sand.knots = c(.2,.4,.6,.8)
> clay.knots = c(.15,.3,.45,.6)
> abslat.knots = c(10,20,30,45)
> lon.knots = c(-50,0,50,125)
>
> dum = as.vector(rep(1,length(trialid)))
>
> doyee = NA
> r.ints = tryCatch(gam(RR ~
> as.factor(pot.trial)
> + as.factor(year)
> + as.factor(crop.legume)
> + as.factor(crop.fruit)
> + as.factor(feedstock)
> + s(trialid,bs="re",by=dum)
> + s(BCAR.imp,bs="cr",k=length(BCAR.knots),by=as.factor(pot.trial))
> +
> s(INAR.imp,bs="cr",k=length(INAR.knots),by=as.factor(crop.legume))
> + s(bcph.imp,bs="cr",k=length(bcph.knots),by=as.factor(year))
> + s(htt.imp,bs="cr",k=length(htt.knots))
> + s(bc.prc.C.imp,bs="cr",k=length(bc.prc.C.knots))
> + s(phi.imp,bs="cr",k=length(phi.knots),by=as.factor(year))
> + s(CEC.imp,bs="cr",k=length(CEC.knots))
> + s(soc.imp,bs="cr",k=length(soc.knots))
> + s(sand.imp,bs="cr",k=length(sand.knots),by=as.factor(year))
> + s(clay.imp,bs="cr",k=length(clay.knots))
> + s(abslat,bs="cr",k=length(abslat.knots))
> + te(INAR.imp,soc.imp,CEC.imp,k=c(4,4,4))
> + te(soc.imp,BCAR.imp,k=c(4,4))
> + te(phi.imp,bcph.imp,k=c(4,4))
> + te(clay.imp,CEC.imp,k=c(4,4))
> + te(htt.imp,bc.prc.C.imp,k=c(4,4),by=as.factor(feedstock))
> ,data=grain.data
> ,knots= list(
> BCAR.imp=BCAR.knots,INAR.imp=INAR.knots,bcph.imp=bcph.knots,htt.imp=htt.knots,bc.prc.C.imp=bc.prc.C.knots,
> phi.imp=phi.knots,CEC.imp=CEC.knots,soc.imp=soc.knots,sand.imp=sand.knots,clay.imp=clay.knots,
> abslat.imp=abslat.knots
> )
> ,method = "REML"
> ,weights = 1/nsame
> ), error=function(e) e, finally=doyee)
> if(inherits(r.ints, "error")) {r.ints=doyee; print("an error happened
> but it got handled.")}
>
>
>
--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603 http://people.bath.ac.uk/sw283
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