[R] Positive Smoothing in fda package

[Oscar Rueda]

Dear all,
I'm trying to build some fda objects using smooth.pos() from fda package.

Here is what I try:

>X <-c(0.4541139,  0.4802537,  0.5091228,  0.3894931,  2.1512258,
>7.9301281, 62.3876109, 54.1168247, 67.8769904, 91.0670615, 20.0682440)
>basis <- create.bspline.basis(c(-100, 100), 7, 5)
>MDA.fdPar <- fdPar(basis, 2, 0.01)
>MDA.fda.joint <- smooth.pos(argvals=seq(from=-100, to=100, length=11),
>y=X, WfdParobj=MDA.fdPar)
Iter.   PENSSE   Grad Length
0        1780.78      -1780.78
1        1753.525      14.318
2        1749.296      15.0611
3        1747.625      15.3031
4        1739.389      16.6266
5        1737.713      16.8989
6        1729.524      18.3147
7        1727.862      18.5791
8        1719.89      19.9475
9        1718.21      20.2311
10        1710.436      21.6275
11        1708.752      21.9372
12        1702.136      23.2679
13        1700.604      23.1824
14        1697.774      23.8055
15        1696.296      23.944
16        1691.261      25.1618
17        1689.009      25.2832
18        1688.607      25.1727
19        1685.972      25.798
20        1685.278      25.6813Error in if (any(stepi[index] < bot[index]
- cvec[index]) & any(deltac[index] !=  :
  missing value where TRUE/FALSE needed

Changing the parameters of the basis I can get a fit, but I'm trying to
fit thousands of objects and I haven't found a combination that works for
all of them.


Another question is how to fit simultaneously several fda objects. If I do

>X <- cbind(c(3, 5, 6, 7, 9, 5, 6, 4, 8, 3, 11), X)
>MDA.fda.joint <- smooth.pos(argvals=seq(from=-100, to=100, length=11),
>y=X, WfdParobj=MDA.fdPar)



Results for curve 1

Iter.   PENSSE   Grad Length
0        31.6364      -31.6364
1        23.6767      3.1061
2        15.9816      3.0551
3        14.4794      2.4754
4        10.2167      2.2024
5        8.462      1.8876
6        7.1204      1.8919
7        6.7124      1.8915
8        6.5114      1.9193
9        6.3748      1.864
Error: subscript out of bounds

Would someone in the list help me with these errors?

Cheers,
Oscar


Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Caldas Lab, Breast Cancer Functional
Genomics.
University of Cambridge. Cancer Research UK Cambridge Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England

Please note that my email address will be changing to:
Oscar.Rueda at cruk.cam.ac.uk