Thanks, David! That makes sense. I shall re-read the manual page again. Regards,
Mike Nielsen On Wed, Feb 27, 2013 at 12:19 PM, David Winsemius <dwinsem...@comcast.net>wrote: > > On Feb 27, 2013, at 6:39 AM, Mike Nielsen wrote: > > > Hi r-helpers. > > > > Please forgive my ignorance, but I would like to plot a smoothing spline > > (smooth.spline) from package "stats", and show the knots in the plot, > and I > > can't seem to figure out where smooth.spline has located the knots (when > I > > use nknots). Unfortunately, I don't know a lot about splines, but I know > > that they provide me an easy way to estimate the location of local maxima > > and minima on varying time-scales (number of knots) in my original data. > > > > I see there is a fit$knot, but it's not clear to me what those values > are: > > for some reason I had expected that they would be contained in my > original > > y values, but they're not. > > It appears they are in the range of [0-1] and the ss$fit$min and > ss$fit$range provide the scaling data (.... for the x-values rather than > the y-values): > > > unique(ss$fit$knot) > [1] 0.00000000 0.04095904 0.08291708 0.12487512 0.16583417 0.20779221 > 0.24975025 0.29070929 > [9] 0.33266733 0.37462537 0.41658342 0.45754246 0.49950050 0.54145854 > 0.58241758 0.62437562 > [17] 0.66633367 0.70829171 0.74925075 0.79120879 0.83316683 0.87412587 > 0.91608392 0.95804196 > [25] 1.00000000 > > I would think that in your case with x0 being 0 you could just use > ss$fit$range*unique(ss$fit$knot) as your knot positions. In the more > geneneral case you would need to add ss$fit$min. I tried confirming this > hunch by looking "statiscal Models in S", inMASSe4, and at the R code but > the R code calls a FORTRAN routine, so you would need to pull the source to > confirm. > > -- > David. > > > I tried generating nknots equally spaced points > > in my x, but when I plotted the points that corresponded to my original y > > values at those equally-spaced x values, I found that the spline did not > > pass through them, which, perhaps naively, I thought it might. > > > > Also, the manual says that yin comprises "the y values used at the > unique y > > values" -- should this read "at the unique x values"? > > > > Could someone kindly point to a resource where I can get a slightly > fuller > > explanation? I looked at the code for smooth.spline, but can't readily > > follow it. > > > > Here's a toy example: > > > >> x<-seq(from=0,to=4*pi,length=1002) > >> y<-sin(x) > >> ss<-smooth.spline(x,y=y,all.knots=F,nknots=25) > >> ss > > Call: > > smooth.spline(x = x, y = y, all.knots = F, nknots = 25) > > > > Smoothing Parameter spar= -0.4573636 lambda= 1.006117e-09 (14 > iterations) > > Equivalent Degrees of Freedom (Df): 26.99935 > > Penalized Criterion: 3.027077e-06 > > GCV: 3.190666e-09 > >> str(ss) > > List of 15 > > $ x : num [1:1002] 0 0.0126 0.0251 0.0377 0.0502 ... > > $ y : num [1:1002] 2.88e-05 1.26e-02 2.51e-02 3.77e-02 5.02e-02 ... > > $ w : num [1:1002] 1 1 1 1 1 1 1 1 1 1 ... > > $ yin : num [1:1002] 0 0.0126 0.0251 0.0377 0.0502 ... > > $ data :List of 3 > > ..$ x: num [1:1002] 0 0.0126 0.0251 0.0377 0.0502 ... > > ..$ y: num [1:1002] 0 0.0126 0.0251 0.0377 0.0502 ... > > ..$ w: num [1:1002] 1 1 1 1 1 1 1 1 1 1 ... > > $ lev : num [1:1002] 0.2238 0.177 0.1399 0.1111 0.0891 ... > > $ cv.crit : num 3.19e-09 > > $ pen.crit: num 3.03e-06 > > $ crit : num 3.19e-09 > > $ df : num 27 > > $ spar : num -0.457 > > $ lambda : num 1.01e-09 > > $ iparms : Named int [1:3] 1 0 14 > > ..- attr(*, "names")= chr [1:3] "icrit" "ispar" "iter" > > $ fit :List of 5 > > ..$ knot : num [1:31] 0 0 0 0 0.041 ... > > ..$ nk : num 27 > > ..$ min : num 0 > > ..$ range: num 12.6 > > ..$ coef : num [1:27] 2.88e-05 1.72e-01 5.19e-01 9.04e-01 1.05 ... > > ..- attr(*, "class")= chr "smooth.spline.fit" > > $ call : language smooth.spline(x = x, y = y, all.knots = F, nknots = > > 25) > > - attr(*, "class")= chr "smooth.spline" > >> > > > > Many thanks! > > > > > > Regards, > > > > Mike Nielsen > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > David Winsemius > Alameda, CA, USA > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
