ffcsaps {dplR}

Smoothing Spline with User-Specified Rigidity and Frequency Cutoff

Description

Applies a smoothing spline to y with rigidity determined by two parameters: frequency response f at a wavelength of nyrs years.

Usage

ffcsaps(y, x = seq_along(y), nyrs = length(y)/2, f = 0.5)

Arguments

y

a numeric vector, typically a tree-ring series.

x

a numeric vector with the same length as y, typically giving the years of y.

nyrs

a number greater than 1, affecting the rigidity of the spline. When f is kept constant, a larger nyrs produces a more rigid spline. Defaults to length(y)/2.

f

a number between 0 and 1 giving the frequency response at a wavelength of nyrs years. When nyrs is kept constant, a smaller f produces a more rigid spline: At one extreme, f = 0 causes the function to return the least-squares straight line fit to the data. At the other extreme, f = 1 results in the natural spline, i.e. the function outputs y. The default value is 0.5.

Details

This applies a smoothing spline similar to the spline applied in most dendrochronological software. See references for more information.

In dplR in version 1.7.3 the function caps was introduced. This essentially replaces ffcsaps for most uses. Where ffcsaps is written entirely in R, caps is a wrapper for a Fortran subroutine from ARSTAN that is thousands of times faster.

Value

A filtered vector.

Note

DendroLab website: https://dendrolaborg.wordpress.com/

Author(s)

Code provided by DendroLab based on programming by F. Qeadan and F. Biondi, University of Nevada Reno, USA and adapted for dplR by Andy Bunn. Patched and improved by Mikko Korpela.

References

Cook, E. R. and Kairiukstis, L. A., editors (1990) Methods of Dendrochronology: Applications in the Environmental Sciences. Springer. ISBN-13: 978-0-7923-0586-6.

Cook, E. R. and Peters, K. (1981) The Smoothing Spline: A New Approach to Standardizing Forest Interior Tree-Ring Width Series for Dendroclimatic Studies. Tree-Ring Bulletin, 41, 45-53.

See Also

caps, detrend

Examples

library(graphics)
## Use first series from the Mesa Verde data set
data(co021)
series <- co021[, 1]
series <- series[!is.na(series)]
plot(series, type = "l", ylab = "Ring Width (mm)", col = "grey")
lines(ffcsaps(series, nyrs = 10), col = "red", lwd = 2)
lines(ffcsaps(series, nyrs = 100), col = "green", lwd = 2)
## nyrs defaults to 0.5*length(series) = 347
lines(ffcsaps(series), col = "blue", lwd = 2)
legend("topright",
       c("Series", "nyrs=10", "nyrs=100",
         paste("Default nyrs (", length(series) / 2, ")", sep="")),
       fill=c("grey", "red", "green", "blue"))

## Compare to caps
all.equal(caps(series),ffcsaps(series))

## Note behavior when NA is encountered and
## take appropriate measures as demonstrated above
y <- c(NA,NA,rnorm(100))
ffcsaps(y)