rcs: Regional Curve Standardization

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/rcs.R

Description

Detrend multiple ring-width series simultaneously using a regional curve.

Usage

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rcs(rwl, po, nyrs = NULL, f = 0.5, biweight = TRUE, ratios = TRUE,
    rc.out = FALSE, make.plot = TRUE, ..., rc.in = NULL, check = TRUE)

Arguments

rwl

a data.frame with series as columns and years as rows such as that produced by read.rwl

po

a data.frame containing two variables. Variable one (series in the example below) gives the series ID as either characters or factors. These must exactly match colnames(rwl). Variable two (pith.offset in the example below) must be integral values and give the years from the beginning of the core to the pith (or center) of the tree. The minimum value is 1.

nyrs

a number giving the rigidity of the smoothing spline, defaults to 0.1 of length of the maximum cambial age (i.e., the length of the regional curve) if nyrs is NULL.

f

a number between 0 and 1 giving the frequency response or wavelength cutoff. Defaults to 0.5.

biweight

logical flag. If TRUE then a robust mean is calculated using tbrm.

ratios

logical flag. If TRUE (the default) then indices are calculated by division, if FALSE indices are calculated by subtraction.

rc.out

logical flag. Returns the regional curve along with the ring-width indices if TRUE.

make.plot

logical flag. Makes plots of the raw data and regional curve if TRUE.

...

other arguments passed to plot.

rc.in

for internal use.

check

a logical flag. Bypass input checks by setting this to FALSE.

Details

This method detrends and standardizes tree-ring series by calculating an age-related growth curve specific to the rwl. The detrending is the estimation and removal of the tree’s natural biological growth trend. The standardization is done by either dividing each series by the growth trend or subtracting the growth trend from each series to produce units in the dimensionless ring-width index (RWI). The option to produce indices by subtraction is intended to be used on series that have been subject to variance stabilization (e.g., using powt).

The spline approach uses an n-year spline where the frequency response is 0.50 at a wavelength of 10 percent of the maximum cambial age unless specified differently using nyrs and f in the function ffcsaps.

This attempts to remove the low frequency variability that is due to biological or stand effects. See the references below for further details on detrending in general, and Biondi and Qeadan (2008) for an explanation of RCS.

Value

A data.frame containing the dimensionless and detrended ring-width indices with column names, row names and dimensions of rwl. If rc.out is TRUE then a list will be returned with a data.frame containing the detrended ring widths as above and a vector containing the regional curve.

Note

DendroLab website: http://dendrolab.org/

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

Biondi, F. and Qeadan, F. (2008) A theory-driven approach to tree-ring standardization: Defining the biological trend from expected basal area increment. Tree-Ring Research, 64(2), 81–96.

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.

Fritts, H. C. (2001) Tree Rings and Climate. Blackburn. ISBN-13: 978-1-930665-39-2.

See Also

detrend, chron, cms, ffcsaps

Examples

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library(utils)
data(gp.rwl)
data(gp.po)
gp.rwi <- rcs(rwl = gp.rwl, po = gp.po, biweight = TRUE,
              rc.out = TRUE, make.plot = FALSE)
str(gp.rwi)
gp.rwi <- rcs(rwl = gp.rwl, po = gp.po, biweight = TRUE,
              make.plot = TRUE, main = "Regional Curve")

dplR documentation built on Nov. 4, 2018, 3 a.m.