detrend: Detrend Multiple Ring-Width Series Simultaneously

Description

This is a wrapper for detrend.series to detrend many ring-width series at once.

Usage

detrend(rwl, y.name = names(rwl), make.plot = FALSE,
        method = c("Spline", "ModNegExp", "Mean", "Ar", "Friedman"),
        nyrs = NULL, f = 0.5, pos.slope = FALSE,
        constrain.modnegexp = c("never", "when.fail", "always"),
        verbose = FALSE, return.info = FALSE,
        wt, span = "cv", bass = 0)

Arguments

rwl

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

y.name

a character vector of length(ncol(rwl)) that gives the ID of each series. Defaults to the column names of rwl.

make.plot

a logical flag. Makes plots of the raw data and detrended data if TRUE. See details below.

method

a character vector to determine the detrending methods. See details below. Possible values are all subsets of c("Spline", "ModNegExp", "Mean", "Ar", "Friedman"). Defaults to using all the available methods.

nyrs

a number giving the rigidity of the smoothing spline, defaults to 0.67 of series length if nyrs is NULL.

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

pos.slope

a logical flag. Will allow for a positive slope to be used in method "ModNegExp". If FALSE the line will be horizontal.

constrain.modnegexp

a character string which controls the constraints of the "ModNegExp" model. See detrend.series for further details.

verbose

logical. Write out details?

return.info

a logical flag. If TRUE, details about models and data will be added to the return value. See ‘Value’.

a numeric vector of case weights for method "Friedman". The default means equals weights.

span

a numeric value controlling method "Friedman", or "cv" (default) for automatic choice by cross-validation. See supsmu.

bass

a numeric value controlling the smoothness of the fitted curve in method "Friedman". See supsmu.

Value

If one detrending method is used, a data.frame containing the dimensionless detrended ring widths with column names, row names and dimensions of rwl. If more methods are used, a list with ncol(rwl) elements each containing a data.frame with the detrended ring widths in each column.

If return.info is TRUE, the return value is a list with three parts:

series

the main result described above (data.frame or list of data.frames)

model.info

Information about the models corresponding to each output series. A list with one element for each column of rwl. See detrend.series (‘Value’, model.info) for a description of the contents.

data.info

Information about the input series. A list with one element for each column of rwl. See detrend.series (‘Value’, data.info).

Details

See detrend.series for details on detrending methods. Setting make.plot = TRUE will cause plots of each series to be produced. These could be saved using Devices if desired.

Examples

Run this code

# NOT RUN {
library(utils)
data(ca533)
## Detrend using modified exponential decay. Returns a data.frame
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")

# }
# NOT RUN {
library(grDevices)
## Detrend using all methods. Returns a list
ca533.rwi <- detrend(rwl = ca533)
## Save a pdf of all series
fname <- tempfile(fileext=".pdf")
print(fname) # tempfile used for output
pdf(fname)
ca533.rwi <- detrend(rwl = ca533, method = c("Spline", "ModNegExp"),
                     make.plot = TRUE)
dev.off()

unlink(fname) # remove the file
# }