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dplR

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",
                   "ModHugershoff"),
        nyrs = NULL, f = 0.5, pos.slope = FALSE,
        constrain.nls = c("never", "when.fail", "always"),
        verbose = FALSE, return.info = FALSE,
        wt, span = "cv", bass = 0, difference = FALSE)

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", "ModHugershoff")`. 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`.
`f`	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"` and `"ModHugershoff"`. If `FALSE` the line will be horizontal.
`constrain.nls`	a `character` string which controls the constraints of the `"ModNegExp"` model and the `"ModHugershoff"`. 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’.
`wt`	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`.
`difference`	a `logical` flag. Compute residuals by substraction if TRUE, otherwise use division.

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.

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 four parts:

`series`	the main result described above (`data.frame` or list of data.frames)
`curves`	the curve or line used to detrend `series`. Either a `data.frame` or a 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`).

Note

This function uses the foreach looping construct with the %dopar% operator. For parallel computing and a potential speedup, a parallel backend must be registered before running the function. If verbose is TRUE, parallel computation is disabled.

Author(s)

Andy Bunn. Improved by Mikko Korpela.

Examples

library(utils)
data(ca533)
## Detrend using modified exponential decay. Returns a data.frame
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
## Detrend using a slines on power transformed data and compute
## residuals via subtraction
ca533.rwi <- detrend(rwl = powt(ca533), method = "Spline",
                     difference = TRUE)

## Detrend using modified Hugershoff curve and return info on the model
## fits. Returns a list with: series, curves, modelinfo and data.info
data(co021)
co021.rwi <- detrend(rwl = co021, method = "ModHugershoff",
                     return.info=TRUE)

## 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

## End(Not run)

dplR

Dendrochronology Program Library in R

v1.7.2

GPL (>= 2)

Authors

Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, cph, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb], Klesse Stefan [ctb], Frank David [ctb], Visser Ronald [ctb]

Initial release

2021-01-27

detrend

Description

Usage

Arguments

Details

Value

Note

Author(s)

See Also

Examples

dplR

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