Package ‘detrendeR’

February 19, 2015

Type Package
Title Start the detrendeR Graphical User Interface (GUI)
Version 1.0.4
Date 2012-10-19
Author Filipe Campelo
Maintainer Filipe Campelo <[email protected]>
Description Simple GUI to perform some standard tree-ring analyses.
Depends tcltk, dplR
License GPL (>= 2)
Repository CRAN
Date/Publication 2012-10-22 10:17:42
NeedsCompilation no

R topics documented:
detrendeR-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
detrender . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
EPS.value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
RwlInfo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Index 8

detrendeR-package detrendeR - A Graphical User Interface to process and visualize tree-

ring data using R

Description
This packages contains a Graphical User Interface to perform some standard tree-ring analyses.

Details

1
2 detrender

Package: detrendeR
Type: Package
Version: 1.0.4
License: GPL

Author(s)

Filipe Campelo <[email protected]>

References

Bunn, A. 2008. A dendrochronology program library in R (dplR). Dendrochronologia 26:115-124.

Bunn, A. 2010. Statistical and visual crossdating in R using library. Dendrochronologia 28:251-
258.
Cook, E.R., Kairiukstis, L.A. 1990. Methods of Dendrochronology: applications in the environ-
mental sciences. Kluwer Academic Publishers.
Fox, J. 2005. The R Commander: A basic-statistics graphical user interface to R. Journal of Statis-
tical Software 14:142.
Thioulouse, J., Dray, S. 2009. ade4TkGUI: ade4 Tcl/Tk Graphical User Interface. R package
version 0.25. http://CRAN.R-project.org/package=ade4TkGUI.

Examples
detrender()

detrender R detrendeR

Description

Start a Graphical User Interface to perform tree-ring analyses.

Usage

detrender()
detrender 3

Details

This function starts a Graphical User Interface (GUI). The window of the detrendeR GUI contains
the menu bar, and three toolbars below, each comprising several buttons. The three toolbars, from
up to down, are aimed at: i) managing the data set of tree-ring series to be processed; ii) provide
general information about the active data set; iii) apply the statistical functions related to detrending
and chronology building. The order of the different bars corresponds to the consecutive steps the
user should follow to build a chronology.
The File menu provides functions to read and save files, to exit detrendeR and to Quit R: "Read file"
allows to read a data file and store the information in a new dataset. The option "clipboard" can be
used to read a data table just copied from a spreadsheet program (like Excel). The items "Read rwl"
and "Read crn" open a dialog box that allows to read data files in the Tucson measurement (*.rwl)
and in the Tucson chronology format (*.crn). The items "Save rwl", "Save crn" and "Save csv"
allows to save the active dataset into different formats (*.rwl, *.crn, *.csv). "Save Workspace..."
saves the current workspace to the specified file. The saved objects can be read back from the file
later by using the function load. "Quit detrendeR" closes the detrendeR window. "Quit R" opens a
dialog box to ask if the environment should be saved before terminate the current R session.
Using the File menu, datasets can be opened from different files, and a large variety of file types
are supported, including Tucson measurement (*.rwl) and Tucson chronology format (*.crn). To
read a data file or data from the clipboard into R, select File -> Read file. The default name of the
dataset is the name of the file to be opened, but the user is allowed to change it. In R the names of
datasets must start with a letter and consist entirely of letters, digits, periods (.) and underscores (_).
The user should also remember that R is case-sensitive and embedded blanks are not allowed in a
dataset name. The active dataset can also be saved into several formats (*.rwl, *.crn, *.csv) using
the items Save rwl, Save crn and Save csv in the File menu.
The Tools menu allows to define settings and to launch detrendeR in batch mode: "Define settings"
brings up a dialog box, where the user can use this dialog box to define tree mask, type of detrending
and other settings. "Batch mode" releases a dialog box identical to the one used to define settings,
but in this case the user can choose the files to be processed by pressing the button "Ok".
The active data set is shown in the first toolbar, immediately below the menu bar. This bar has two
buttons, the first indicating the name of the active dataset, or the label "<Please select a dataset>" or
"<No active dataset>" if no dataset is selected. The user can load several datasets into memory, and
change the active dataset just by clicking the flat button with the active dataset name. However, at
any given time, only one dataset is active. Once selected, the subsequent functions are only applied
to the active dataset. The second button, Delete, allows the user to remove the active dataset and/or
other datasets from the R environment.
The second toolbar contains four buttons related to general information about the active dataset.
The "Information" button displays the series identification, first and last year, and length of the
series. The button "TreeIds" provides the tree mask of the active dataset. "Missing rings" indicates
the existence of missing rings within the series. The last button "RwlInfo" computes some common
descriptive statistics on individual series, such as the correlation with the master chronology, mean,
median, standard deviation, mean sensitivity and first-order autocorrelation, and prints them to the
R editor window, using the RwlInfo function.
The lowest toolbar constitutes the core of the program, and contains four buttons that brings up dif-
ferent dialog boxes providing a variety of mathematical and statistical functions for trend removal,
chronology building and measuring the quality of a chronology.
4 detrender

The button "Detrending" extends a drop-down menu with two additional commands: "1 step" and
"2 steps", that open the Detrending options dialog box window. In the first case, a single detrending
method is applied to the selected dataset and two new datasets are added to the R environment, the
sufixes ".cv1" and ".in1" are placed after the name of the original dataset to identify the curve and
the index datasets, respectively. In the second case, four new datasets are produced by a two-step
detrending, having the suffixes ".cv1", ".cv2", ".in1" and ".in2".
detrendeR provides four different detrending methods: modified negative exponential, cubic smooth-
ing spline, simple linear regression and through the mean. The spline algorithm used was the
Andrew Bunn’s fsscap function from the dplR package (Bunn, 2008). In the dialog box window
"Detrending options" the checkbox "Interactive detrending" allows the user to verify how well the
detrending curve fits each series, and use different methods for different series. The smoothing
spline has the parameter ’bandwidth’ to modify the trend elimination. Large bandwidths lead to a
stiff trend line while a small bandwidth adapts smoothly to the time series, the effect of different
bandwidth can be easily observed by applying the interactive detrending.
The interactive detrending window can be closed at any time by pressing the button "Close without
saving" or the button "Close and Save changes". The second detrending options have the same
options as explained for the first detrending. The statistics of the detrended series are displayed in
the console, by applying the RwlInfo function to the index series.
The button "AR model" can be used to remove the autocorrelation from each series, using the
R function ar. The maximum order to be applied during the univariate autoregressive process is
chosen by the user, but the selected order for each series is determined by the first minimum Akaike
Information Criterion. The resulting series without persistence will be stored into a new dataset,
having the suffix ".res" placed after the name of the input dataset by default.
The button "Chrono" combines tree-ring index or raw-width series into a mean value chronology
by averaging each year using an arithmetic mean or a biweight robust estimate of the mean. If
the series used to produce the chronology are detrended (standardized) a Standard chronology will
be produced. A Residual or a Prewhitened chronology is produced when the averaged series are
residuals from the autoregressive model of the detrended series. Usually, this chronology shows
a strong signal without persistence, however if some persistence remains, an autoregressive model
can be applied to remove it.
The last button, "EPS", produces several statistics that indicate the common signal to all series
using the mean correlation between trees (rbt) and the Expressed Population Signal (EPS). By
pressing this button the EPS analysis dialog box is launched and allows performing three analyses
simultaneously, using the EPS.value function, a changed version of the rwi.stats function from the
dplR package (Bunn, 2008). This function provides a variety of statistics, such as the mean within-
and between-tree correlation (rwt, rbt) and the EPS (for a better explanation of the algorithm see
Cook et al., 1990). In the Common interval analysis only the period where all series are represented
are used to calculate the rbt and EPS values. The user can choose a certain time span and determine
the rbt and EPS values for that period. The output is printed in the R console editor. The analysis
can also be performed for a specified length ("Window length") and slide this window with regular
steps ("Lag").
There are two ways to end the detrendeR session. The user can select File -> Quit detrendeR and
will be asked whether the R workspace should be saved. The R session will be kept working and
the detrendeR can be started later by writing the command detrender() in the R console editor. The
user can also select File -> Quit R and, in this case, the program will ask whether to save the R
workspace (i.e., the data that R keeps in memory). This allows the user to maintain different saved
workspaces for different projects.
EPS.value 5

References
Bunn, A. 2008. A dendrochronology program library in R (dplR). Dendrochronologia 26:115-124.
Bunn, A. 2010. Statistical and visual crossdating in R using library. Dendrochronologia 28: 251-
258.
Cook, E.R., Kairiukstis, L.A. 1990. Methods of Dendrochronology: applications in the environ-
mental sciences. Kluwer Academic Publishers.
Fox, J. 2005. The R Commander: A basic-statistics graphical user interface to R. Journal of Statis-
tical Software 14:142.
Thioulouse, J., Dray, S. 2009. ade4TkGUI: ade4 Tcl/Tk Graphical User Interface. R package
version 0.25. http://CRAN.R-project.org/package=ade4TkGUI.

Examples
detrender()

EPS.value Computes general statistics on ring-width series.

Description
This function computes general statistics on a data.frame of ring-width series. This function is a
changed version of the Andrew Bunn’s rwi.stats function from the dplR package (Bunn, 2008)

Usage
EPS.value(rwl, stc = c(5,2,1))

Arguments
rwl a data.frame of ring widths
stc a vector of three integers giving the Site-Tree-Core mask. Defaults to c(5,2,1)
and these three values should sum to eigth. The stc[1] gives the number of
characters used to define the site code, stc[2] defines the tree mask and the core
ids is given by the last element of the vector stc[3].

Value
A data.frame with the following values: ’start’, ’end’, ’tree’, ’core’, ’n.tot’, ’n.wt’, ’n.bt’,’r.tot’,’r.wt’,
’r.bt’, ’c.eff’, ’r.eff’, and ’eps’.

start the first year.

end the last year.
tree the number of trees.
core the number of cores.
6 RwlInfo

n.tot the number of unique combinations of the input series (i.e., 1/2*n*[n-1]).
n.wt the total number of unique combinations of the within-tree series.
n.bt the total number of unique combinations of the between-tree series.
r.tot the mean of all correlation between different cores.
r.wt the mean of correlations between series from the same tree over all trees.
r.bt the mean interseries correlation between all series from different trees.
c.eff the effective number of cores.
r.eff the effective signal calculated as [rbar.bt / (rbar.wt + (1-rbar.wt) / c.eff)].
eps the expressed population signal.

References
Bunn, A. 2008. A dendrochronology program library in R (dplR). Dendrochronologia 26:115-124.
Cook, E.R., Kairiukstis, L.A. 1990. Methods of Dendrochronology: applications in the environ-
mental sciences. Kluwer Academic Publishers.

Examples

data(co021, package="dplR")

years<-as.integer(rownames(co021))
co021.subset<-(subset(co021, subset=years>=1900 & years<=1950))
co021.subset<-co021.subset[,-c(28,30,31)] ## to remove the following series "645232","646107" and "646118"

EPS.value(co021.subset, stc=c(0,8,0))

RwlInfo Computes some common statistics on individual ring-width series.

Description
This function computes some common descriptive statistics on individual series, such as the correla-
tion with the master chronology, mean, median, standard deviation, mean sensitivity and first-order
autocorrelation, and the output can be printed to the R editor window

Usage
RwlInfo(rwl, print=TRUE, chrono=NULL)

Arguments
rwl a data.frame with ring-width series as columns and years as rows.
print logical flag. If TRUE the output is printed in the console.
chrono If NULL the function computes a mean chronology using all series presented in
the data.frame (rwl).
RwlInfo 7

Value
A data.frame with the descriptive statistics for each series.

References
Bunn, A. 2008. A dendrochronology program library in R (dplR). Dendrochronologia 26:115-124.

Examples

data(co021, package="dplR")
RwlInfo(co021)
RwlInfo(co021, print=FALSE)->co021.info
write(co021.info)
Index

∗Topic package
detrendeR-package, 1

detrendeR (detrendeR-package), 1
detrender, 2
detrendeR-package, 1

EPS.value, 5

RwlInfo, 6