pointer.rgc: Calculate pointer years using the relative growth change...

View source: R/pointer.rgc.R

pointer.rgcR Documentation

Calculate pointer years using the relative growth change method

Description

The function calculates event and pointer years on a data.frame with tree-ring series using the relative growth change method, described as abrupt growth change method in Schweingruber et al. (1990). This method relates tree growth in year i to the average growth of n preceding years. Thresholds for event- and pointer-year calculations can be adjusted.

Usage

pointer.rgc(data, period = NULL, nb.yrs = 4, rgc.thresh.pos = 60, rgc.thresh.neg = 40, 
            series.thresh = 75, make.plot = FALSE)

Arguments

data

a data.frame with tree-ring series (raw or detrended) as columns and years as rows (e.g., output of read.rwl or detrend of package dplR).

period

a vector specifying the start and end year of the analysis. Defaults to the full period covered by the data.

nb.yrs

an integer specifying the number of preceding years to be used in calculating relative growth changes. Defaults to 4.

rgc.thresh.pos

a numeric specifying the threshold above which a relative growth change (in percentage) for a specific tree and year is considered a positive event year. Defaults to 60.

rgc.thresh.neg

a numeric specifying the threshold below which a relative growth change (in percentage) for a specific tree and year is considered a negative event year. Defaults to 40.

series.thresh

a numeric specifying the minimum percentage of trees that should display a positive (or negative) event year for that year to be considered as positive (or negative) pointer year. Defaults to 75.

make.plot

a logical specifying whether a bar plot, showing mean relative growth changes, should be created. Pointer years are indicated with dark-gray bars. Defaults to FALSE.

Details

The function calculates the ratio of tree growth in year t and the average growth of n preceding years for individual trees. Resulting relative growth changes are used to identify event years for trees, and these event years to define pointer years for the site.

Following Schweingruber et al. (1990), nb.yrs, rgc.thresh.pos, rgc.thresh.neg and series.thresh are set to 4, 60, 40 and 75 respectively, meaning that a positive or negative pointer year will be defined when at least 75% of the tree-ring series display an event year with a growth increase or decrease of at least 60% or 40%, respectively, relative to the average growth in the four preceding years. Depending on the sensitivity of the tree-ring series, the thresholds rgc.thresh.pos and rgc.thresh.neg may be adjusted (e.g., lowered for more complacent series; Jetschke et al. 2019).

Note that the resulting time series are truncated by nb.yrs at the beginning inherent to the calculation method.

Value

The function returns a list containing the following components:

rgc

a matrix with relative growth changes for individual tree-ring series

EYvalues

a matrix indicating positive (1), negative (-1) and non-event years (0) for individual tree-ring series

out

a data.frame containing the following columns: year - time stamp, nb.series - number of series considered, perc.pos - percentage of trees showing a positive event year, perc.neg - percentage of trees showing a negative event year, nature - number indicating whether the year is a positive (1), negative (-1) or no pointer year (0), dev_mean - mean growth deviation in percentage over the available series for each year, and dev_sd - standard deviation of the growth deviation for each year

spec.param

a data.frame specifying the arguments used in the calculation

Author(s)

Marieke van der Maaten-Theunissen and Ernst van der Maaten.

References

Jetschke, G., van der Maaten, E. and van der Maaten-Theunissen, M. (2019) Towards the extremes: A critical analysis of pointer year detection methods. Dendrochronologia 53: 55-62.

Schweingruber, F.H., Eckstein, D., Serre-Bachet, F. and Bräker, O.U. (1990) Identification, presentation and interpretation of event years and pointer years in dendrochronology. Dendrochronologia 8: 9-38.

In writing the function, the code of the dplR function pointer (Pierre Mérian) was used as a reference.

Examples

## Calculate pointer years on tree-ring series
data(s033)
py1 <- pointer.rgc(s033)
head(py1$out)

## Calculate pointer years with user-defined arguments
data(s033)
py2 <- pointer.rgc(s033, period = c(1950,2010), nb.yrs = 5, rgc.thresh.pos = 50,
                   rgc.thresh.neg = 50, series.thresh = 50, make.plot = TRUE)
head(py2$out)


pointRes documentation built on May 8, 2022, 1:05 a.m.