res.comp: Calculate resilience components: resistance, recovery,...

Description Usage Arguments Details Value Author(s) References Examples

View source: R/res.comp.R

Description

The function calculates resilience components on a data.frame of tree-ring series after Lloret et al. (2011), useful to analyze growth of individual trees prior, during and after extreme events / disturbances. The component 'resistance' is conceptually identical to 'abrupt growth changes' as described in Schweingruber et al. (1990). To identify negative event and pointer years, thresholds can be set as for the function pointer.rgc. 'Recovery' is the ability of tree growth to recover after disturbance, whereas 'resilience' reflects the ability of trees to reach pre-disturbance growth levels. Weighting of the resilience by the experienced growth reduction results in 'relative resilience'.

Usage

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res.comp(data, nb.yrs = 4, post = NULL, res.thresh.neg = 40, series.thresh = 75)

Arguments

data

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

nb.yrs

an integer specifying the number of years for pre- and (or) post-disturbance periods to be considered in calculating resilience components. Defaults to 4.

post

an integer specifying the number of years for post-disturbance periods. Defaults to nb.yrs. Optional argument in case pre- and post-period lengths should differ.

res.thresh.neg

a numeric specifying the threshold below which the resistance, expressed as a percentual change (i.e. relative growth reduction), is considered a negative event year for individual trees and years. Defaults to 40.

series.thresh

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

Details

The function calculates the resilience components resistance, recovery, resilience and relative resilience as described in Lloret et al. (2011). A threshold on resistance can be set to identify negative event years for trees (cf. rgc.thresh.neg in function pointer.rgc), which are used to define negative pointer years for the site.

If nb.yrs, res.thresh.neg and series.thresh are set to 4, 40 and 75 respectively, a negative pointer year will be defined when at least 75% of the tree-ring series display an event year with resistance values indicating a growth decrease of at least 40%, relative to the average growth in the 4 preceding years. The output provides the resilience components for all possible years, as well as for the selected pointer years separately.

Note that the resulting time series are truncated at both ends by the number of years specified in nb.yrs (and post), inherent to the calculation methods.

Value

#' The function returns a list containing the following components:

resist

a matrix with resistance values (i.e. relative growth changes) for individual tree-ring series

EYvalues

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

recov

a matrix with recovery values for individual tree-ring series

resil

a matrix with resilience values for individual tree-ring series

rel.resil

a matrix with relative resilience values for individual tree-ring series

out

a data.frame containing the following columns:

year - time stamp

nb.series - number of series considered

perc.neg - percentage of trees showing a negative event year

nature - number indicating whether the year is a negative (-1) or no pointer year (0)

resist_mean - mean resistance as percentual change over the available series

resist_sd - standard deviation of the resistance

recov_mean - mean recovery as percentual change over the available series

recov_sd - standard deviation of the recovery

resil_mean - mean resilience as percentual change over the available series

resil_sd - standard deviation of the resilience

rel.resil_mean - mean relative resilience calculated over the available series

rel.resil_sd - standard deviation of the relative resilience

out.select

a data.frame containing a subset of rows from out that provide all statistics for years that were identified as negative pointer years

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

Lloret, F., Keeling, E.G. and Sala, A. (2011) Components of tree resilience: effects of successive low-growth episodes in old ponderosa pine forests. Oikos 120: 1909-1920.

Schweingruber, F.H., Eckstein, D., Serre-Bachet, F. and Br<c3><a4>ker, O.U. (1990) Identification, presentation and interpretation of event years and pointer years in dendrochronology. Dendrochronologia 8: 9-38.

Examples

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## Calculate resilience components on tree-ring series
data(s033)
res <- res.comp(s033, nb.yrs = 4, post = NULL, res.thresh.neg = 40, series.thresh = 75)
res$out
res$out.select

pointRes documentation built on May 1, 2019, 8:45 p.m.