phase.sc: Application of the stem-cycle approach to calculate cyclic...

In dendRoAnalyst: A Tool for Processing and Analyzing Dendrometer Data

Application of the stem-cycle approach to calculate cyclic phases and tree-level phase statistics.

Description

This function analyses dendrometer data using the stem-cycle approach (Downs et al. 1999; Deslauriers et al. 2011). It defines three phases: 1) shrinkage, when the dendrometer reading is lower than the previous reading, 2) expansion, when the dendrometer reading is higher than or equal to the previous reading but does not exceed the previous maximum, and 3) increment, when the dendrometer reading is higher than the previous maximum. The function also calculates phase-level statistics and adds the analysed tree identifier to both output tables.

Usage

phase.sc(df, TreeNum, smoothing = NULL)

Arguments

df	Dataframe with the first column containing date and time in the format yyyy-mm-dd HH:MM:SS. It should contain data with constant temporal resolution for best results.
TreeNum	Numeric value indicating the tree to be analysed. For example, TreeNum = 1 refers to the first dendrometer data column after the timestamp column, i.e. df[[2]].
smoothing	Numeric value from 1 to 24 indicating the smoothing window in hours. Default is NULL for no smoothing. The function smooth.Pspline is used for smoothing.

Value

A list of two dataframes. The first dataframe, SC_cycle, contains cyclic phases and their statistics. The second dataframe, SC_phase, contains the timestamp-level phase assignment. Both tables include a Tree column derived from the dendrometer column selected by TreeNum.

The contents of SC_cycle are:

Columns		Description
Tree		Analysed dendrometer series name derived from df.
Phases		Cyclic phases. 1, 2, and 3 for shrinkage, expansion, and increment respectively.
Start		Time when the corresponding phase starts.
End		Time when the corresponding phase ends.
Duration_h		Duration of the corresponding phase in hours.
Duration_m		Duration of the corresponding phase in minutes.
Magnitude		Radial/circumferential change during the corresponding phase in millimeters.
rate		Rate of radial/circumferential change in micrometers per hour.
DOY		Day of year for the corresponding phase.

The contents of SC_phase are:

Columns		Description
Tree		Analysed dendrometer series name derived from df.
TIME		Timestamp.
dm		Dendrometer measurement of the selected tree.
Phases		Timestamp-level phase assignment.

References

Deslauriers A, Rossi S, Turcotte A, Morin H, Krause C (2011) A three-step procedure in SAS to analyze the time series from automatic dendrometers. Dendrochronologia 29:151-161. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.dendro.2011.01.008")}

Downes G, Beadle C, Worledge D (1999) Daily stem growth patterns in irrigated Eucalyptus globulus and E. nitens in relation to climate. Trees 14:102-111. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/PL00009752")}

Examples

library(dendRoAnalyst)
data(gf_nepa17)
sc.phase <- phase.sc(df = gf_nepa17, TreeNum = 1, smoothing = 12)
head(sc.phase$SC_cycle, 10)
head(sc.phase$SC_phase, 10)

dendRoAnalyst documentation built on Oct. 2, 2026, 9:06 a.m.