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

In dendRoAnalyst: A Tool for Processing and Analyzing Dendrometer Data

Application of the stem-cycle approach to calculate different phases, their duration and to plot them.

Description

This function analyses the dendrometer data using Stem-cycle approach (Downs et al. 1999; Deslauriers et al. 2011). A function that defines three phases: 1) Shrinkage, when the dendrometer reading is less than previous reading, 2) Expansion, when current reading is more than previous reading and 3) Increment, when current reading is higher than the previous maximum. Additionally, it calculates various statistics for each phase.

Usage

phase.sc(
  df,
  TreeNum,
  smoothing = NULL,
  outputplot = FALSE,
  days,
  cols = c("#fee8c8", "#fdbb84", "#e34a33"),
  phNames = c("Shrinkage", "Expansion", "Increment"),
  cex = NULL,
  cex.axis = NULL,
  cex.legend = NULL,
  font.axis = NULL,
  col.axis = NULL,
  ...
)

Arguments

df	dataframe with 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	numerical value indicating the tree to be analysed. E.g. '1' refers to the first dendrometer data column in df.
smoothing	numerical value from 1 to 12 which indicates the length of the smoothing spline, i.e. 1 = 1 hour and 12 = 12 hours. Default is NULL for no smoothing.The function smooth.Pspline is used for smoothing the data.
outputplot	logical, to plot the phase diagram.
days	array with initial and final day for plotting. E.g. c(a,b), where a = initial date and b = final date.
cols	array with three elements representing colors for shrinking, expanding and increasing phases respectively.
phNames	array with three elements for three different phases. Default is "Shrinkage", "Expansion" and "Increment".
cex	numeric, for the size of the points. Default is NULL.
cex.axis	numeric, for the size of the axis tick labels. Default is NULL.
cex.legend	numeric, for the size of the legend labels. Default is NULL.
font.axis	numeric, for the font type of the axis tick labels. Default is NULL.
col.axis	color names, for the color of the axis tick labels. Default is NULL.
...	other graphical parameters.

Value

A list of two dataframes. The first dataframe SC_cycle with cyclic phases along with various statistics and the second dataframe SC_phase with assigned phases for each data point.The dataframe SC_cycle contains the beginning, end, duration, magnitude and rate of each phase. The dataframe SC_phase contains time and corresponding phases during that time. The contents of SC_cycle are:

Columns		Description
Phase		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.

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. 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. doi: 10.1007/PL00009752

Examples

library(dendRoAnalyst)
data(gf_nepa17)
sc.phase<-phase.sc(df=gf_nepa17, TreeNum=1, smoothing=12, outputplot=TRUE, days=c(150,160))
head(sc.phase[[1]],10)
head(sc.phase[[2]],10)

dendRoAnalyst documentation built on Nov. 16, 2022, 9:07 a.m.