phase.zg: Application of the zero-growth approach to calculate...

In dendRoAnalyst: A Tool for Processing and Analyzing Dendrometer Data

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

Description

This function analyses data using the zero-growth approach. Initially, it divides the data in two categories: 1) Tree water deficiency (TWD), i.e. the reversible shrinkage and expansion of the tree stem when the current reading is below the previous maximum and, 2) Increment (GRO), the irreversible expansion of the stem when the current reading is above the previous maximum. Then it calculates the TWD for each data point as the difference between the modelled "growth line" and the observed measurement. See Zweifel et. al.,(2016) for details.

The severity value of each TWD was introduced in version 0.1.4 of the package. This value is calculated as product of angle of depression of the TWD period and its duration in days.

Usage

phase.zg(
  df,
  TreeNum,
  outputplot,
  days,
  linearCol = "#2c7fb8",
  twdCol = "#636363",
  twdFill = NULL,
  twdFillCol = "#f03b20",
  xlab = "DOY",
  ylab1 = "Stem size variation [mm]",
  ylab2 = "TWD [mm]",
  twdYlim = NULL,
  cex.axis = NULL,
  cex.lab = NULL,
  font.lab = NULL,
  col.lab = 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.
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.
linearCol	color for the modelled curve.
twdCol	color for the TWD curve.
twdFill	filling method for the area under the TWD curve. Equivalent to density argument of the polygon function in the graphics package of R. Default value is NULL.
twdFillCol	color to fill the area under the TWD curve.
xlab	string, x label of the plot.
ylab1	string, y label of the upper plot.
ylab2	string, y label of the lower plot.
twdYlim	numeric, to define the limit of the y-axis of the lower plot. Default is NULL, which automatically adjusts the y-axis limit.
cex.axis	numeric, for the size of the axis tick labels. Default is NULL.
cex.lab	numeric, for the size of the axis labels. Default is NULL.
font.lab	numeric, for the font type of the axis labels. Default is NULL.
col.lab	color names, for the color of the axis 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.

Value

A list of two dataframes. The first dataframe ZG_cycle contains the cyclic phases along with various statistics and the second dataframe ZG_phase with assigned phases for each data point.The contents of ZG_cycle are:

Columns		Description
DOY		Day of year for the corresponding phase.
Phase		TWD for tree water deficit and GRO for irreversible expansion.
start		Time when the corresponding phase starts.
end		Time when the corresponding phase ends.
Duration_h		Duration of the corresponding phase in hours.
Magnitude		Radial/circumferential change in millimeters.
rate		Rate of Radial/circumferential change in micrometers per hour.
Max.twd		Maximum TWD recorded for the corresponding TWD phase.
twd.severity		The severity of the individual TWD period (see description below).
Max.twd.time		Time of occurrence of maximum TWD value for each TWD phase.
Avg.twd		Average of TWD values for each TWD phase.
STD.twd		Standard deviation of TWD values for each TWD phase.

References

Zweifel R, Haeni M, Buchmann N, Eugster W (2016) Are trees able to grow in periods of stem shrinkage? New Phytol 211:839–849. doi: 10.1111/nph.13995

Examples

library(dendRoAnalyst)
data(gf_nepa17)
zg.phase<-phase.zg(df=gf_nepa17[1:600,], TreeNum=1, outputplot=TRUE, days=c(2,6))
head(zg.phase[[1]],10)
head(zg.phase[[2]],10)

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