plotWoodCalendar {CAVIAR}R Documentation

plotWoodCalendar

Description

Plots wood formation calendar

Usage

plotWoodCalendar(data, xmin = NA, xmax = NA, title = " ", subtitle = " ", plotype = 4)

Arguments

data a data frame of critical dates and durations with 8 compulsory columns located by their names (bE, bL, bM, cE, cL, dE, dL, dX), typically output from computeCriticalDates function
xmin an optional numeric indicating the x-axis minimum value
xmax an optional numeric indicating the x-axis maximum value
title an optional character containing the plot title
subtitle an optional character containing the plot subtitle
plotype an optional integer indicating the type of plot 1: individual critical dates plot,
2: group critical dates plot,
3: group critical durations plot,
4: group critical dates and durations plots (default).

Details

Critical dates can be first plotted for each individual tree (5 trees per page) in order to allow a visual checking of date consistencies using plotype = 1.
Consistent dates can then be used to draw a wood formation calendar using plotype = 2 for dates and plotype = 3 for durations.
Xylem development phase (enlarging: E, maturing: L, mature: M) onsets and cessations are represented by diamond-crossed-by-a-line marks. The left end of the line represents the minimum, the left end of the diamond the first quartile, the middle of the diamond the median, the right end of the diamond the third quartile and the right end of the line the maximum. plotype = 4 plots dates and durations at the same time.
NB. These representations are specially designed for five trees datasets. They also work when more trees are available, but then the graph represents a summary of the dataset and not all the data individually.

Value

A data frame of the critical dates and durations median and median absolute deviation.

Note

Version: 4.0
Last modifications: 11 February 2010

Author(s)

Cyrille Rathgeber - LERFoB, UMR1092 - INRA Nancy (France)
Email: cyrille.rathgeber@nancy.inra.fr

References

Rathgeber C.B.K., Longuetaud F. , Mothe F., Cuny H., Le Moguedec G. 2010. Phenology of wood formation: data processing, analysis and visualisation using R. Accepted in Dendrochronologia.

See Also

CAVIAR-package, computeBootstrapTest and computeCriticalDates

Examples

## Loading the AMA2006 dataset:
data(AMA2006)

## Computing wood formation critical dates for firs and pines:
Fir.cdd <- computeCriticalDates(AMA2006[AMA2006$Sp=="ABAL", ])
Pine.cdd <- computeCriticalDates(AMA2006[AMA2006$Sp=="PISY", ])

# Computing medians and medians absolute deviation for firs critical dates and durations
Fir.medians <- plotWoodCalendar(Fir.cdd)

## Visualising wood formation critical dates and durations on the screen for firs:
# Dates by trees individually
plotWoodCalendar(Fir.cdd, plotype=1)
# Dates by group of trees
plotWoodCalendar(Fir.cdd, plotype=2)
# Duration by group of trees
plotWoodCalendar(Fir.cdd, plotype=3)

## Plotting wood formation calendar for firs and pines in a PDF file
# General settings
pdf(file="Wood formation calendar.pdf")
layout(matrix(c(1, 2, 3, 4), nrow=2, ncol=2, byrow=TRUE))
par(mar=c(4, 4, 4, 1))

# Drawing the first plot - Firs critical dates
plotWoodCalendar(Fir.cdd, xmin=100, xmax=305, subtitle="a. Fir critical dates", plotype=2)

# Drawing the second plot - Firs critical durations
plotWoodCalendar(Fir.cdd, xmax=210, subtitle="b. Fir critical durations", plotype=3)

# Drawing the third plot - Pines critical dates
plotWoodCalendar(Pine.cdd, xmin=100, xmax=305, subtitle="c. Pine critical dates", plotype=2)

# Drawing the fourth plot - Pines critical durations
plotWoodCalendar(Pine.cdd, xmax=210, subtitle="d. Pine critical durations", plotype=3)

dev.off()

[Package CAVIAR version 0.1-0 Index]