ringPlot {tracheideR}

Plot intra-ring variation of tracheid features (with the possibility of plotting a climatic variable)

Description

This function plots the intra-ring variation of a tracheid feature (e.g. LD, CWT or LD/CWT) along the growing season and, optionally, the intra-annual variation of a climatic variable can be added to the same plot.

Usage

ringPlot(traq, varMean = NULL, varYear = NULL, m0 = 3, mt = 6.75,
  m1 = 11, type = c("LD", "CWT", "LWratio"), ylab = match.arg(type),
  main = "", addGS = TRUE, addMonths = addGS, ...,
  varMeanCol = "grey80", varYearCol = "red", varName = "")

Arguments

traq

ordered sequence of a tracheid feature (e.g. LD)

varMean

vector with monthly values of a given environmental variable

varYear

vector with monlthy values of an environmental variable for a specific year

m0

the start of the growing season (in months); the default value is 3 that corresponds to day of the year (doy) 60.

mt

the moment of transition from earlywood to latewood; the default value is 6.75.

m1

the end of the growing season; default value is 11.

type

a string that defines the tracheid features to be plotted, defaults "LD"

ylab

the y axis title (for the tracheid feature variable), default value is type

main

an overall title for the plot, if no string is supplied no title is added to the plot

addGS

logical; if TRUE add the growing season length to the axis 1, defaults TRUE

addMonths

logical; if TRUE add months to the axis 1, defaults TRUE

...

graphical parameters for plot may also be passed as arguments to this function

varMeanCol

the default value, "grey80", gives the color to plot the mean environmental variable

varYearCol

the color to plot monthly environmental values; the default value is "red"

varName

the y axis title (for the environmental variable),default value is ""; if no string is supplied no title is added to environmental axis

Details

This function returns an invisible data.frame (used to produced the graph)

Examples

## Not run:

# year 2010
y2010raw <- getTrac(tch$y2010, scale = .169)
y2010std <- tracheider(y2010raw)
par(oma = c(2,1,1,0.5))
par(mar = c(2,4,1,4))
y2010LD <- ringPlot(traq = y2010std, varMean = colMeans(sw),
varYear = sw["2010",], main=2010,type = "LD",  ylim = c(0,45),
ylab = expression(paste("LD (", mu,"m)")),varName = "Soil moisture")

# year 2013
y2013raw <- getTrac(tch$y2013, scale = .169)
y2013std <- tracheider(y2013raw)
y2013LD <- ringPlot(traq = y2013std, varMean = colMeans(sw),
varYear = sw["2013",], main=2013,type = "LD",  ylim = c(0,45),
ylab = expression(paste("LD (", mu,"m)")),varName = "Soil moisture")

# 2010 & 2013 in the same plot
par(mfcol = c(2,1))
par(oma = c(2,1,1,0.5))
par(mar = c(2,4,1,4))

ringPlot(y2010std,  varMean = colMeans(sw), varYear = sw["2010",],
type = "LD", ylab = "", main=2010, addGS = FALSE, addMonths = FALSE)

ringPlot(y2013std,  varMean = colMeans(sw), varYear = sw["2013",],
type = "LD", ylab=expression(paste("LD (", mu,"m)")),
main = 2013, addGS = TRUE, varName= "Soil moisture")

## End(not run)