FREddyPro (version 1.0)

plotDaily: Plot average daily patterns

Description

Calculating and plotting the daily pattern of any variable with the option to use mean or both mean and median. There is also an option to plot quantiles.

Usage

plotDaily(x, day.x, y = NULL, day.y = NULL, median = FALSE,
quantiles = FALSE, probs = c(0.05, 0.95), legend = FALSE, legendSide =
NULL, legendText = NULL, type = "l", lty = c(1, 4), col = c(1, 2),
cex.legend = 1, horiz.legend = TRUE, ylab = "Mean and median", xlab =
"Day", ...)

Arguments

x

The variable to plot

day.x

The day variable associated with the X variable

y

A second optional variable to plot.

day.y

The day variable associated with the Y variable, also optional.

median

Logical. If TRUE the median is also plotted with the mean.

quantiles

Logical. If TRUE the quantiles will be plotted as a colour band

probs

An array of the quantiles to use. The default is 0.05 and 0.95 (5th and 95th).

legend

Logical. If TRUE a legend will be plotted.

legendSide

The side of the plot to place the legend.

legendText

The text to use for legend.

type

The type of plot. The default is a line plot.

lty

The type of line when a line plot is used.

col

The colour to use for the lines or points. It can be a single values or an array.

cex.legend

The size of the legend labels.

horiz.legend

A logical parameter. If TRUE the legend is will be placed horizontally.

ylab

The y-axis label.

xlab

The x-axis label.

...

Further graphical options.

Details

The function first aggregates the given variable daily and plots by default the mean. The median can also be plotted with the mean. There is an optional graphical output for quantiles. By default is the 5th and 95th but other quantiles can be used. There are two separate daily inputs to the functions to allow plotting variables from different data frames.

Examples

## Load the data
data(fluxes)

## Clean and despike the fluxes
fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,distCor=TRUE,timesList=3,
thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	

## Plot the daily patterns

plotDaily(x=fluxes$co2_flux,day.x=fluxes$yday,type='o',
median=TRUE,ylim=c(-30,20),lty=c(1,2),col=c(1,2),quantiles=TRUE,
legend=TRUE,legendSide='topleft',
lwd=2,ylab="Fc (umol m"^2~" s"^-1~")",main="Harwood forest",cex.legend=0.9,
horiz.legend=FALSE)
abline(h=0,lty=2)