IsoplotR (version 0.5)

kde: Create (a) kernel density estimate(s)

Description

Creates one or more kernel density estimates using a combination of the Botev (2010) bandwidth selector and the Abramson (1982) adaptive kernel bandwidth modifier.

Usage

kde(x, ...)
"kde"(x, from = NA, to = NA, bw = NA, adaptive = TRUE, log = FALSE, n = 512, plot = TRUE, pch = NA, xlab = "age [Ma]", ylab = "", kde.col = rgb(1, 0, 1, 0.6), hist.col = rgb(0, 1, 0, 0.2), show.hist = TRUE, bty = "n", binwidth = NA, ncol = NA, ...)
"kde"(x, from = NA, to = NA, bw = NA, adaptive = TRUE, log = FALSE, n = 512, plot = TRUE, pch = NA, xlab = "age [Ma]", ylab = "", kde.col = rgb(1, 0, 1, 0.6), hist.col = rgb(0, 1, 0, 0.2), show.hist = TRUE, bty = "n", binwidth = NA, ncol = NA, type = 4, cutoff.76 = 1100, cutoff.disc = c(-15, 5), ...)
"kde"(x, from = NA, to = NA, bw = NA, adaptive = TRUE, log = FALSE, n = 512, plot = TRUE, pch = NA, xlab = "age [Ma]", ylab = "", kde.col = rgb(1, 0, 1, 0.6), hist.col = rgb(0, 1, 0, 0.2), show.hist = TRUE, bty = "n", binwidth = NA, ncol = NA, samebandwidth = TRUE, normalise = TRUE, ...)

Arguments

x

a vector of numbers or an object of class UPb or detrital

...

optional arguments to be passed on to density

from

minimum age of the time axis. If NULL, this is set automatically

to

maximum age of the time axis. If NULL, this is set automatically

bw

the bandwidth of the KDE. If NULL, bw will be calculated automatically using botev()

adaptive

boolean flag controlling if the adaptive KDE modifier of Abramson (1982) is used

log

transform the ages to a log scale if TRUE

n

horizontal resolution of the density estimate

plot

show the KDE as a plot

pch

the symbol used to show the samples. May be a vector. Set pch = NA to turn them off.

xlab

the label of the x-axis

ylab

the label of the y-axis

kde.col

the fill colour of the KDE specified as a four element vector of r, g, b, alpha values

hist.col

the fill colour of the histogram specified as a four element vector of r, g, b, alpha values

show.hist

boolean flag indicating whether a histogram should be added to the KDE

bty

change to "o", "l", "7", "c", "u", or "]" if you want to draw a box around the plot

binwidth

scalar width of the histogram bins, in Myr if x$log==FALSE, or as a fractional value if x$log==TRUE. Sturges' Rule is used if binwidth==NA

ncol

scalar value indicating the number of columns over which the KDEs should be divided. This option is only used if x is of class detritals.

type

scalar indicating whether to plot the $^{207}$Pb/$^{235}$U age (type=1), the $^{206}$Pb/$^{238}$U age (type=2), the $^{207}$Pb/$^{206}$Pb age (type=3), the $^{207}$Pb/$^{206}$Pb-$^{206}$Pb/$^{238}$U age (type=4), or the (Wetherill) concordia age (type=5)

cutoff.76

the age (in Ma) below which the $^{206}$Pb/$^{238}$U and above which the $^{207}$Pb/$^{206}$Pb age is used. This parameter is only used if type=4.

cutoff.disc

two element vector with the maximum and minimum percentage discordance allowed between the $^{207}$Pb/$^{235}$U and $^{206}$Pb/$^{238}$U age (if $^{206}$Pb/$^{238}$U < cutoff.76) or between the $^{206}$Pb/$^{238}$U and $^{207}$Pb/$^{206}$Pb age (if $^{206}$Pb/$^{238}$U > cutoff.76). Set cutoff.disc=NA if you do not want to use this filter.

samebandwidth

boolean flag indicating whether the same bandwidth should be used for all samples. If samebandwidth = TRUE and bw = NULL, then the function will use the median bandwidth of all the samples.

normalise

boolean flag indicating whether or not the KDEs should all integrate to the same value.

Value

if plot==TRUE, returns an object of class KDE, i.e. a list containing the following items:

x

horizontal plot coordinates

y

vertical plot coordinates

bw

the base bandwidth of the density estimate

ages

the data values from the input to the KDE function

or, if class(x)=='detritals', an object of class KDEs, i.e. a list containing the following items:

kdes

a named list with objects of class KDE

from

the beginning of the common time scale

to

the end of the common time scale

themax

the maximum probability density of all the KDEs

xlabel

the x-axis label to be used by plot.KDEs

Examples

data(examples)
kde(examples$DZ[['N1']],kernel="epanechnikov")
kde(examples$DZ,from=0,to=3000)