cad: Plot continuous data as cumulative age distributions

Description Usage Arguments Details References See Also Examples

View source: R/cad.R

Description

Plot a dataset as a Cumulative Age Distribution (CAD), also known as a ‘empirical cumulative distribution function’.

Usage

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cad(x, ...)

## Default S3 method:
cad(x, pch = NA, verticals = TRUE,
  xlab = "age [Ma]", col = "black", hide = NULL, ...)

## S3 method for class 'detritals'
cad(x, pch = NA, verticals = TRUE,
  xlab = "age [Ma]", col = "heat.colors", hide = NULL, ...)

## S3 method for class 'UPb'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", type = 4, cutoff.76 = 1100,
  cutoff.disc = list(-15, 5, TRUE), common.Pb = 0, hide = NULL, ...)

## S3 method for class 'PbPb'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", common.Pb = 1, hide = NULL, ...)

## S3 method for class 'ArAr'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", i2i = FALSE, hide = NULL, ...)

## S3 method for class 'KCa'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", i2i = FALSE, hide = NULL, ...)

## S3 method for class 'ThU'
cad(x, pch = NA, verticals = TRUE, xlab = "age [ka]",
  col = "black", i2i = FALSE, detritus = 0, hide = NULL, ...)

## S3 method for class 'ReOs'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", i2i = TRUE, hide = NULL, ...)

## S3 method for class 'SmNd'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", i2i = TRUE, hide = NULL, ...)

## S3 method for class 'RbSr'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", i2i = TRUE, hide = NULL, ...)

## S3 method for class 'LuHf'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", i2i = TRUE, hide = NULL, ...)

## S3 method for class 'UThHe'
cad(x, pch = NA, verticals = TRUE, xlab = "age [Ma]",
  col = "black", hide = NULL, ...)

## S3 method for class 'fissiontracks'
cad(x, pch = NA, verticals = TRUE,
  xlab = "age [Ma]", col = "black", hide = NULL, ...)

Arguments

x

a numerical vector OR an object of class UPb, PbPb, ArAr, KCa, UThHe, fissiontracks, ReOs, RbSr, SmNd, LuHf, ThU or detritals

...

optional arguments to the generic plot function

pch

plot character to mark the beginning of each CAD step

verticals

logical flag indicating if the horizontal lines of the CAD should be connected by vertical lines

xlab

x-axis label

col

either the name of one of R's built-in colour palettes (e.g., 'heat.colors', 'terrain.colors', 'topo.colors', 'cm.colors') (if x has class detritals) OR the name or code for a colour to give to single sample datasets (otherwise).

hide

vector with indices of aliquots that should be removed from the plot.

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), the concordia age (type=5), or the ^{208}Pb/^{232}Th age (type=6).

cutoff.76

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

cutoff.disc

discordance cutoff filter. This is a three element list.

The first two items contain the minimum (negative) and maximum (positive) 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).

The third item is a boolean flag that controls whether the discordance filter should be applied before (TRUE) or after (FALSE) the common-Pb correction.

Set cutoff.disc=NA to turn off this filter.

common.Pb

common lead correction:

0: none

1: use the Pb-composition stored in

settings('iratio','Pb206Pb204') (if x has class UPb and x$format<4);

settings('iratio','Pb206Pb204') and settings('iratio','Pb207Pb204') (if x has class PbPb or x has class UPb and 3<x$format<7); or

settings('iratio','Pb208Pb206') and settings('iratio','Pb208Pb207') (if x has class UPb and x$format=7 or 8).

2: use the isochron intercept as the initial Pb-composition

3: use the Stacey-Kramers two-stage model to infer the initial Pb-composition (only applicable if x has class UPb)

i2i

‘isochron to intercept’: calculates the initial (aka ‘inherited’, ‘excess’, or ‘common’) ^{40}Ar/^{36}Ar, ^{40}Ca/^{44}Ca, ^{207}Pb/^{204}Pb, ^{87}Sr/^{86}Sr, ^{143}Nd/^{144}Nd, ^{187}Os/^{188}Os, ^{230}Th/^{232}Th or ^{176}Hf/^{177}Hf ratio from an isochron fit. Setting i2i to FALSE uses the default values stored in settings('iratio',...) or zero (for the Pb-Pb method). When applied to data of class ThU, setting i2i to TRUE applies a detrital Th-correction.

detritus

detrital ^{230}Th correction (only applicable when x$format=1 or 2).

0: no correction

1: project the data along an isochron fit

2: correct the data using an assumed initial ^{230}Th/^{232}Th-ratio for the detritus.

3: correct the data using the measured present day ^{230}Th/^{238}U, ^{232}Th/^{238}U and ^{234}U/^{238}U-ratios in the detritus.

Details

Empirical cumulative distribution functions or cumulative age distributions are the most straightforward way to visualise the probability distribution of multiple dates. Suppose that we have a set of n dates t_i. The CAD is a step function that sets out the rank order of the dates against their numerical value:

CAD(t) = ∑_i 1(t<t_i)/n

where 1(\ast) = 1 if \ast is true and 1(\ast) = 0 if \ast is false. CADs have two desirable properties (Vermeesch, 2007). First, they do not require any pre-treatment or smoothing of the data. This is not the case for histograms or kernel density estimates. Second, it is easy to superimpose several CADs on the same plot. This facilitates the intercomparison of multiple samples. The interpretation of CADs is straightforward but not very intuitive. The prominence of individual age components is proportional to the steepness of the CAD. This is different from probability density estimates such as histograms, in which such components stand out as peaks.

References

Vermeesch, P., 2007. Quantitative geomorphology of the White Mountains (California) using detrital apatite fission track thermochronology. Journal of Geophysical Research: Earth Surface, 112(F3).

See Also

kde, radialplot

Examples

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data(examples)
cad(examples$DZ,verticals=FALSE,pch=20)

pvermees/IsoplotR documentation built on Jan. 8, 2020, 7:03 p.m.