R: Calculate isotopic ages

age {IsoplotR}

R Documentation

Calculate isotopic ages

Description

Calculates U-Pb, Pb-Pb, Th-Pb, Ar-Ar, K-Ca, Re-Os, Sm-Nd, Rb-Sr, Lu-Hf, U-Th-He, Th-U and fission track ages and propagates their analytical uncertainties. Includes options for single grain, isochron and concordia_ages.

Usage

age(x, ...)

## Default S3 method:
age(
  x,
  method = "U238-Pb206",
  oerr = 1,
  sigdig = NA,
  exterr = FALSE,
  J = c(NA, NA),
  zeta = c(NA, NA),
  rhoD = c(NA, NA),
  d = diseq(),
  ...
)

## S3 method for class 'UPb'
age(
  x,
  type = 1,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  common.Pb = 0,
  discordance = discfilter(),
  ...
)

## S3 method for class 'PbPb'
age(
  x,
  isochron = TRUE,
  common.Pb = 2,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'ArAr'
age(
  x,
  isochron = FALSE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'KCa'
age(
  x,
  isochron = FALSE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'UThHe'
age(x, isochron = FALSE, central = FALSE, i = NULL, oerr = 1, sigdig = NA, ...)

## S3 method for class 'fissiontracks'
age(x, central = FALSE, i = NULL, oerr = 1, sigdig = NA, exterr = FALSE, ...)

## S3 method for class 'ThU'
age(
  x,
  isochron = FALSE,
  Th0i = 0,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  ...
)

## S3 method for class 'ThPb'
age(
  x,
  isochron = TRUE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'ReOs'
age(
  x,
  isochron = TRUE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'SmNd'
age(
  x,
  isochron = TRUE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'RbSr'
age(
  x,
  isochron = TRUE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'LuHf'
age(
  x,
  isochron = TRUE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

## S3 method for class 'PD'
age(
  x,
  nuclide,
  isochron = TRUE,
  i2i = TRUE,
  exterr = FALSE,
  i = NULL,
  oerr = 1,
  sigdig = NA,
  projerr = FALSE,
  ...
)

Arguments

`x`	can be: a scalar containing an isotopic ratio, a two element vector containing an isotopic ratio and its standard error, or the spontaneous and induced track densities `Ns` and `Ni`, a two element vector containing `Ar40Ar39`, `s[Ar40Ar39]`, a two element vector containing `K40Ca40` and `s[K40Ca40]`, a six element vector containing `U`, `s[U]`, `Th`, `s[Th]`, `He` and `s[He]`, an eight element vector containing `U`, `s[U]`, `Th`, `s[Th]`, `He`, `s[He]`, `Sm` and `s[Sm]` a two element vector containing `Sr87Rb87` and `s[Sr87Rb87]` a two element vector containing `Os187Re187` and `s[Os187Re187]` a two element vector containing `Nd143Sm147` and `s[Nd144Sm147]` a two element vector containing `Hf176Lu176` and `s[Hf176Lu176]` a five element vector containing `Th230U238`, `s[Th230/U238]`, `U234U238`, `s[U234U238]` and `cov[Th230U238,U234U238]` OR an object of class `UPb`, `PbPb`, `ThPb`, `ArAr`, `KCa`, `ThU`, `RbSr`, `SmNd`, `ReOs`, `LuHf`, `UThHe` or `fissiontracks`.
`...`	additional arguments
`method`	one of either `'U238-Pb206'`, `'U235-Pb207'`, `'Pb207-Pb206'`, `'Th232-Pb208'`, `'Ar-Ar'`, `'K-Ca'`, `'Th-U'`, `'Re-Os'`, `'Sm-Nd'`, `'Rb-Sr'`, `'Lu-Hf'`, `'U-Th-He'` or `'fissiontracks'`
`oerr`	indicates whether the analytical uncertainties of the output are reported as: `1`: 1`\sigma` absolute uncertainties. `2`: 2`\sigma` absolute uncertainties. `3`: absolute (1-`\alpha`)% confidence intervals, where `\alpha` equales the value that is stored in `settings('alpha')`. `4`: 1`\sigma` relative uncertainties (`\%`). `5`: 2`\sigma` relative uncertainties (`\%`). `6`: relative (1-`\alpha`)% confidence intervals, where `\alpha` equales the value that is stored in `settings('alpha')`. (only used when `isochron` and `central` are `FALSE`)
`sigdig`	number of significant digits for the uncertainty estimate (only used if `type=1`, `isochron=FALSE` and `central=FALSE`).
`exterr`	propagate the external (decay constant and calibration factor) uncertainties?
`J`	two-element vector with the J-factor and its standard error.
`zeta`	two-element vector with the zeta-factor and its standard error.
`rhoD`	two-element vector with the track density of the dosimeter glass and its standard error.
`d`	an object of class `diseq`.
`type`	scalar flag indicating whether `1`: each U-Pb analysis should be considered separately, `2`: all the measurements should be combined to calculate a concordia_age, `3`: a discordia_line should be fitted through all the U-Pb analyses using the maximum likelihood algorithm of Ludwig (1998), which assumes that the scatter of the data is solely due to the analytical uncertainties. `4`: a discordia_line should be fitted ignoring the analytical uncertainties. `5`: a discordia_line should be fitted using a modified maximum likelihood algorithm that accounts for overdispersion by adding a geological (co)variance term.
`i`	index of a particular aliquot
`common.Pb`	common lead correction: `0`: none `1`: use the Pb-composition stored in `settings('iratio','Pb207Pb206')` (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','Pb206Pb208')` and `settings('iratio','Pb207Pb208')` (if `x` has class `UPb` and `x$format=7` or `8`). `2`: use the isochron intercept as the initial Pb-composition `3`: use the Stacey-Kramer two-stage model to infer the initial Pb-composition
`discordance`	discordance calculator. This is an object of class `discfilter`, or a two element list containing: `option`: one of `1` or `'t'` (absolute age filter); `2` or `'r'` (relative age filter); `3` or `'sk'` (Stacey-Kramers common Pb filter); `4` or `'a'` (perpendicular Aitchison distance); `5` or `'c'` (concordia distance); `6` or `'p'` (p-value of concordance); or `NA` (omit the discordance from the output) `before`: logical flag indicating whether the discordance should be calculated before (`TRUE`) or after (`FALSE`) the common-Pb correction.
`isochron`	logical flag indicating whether each analysis should be considered separately (`isochron=FALSE`) or an isochron age should be calculated from all analyses together (`isochron=TRUE`).
`projerr`	logical. If `TRUE`, propagates the uncertainty of the non-radiogenic isotope correction (the 'projection error') into the age uncertainty. Note that the resulting single grain age uncertainties may be strongly correlated with each other, but these error correlations are not reported in the output.
`i2i`	‘isochron to intercept’: calculates the initial (aka ‘inherited’, ‘excess’, or ‘common’) `^{40}`Ar/`^{36}`Ar, `^{40}`Ca/`^{44}`Ca, `^{87}`Sr/`^{86}`Sr, `^{143}`Nd/`^{144}`Nd, `^{187}`Os/`^{188}`Os, `^{176}`Hf/`^{177}`Hf or `^{204}`Pb/`^{208}`Pb ratio from an isochron fit. Setting `i2i` to `FALSE` uses the default values stored in `settings('iratio',...)`.
`central`	logical flag indicating whether each analysis should be considered separately (`central=FALSE`) or a central age should be calculated from all analyses together (`central=TRUE`).
`Th0i`	initial `^{230}`Th correction. `0`: no correction `1`: project the data along an isochron fit `2`: if `x$format` is `1` or `2`, correct the data using the measured present day `^{230}`Th/`^{238}`U, `^{232}`Th/`^{238}`U and `^{234}`U/`^{238}`U activity ratios in the detritus. If `x$format` is `3` or `4`, correct the data using the measured `^{238}`U/`^{232}`Th activity ratio of the whole rock, as stored in `x` by the `read.data()` function. `3`: correct the data using an assumed initial `^{230}`Th/`^{232}`Th-ratio for the detritus (only relevant if `x$format` is `1` or `2`).
`nuclide`	a text string corresponding to a valid entry for `settings('lambda',...)`

Value

if x is a scalar or a vector, returns the age using the geochronometer given by method and its standard error.
if x has class UPb and type=1, returns a table with the following columns: t.75, err[t.75], t.68, err[t.68], t.76, err[t.76], (t.82, err[t.82],) t.conc, err[t.conc], (disc) or err[p.conc],) containing the ^{207}Pb/^{235}U-age and standard error, the ^{206}Pb/^{238}U-age and standard error, the ^{207}Pb/^{206}Pb-age and standard error, (the ^{208}Pb/^{232}Th-age and standard error,) the single grain concordia_age and standard error, (and the % discordance or p-value for concordance,) respectively.
if x has class UPb and type=2, 3, 4 or 5, returns the output of the concordia function.
if x has class PbPb, ThPb, ArAr, KCa, RbSr, SmNd, ReOs, LuHf, ThU or UThHe and isochron=FALSE, returns a table of Pb-Pb, Th-Pb, Ar-Ar, K-Ca, Rb-Sr, Sm-Nd, Re-Os, Lu-Hf, Th-U or U-Th-He ages and their standard errors.
if x has class ThU and isochron=FALSE, returns a 5-column table with the Th-U ages, their standard errors, the initial ^{234}U/^{238}U-ratios, their standard errors, and the correlation coefficient between the ages and the initial ratios.
if x has class PbPb, ThPb, ArAr, KCa, RbSr, SmNd, ReOs, LuHf, UThHe or ThU and isochron=TRUE, returns the output of the isochron function.
if x has class fissiontracks and central=FALSE, returns a table of fission track ages and standard errors.
if x has class fissiontracks or UThHe and central=TRUE, returns the output of the central function.

Examples

attach(examples)
tUPb <- age(UPb,type=1)
tconc <- age(UPb,type=2)
tdisc <- age(UPb,type=3)
tArAr <- age(ArAr)
tiso <- age(ArAr,isochron=TRUE,i2i=TRUE)
tcentral <- age(FT1,central=TRUE)