Title: Monazite Dating for the NiLeDAM Team
Version: 0.4
Date: 2025-06-19
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Description: Th-U-Pb electron microprobe age dating of monazite, as originally described in <doi:10.1016/0009-2541(96)00024-1>.
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Depends: R (≥ 2.4.0)
Imports: dplyr, ggplot2, magrittr, methods, nleqslv, rlang, scales, shiny, shinyjs, shinythemes, stats, thematic, tidyr
Suggests: knitr, rmarkdown, spelling, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
Repository: CRAN
RoxygenNote: 7.2.3
Collate: 'init.R' 'describeNiLeDAM.R' 'describeSrilanka.R' 'ages.R' 'calculate.R' 'oneAgeTest.R' 'ageTests.R' 'tests.R' 'ages-oneAgeTest-ageTests.R' 'liveNILEDAM.R'
Language: en-US
NeedsCompilation: no
Packaged: 2025-06-19 13:49:08 UTC; nathalie
Author: Nathalie Vialaneix ORCID iD [aut, trl, cre], Aurélie Mercadié [aut], Jean-Marc Montel [aut], Anne-Magali Seydoux-Guillaume [ctb]
Date/Publication: 2025-06-19 14:00:02 UTC

Monazite Dating for the 'NiLeDAM' Team

Description

The aim here is to provide facilities to date monazite using electron microprobe analysis (EPMA). More precisely, the 'NiLeDAM' package has three main features:

The package contains two main functions: calculateAges(), that calculate the ages and tests(), that test for the number of age populations.

An example is provided with the data srilanka, which can be run using demo(srilanka).

Author(s)

Aurélie Mercadié, aurelie.mercadie@inrae.fr

Jean-Marc Montel, jean-marc.montel@ensg.inpl-nancy.fr

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

Maintainer: Nathalie Vialaneix

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

Examples

## Not run: demo(srilanka)

Class "ageTests"

Description

Results of \chi^2-tests testing to which number of populations the ages calculated by the function calculateAges() are the most likely to come from. The test is the one described in the article Montel et al. (1996).

Fields

nb.pop

Object of class "vector" that contains the tested numbers of populations.

best.nb

Object of class "numeric" that contains the most probable number of populations, which is the smallest number for which the \chi^2-test is accepted.

best.res

Object of class "oneAgeTest" that contains the result of the test for best.nb populations.

Objects from the Class

Objects from this class are created by the function tests() applied to an object of class ages when the option nbmax is not set to NULL but to an integer larger than nbmin.

Methods

Author(s)

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

See Also

ages, tests(), plot.ageTests

Examples

showClass("ageTests")

## Example
data(srilanka)
calculated.ages <- calculateAges(srilanka, nloops = 10)
tests(calculated.ages, nbmax = 3)

Class "ages"

Description

A class for the results of the calculateAges function. It contains the ages calculated for each analytic point from triplets (U,Th,Pb) and corresponding errors.

Fields

data

Object of class "data.frame" that contains the original triplets (U,Th,Pb) and corresponding errors.

ages

Object of class "vector" that contains the ages calculated for each analytic point.

ci

Object of class "matrix", which is a two-column matrix that contains the bounds of the confidence intervals for each age of the slot ages. These are estimated from a MC simulation method as described in calculateAges().

sd

Object of class "vector" that contains the standard deviations for each age of the slot ages. These are estimated from a MC simulation method as described in calculateAges().

nloops

Object of class "numeric" that stores the number of MC simulations used to estimate the confidence intervals and the standard deviations.

level

Object of class "numeric" that stores the level of the confidence intervals.

Objects from the Class

Objects can be created by calls of the function calculateAges().

Methods

Author(s)

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

See Also

calculateAges(), tests()

Examples

showClass("ages")

## Example on the srilanka dataset

data(srilanka)
calculated.ages <- calculateAges(srilanka, nloops = 10)
calculated.ages

Calculate the ages from electron microprobe measurements.

Description

This function calculates the ages, confidence intervals and standard deviations from triplets (U,Th,Ph), obtained by electron microprobe, given together with corresponding errors.

Usage

calculateAges(measures, nloops = 1000, level = 0.05, verbose = TRUE, seed = NULL)

Arguments

measures

a data.frame object with one electron microprobe measurement by row and with columns U, corresponding error for U, Th, corresponding error for Th, Pb, corresponding error for Pb, all expressed in ppm. See an example with data(srilanka).

nloops

the number of Monte Carlo (MC) simulations used to estimate the confidence intervals for the ages. Default is 1000.

level

the level of significance of the confidence intervals for the ages. Default is 0.05.

verbose

logical; activates the verbose mode. Default is TRUE.

seed

if supplied, initialize the random seed. Default is NULL (the random seed is not initialized).

Details

The ages are calculated by solving the Equation (1) of Montel et al. (1996). The equation is solved by the Broyden method implemented in the nleqslv() function.

The standard deviations and the confidence intervals are calculated using a MC approach: randomized observations of the triplets are generated from normal distributions with standard deviations equal to \frac{\textrm{error}}{2} where 'error' denotes the error in the measurement of Th, U or Pb, passed in measures. Standard deviations are estimated by the empirical standard deviations and confidence intervals by quantiles for probabilities \frac{\textrm{\texttt{level}}}{2} and 1-\frac{\textrm{\texttt{level}}}{2}, respectively.

Value

An object of class ages.

Note

You should use at least 1000 MC simulations otherwise the estimated confidence intervals and standard deviations will not be reliable. Such simulations can take a few seconds/minutes for fifty or so triplets and corresponding errors.

Author(s)

Jean-Marc Montel, jean-marc.montel@ensg.inpl-nancy.fr

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

See Also

ages tests

Examples

## Load the data
data(srilanka)

## Calculate the ages
calculateAges(srilanka, nloops=10)

Graphical Web User Interface for 'NiLeDAM'

Description

This function starts the graphical user interface with the default system browser. This interface is more likely to work properly with Firefox https://www.mozilla.org/fr/firefox/new/. In case Firefox is not your default browser, copy/paste http://localhost:8100 into the address bar.

Usage

liveNiLeDAM()

Value

Starts the 'NiLeDAM' GUI.

Author(s)

Aurélie Mercadié, aurelie.mercadie@inrae.fr

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

Class "oneAgeTest"

Description

Results of a \chi^2-test testing if the ages calculated by the function calculateAges() come from a given number of populations. The test is the one described in the article Montel et al. (1996).

Fields

data

Object of class "ages" as created by the function calculateAges(). This is the object passed as an argument to the function tests().

ages

Object of class "vector" that contains the estimated common age(s) of the population(s). Its size is equal to the argument nbmin passed to the function tests().

sd

Object of class "vector" that contains the estimated standard deviations of the common age(s) of the population(s). Its size is equal to the argument nbmin passed to the function tests().

ic

Object of class "matrix" having nbmin rows and two columns corresponding to the confidence intervals at level level as passed as an argument to the function tests().

S

Object of class "numeric" \chi^2 test statistic of the test.

thres

Object of class "numeric" probability threshold of the test.

df

Object of class "numeric" degree of freedom of the test.

level

Object of class "numeric" confidence level of the test. Passed as an argument to the function tests().

h0

Object of class "logical" result of the test: if h0 is TRUE, the test is accepted at level level and if h0 is FALSE, the test is rejected at level level.

which.pop

Object of class "vector" that contains the population number for each analytic point. 1 corresponds to the population with the first age in ages, 2 to the population with the second age in ages...

Objects from the Class

Objects from this class are created by the function tests() applied to an object of class ages when the option nbmax is set to NULL.

Methods

Author(s)

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

See Also

ages, tests(), plot.oneAgeTest

Examples

showClass("oneAgeTest")

## Example

data(srilanka)
calculated.ages <- calculateAges(srilanka, nloops=10)
tests(calculated.ages)

Method "plot" for Classes "oneAgeTest" and "ageTests"

Description

Display densities of the ages calculated by the function calculateAges(), as well as the common age(s) density(ies) as returned by the function tests().

Usage

## S4 method for signature 'oneAgeTest'
plot(x, y = NULL, main = "", col = "red")

Arguments

x

an object of class "oneAgeTest" or "ageTests" (see section Methods)

y

NUll

main

a character string, title of the plot

col

a character string, color of the common age(s) density(ies)

Details

The estimated densities are Gaussian, as supposed by the model described in Montel et al. (1996). Each density is referenced by its number to help identify outliers or invalid measurements.

Also note that if an object of class oneAgeTest is passed to the function, the common age(s) densities is displayed even if the test of the function tests() is rejected.

If argument col is supplied, it is used to display the density(ies) of the common age(s).

Usage

plot(x, ...)

Methods

Author(s)

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

See Also

tests(), oneAgeTest, ageTests

Examples

data(srilanka)
calculated.ages <- calculateAges(srilanka, nloops = 10)
res.tests <- tests(calculated.ages, 1, 3)
plot(res.tests, main = "Densities", col = "lightseagreen")

Method "popline" for Classes "oneAgeTest" and "ageTests"

Description

Display observations as well as their reference's population as calculated by the function tests() given their value of Pb (ppm) and Th*(ppm), where Th* is a function of Th and U variables.

Usage

## S4 method for signature 'oneAgeTest'
popline(x, main2 = "")

Arguments

x

an object of class "oneAgeTest" or "ageTests" (see section Methods)

main2

a character string, title of the plot

Details

Th* is computed thanks to the following formula: Th + 232*U * [238(exp(4.9475*10^{-5}*Age) - 1)]^{-1} * [[exp(9.8485*10^{-4}*Age + 138*exp(1.55125*10^{-4}*Age))][139] - 1]

Slopes, depending directly of the ages computed with the function tests(), are obtained through the following equation: [exp(4.9475*10^{-5}*Age) - 1] * 207.3/232.

Usage

popline(x, main2)

Methods

Author(s)

Aurélie Mercadié, aurelie.mercadie@inrae.fr

Jean-Marc Montel, jean-marc.montel@ensg.inpl-nancy.fr

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

See Also

tests(), oneAgeTest, ageTests

Examples

data(srilanka)
calculated.ages <- calculateAges(srilanka, nloops = 10)
res.tests <- tests(calculated.ages, 1, 3)
popline(res.tests, main2 = "Populations")

An example data set: electron microprobe data.

Description

This dataset is kindly provided by Anne-Magali Seydoux-Guillaume anne.magali.seydoux@univ-st-etienne.fr and has been published in Seydoux-Guillaume et al. (2012).

Usage

data(srilanka)

Format

A data frame with 32 observations on the following 6 variables:

Details

The first 8 observations are group control data (more precisely, they correspond to standard reference analyses). When testing if all the observations are issued from a single population, the assumption is thus rejected. Removing the first 8 observations leads to obtain a positive answer when testing if the observations come from the same population. See demo(srilanka).

References

Seydoux-Guillaume A.M., Montel J.M., Bingen B., Bosse V., de Parseval P., Paquette J.L., Janots E., Wirth R. (2012) Low-temperature alteration of monazite: fluid mediated coupled dissolution-precipitation, irradiation damage and disturbance of the U-Pb and Th-Pb chronometers. Chemical Geology, 330–331, 140–158.

Examples

data(srilanka)

# With control group data
summary(srilanka)

# Without control group data
summary(srilanka[9:32,])

Method "tests" for Class "ages"

Description

Test if a set of ages belongs to a given number of populations or alternatively find out the most probable number of populations within a range.

Usage

## S4 method for signature 'ages'
tests(object, nbmin = 1, nbmax = NULL, level = object@level, verbose = TRUE)

Arguments

object

an object of type ages as produced by the function calculateAges()

nbmin

a numeric. Minimum tested number of populations.

nbmax

a numeric. Maximum tested number of populations.

level

a numeric. Confidence interval level. Default is equal to object@level, i.e., to the level of confidence used to calculate the ages.

verbose

logical. Activates the verbose mode.

Details

The function successively tests all values from nbmin to nbmax and keeps the smallest accepted one (returns an error if all supplied values are rejected). In this case, the output value is an object of class ageTests.

If nbmax is NULL, the results are kept even if the test is rejected. In this case, the output value is an object of class oneAgeTest.

The performed tests are those described in Montel et al. (1996).

Value

An object of class ageTests or oneAgeTest depending on the value of nbmax (see section "Details").

Usage

tests(object, nbmin=1, nbmax=NULL, level=object@level, verbose=TRUE)

Methods

Author(s)

Jean-Marc Montel, jean-marc.montel@ensg.inpl-nancy.fr

Nathalie Vialaneix, nathalie.vialaneix@inrae.fr

References

Montel J.M., Foret S., Veschambre M., Nicollet C., Provost A. (1996) Electron microprobe dating of monazite. Chemical Geology, 131, 37–53.

See Also

calculateAges(), oneAgeTest, ageTests

Examples

data(srilanka)
calculated.ages <- calculateAges(srilanka, nloops = 10)
tests(calculated.ages)
tests(calculated.ages, 1, 3)