Description Usage Arguments Details Value Function version How to cite Author(s) References See Also Examples

View source: R/calc_FiniteMixture.R

This function fits a k-component mixture to a De distribution with differing known standard errors. Parameters (doses and mixing proportions) are estimated by maximum likelihood assuming that the log dose estimates are from a mixture of normal distributions.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 |

`data` |
RLum.Results or data.frame ( |

`sigmab` |
numeric ( |

`n.components` |
numeric ( |

`grain.probability` |
logical ( |

`dose.scale` |
numeric:
manually set the scaling of the y-axis of the first plot with a vector
in the form of |

`pdf.weight` |
logical ( |

`pdf.sigma` |
character ( |

`pdf.colors` |
character ( |

`pdf.scale` |
numeric: manually set the max density value for proper scaling of the x-axis of the first plot |

`plot.proportions` |
logical ( |

`plot` |
logical ( |

`...` |
further arguments to pass. See details for their usage. |

This model uses the maximum likelihood and Bayesian Information Criterion (BIC) approaches.

Indications of overfitting are:

increasing BIC

repeated dose estimates

covariance matrix not positive definite

covariance matrix produces NaNs

convergence problems

**Plot**

If a vector (`c(k.min:k.max)`

) is provided
for `n.components`

a plot is generated showing the the k components
equivalent doses as normal distributions. By default `pdf.weight`

is
set to `FALSE`

, so that the area under each normal distribution is
always 1. If `TRUE`

, the probability density functions are weighted by
the components proportion for each iteration of k components, so the sum of
areas of each component equals 1. While the density values are on the same
scale when no weights are used, the y-axis are individually scaled if the
probability density are weighted by the components proportion.

The standard deviation (sigma) of the normal distributions is by default
determined by a common `sigmab`

(see `pdf.sigma`

). For
`pdf.sigma = "se"`

the standard error of each component is taken
instead.

The stacked barplot shows the proportion of each component (in
per cent) calculated by the FFM. The last plot shows the achieved BIC scores
and maximum log-likelihood estimates for each iteration of k.

Returns a plot (*optional*) and terminal output. In addition an
RLum.Results object is returned containing the
following elements:

`.$summary` |
data.frame summary of all relevant model results. |

`.$data` |
data.frame original input data |

`.$args` |
list used arguments |

`.$call` |
call the function call |

`.$mle` |
covariance matrices of the log likelhoods |

`.$BIC` |
BIC score |

`.$llik` |
maximum log likelihood |

`.$grain.probability` |
probabilities of a grain belonging to a component |

`.$components` |
matrix estimates of the de, de error and proportion for each component |

`.$single.comp` |
data.frame single componente FFM estimate |

If a vector for `n.components`

is provided (e.g. `c(2:8)`

),
`mle`

and `grain.probability`

are lists containing matrices of the
results for each iteration of the model.

The output should be accessed using the function get_RLum

0.4.1

Burow, C., 2019. calc_FiniteMixture(): Apply the finite mixture model (FMM) after Galbraith (2005) to a given De distribution. Function version 0.4.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., 2019. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.6. https://CRAN.R-project.org/package=Luminescence

Christoph Burow, University of Cologne (Germany)

Based on a rewritten S script of Rex Galbraith, 2006.
, RLum Developer Team

Galbraith, R.F. & Green, P.F., 1990. Estimating the component ages in a finite mixture. Nuclear Tracks and Radiation Measurements 17, 197-206.

Galbraith, R.F. & Laslett, G.M., 1993. Statistical models for mixed fission track ages. Nuclear Tracks Radiation Measurements 4, 459-470.

Galbraith, R.F. & Roberts, R.G., 2012. Statistical aspects of equivalent dose and error calculation and display in OSL dating: An overview and some recommendations. Quaternary Geochronology 11, 1-27.

Roberts, R.G., Galbraith, R.F., Yoshida, H., Laslett, G.M. & Olley, J.M., 2000. Distinguishing dose populations in sediment mixtures: a test of single-grain optical dating procedures using mixtures of laboratory-dosed quartz. Radiation Measurements 32, 459-465.

Galbraith, R.F., 2005. Statistics for Fission Track Analysis, Chapman & Hall/CRC, Boca Raton.

**Further reading**

Arnold, L.J. & Roberts, R.G., 2009. Stochastic modelling of multi-grain equivalent dose (De) distributions: Implications for OSL dating of sediment mixtures. Quaternary Geochronology 4, 204-230.

Cunningham, A.C. & Wallinga, J., 2012. Realizing the potential of fluvial archives using robust OSL chronologies. Quaternary Geochronology 12, 98-106.

Rodnight, H., Duller, G.A.T., Wintle, A.G. & Tooth, S., 2006. Assessing the reproducibility and accuracy of optical dating of fluvial deposits. Quaternary Geochronology 1, 109-120.

Rodnight, H. 2008. How many equivalent dose values are needed to obtain a reproducible distribution?. Ancient TL 26, 3-10.

calc_CentralDose, calc_CommonDose, calc_FuchsLang2001, calc_MinDose

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ```
## load example data
data(ExampleData.DeValues, envir = environment())
## (1) apply the finite mixture model
## NOTE: the data set is not suitable for the finite mixture model,
## which is why a very small sigmab is necessary
calc_FiniteMixture(ExampleData.DeValues$CA1,
sigmab = 0.2, n.components = 2,
grain.probability = TRUE)
## (2) repeat the finite mixture model for 2, 3 and 4 maximum number of fitted
## components and save results
## NOTE: The following example is computationally intensive. Please un-comment
## the following lines to make the example work.
FMM<- calc_FiniteMixture(ExampleData.DeValues$CA1,
sigmab = 0.2, n.components = c(2:4),
pdf.weight = TRUE, dose.scale = c(0, 100))
## show structure of the results
FMM
## show the results on equivalent dose, standard error and proportion of
## fitted components
get_RLum(object = FMM, data.object = "components")
``` |

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