Description Usage Arguments Details Value See Also Examples

View source: R/BchronDensity.R

This function runs a non-parametric phase model on 14C and non-14C ages via Gaussian Mixture density estimation

1 2 3 4 | ```
BchronDensity(ages, ageSds, calCurves, pathToCalCurves = system.file("data",
package = "Bchron"), dfs = rep(100, length(ages)), numMix = 50,
iterations = 10000, burn = 2000, thin = 8, updateAges = FALSE,
store_density = TRUE)
``` |

`ages` |
A vector of ages (most likely 14C) |

`ageSds` |
A vector of 1-sigma values for the ages given above |

`calCurves` |
A vector of values containing either 'intcal13', 'shcal13', 'marine13', or 'normal'. Should be the same length the number of ages supplied. Non-standard calibration curves can be used provided they are supplied in the same format as those previously mentioned and are placed in the same directory. Normal indicates a normally-distributed (non-14C) age. |

`pathToCalCurves` |
File path to where the calibration curves are located. Defaults to the system directory where the 3 standard calibration curves are stored |

`dfs` |
Degrees-of-freedom values for the t-distribution associated with the calibration calculation. A large value indicates Gaussian distributions assumed for the 14C ages |

`numMix` |
The number of mixture components in the phase model. Might need to be increased if the data set is large and the phase behaviour is very complex |

`iterations` |
The number of iterations to run for |

`burn` |
The number of starting iterations to discard |

`thin` |
The step size of iterations to keep |

`updateAges` |
Whether or not to update ages as part of the MCMC run. Default is FALSE. Changing this to TRUE will improve performance but will fit a slightly invalid model |

`store_density` |
Whether or not to store the density and age grid. Useful for plotting the output in other packages |

This model places a Gaussian mixture prior distribution on the calibrated ages and so estimates the density of the overall set of radiocarbon ages. It is designed to be a probabilistic version of the Oxcal SUM command which takes calibrated ages and sums the probability distributions with the aim of estimating activity through age as a proxy.

An object of class BchronDensityRun with the following elements:

thetaThe posterior samples of the restricted ages

pPosterior samples of the mixture proportions

muValues of the means of each Gaussian mixture

calAgesThe calibrated ages from

`BchronCalibrate`

GThe number of mixture components. Equal to numMix

age_gridA grid of ages used for the final density estimate

densityThe density estimate based on the above age grid

`Bchronology`

, `BchronRSL`

, `BchronDensityFast`

for a faster approximate version of this function

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

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