Chron.jl

# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#                                   Chron.jl                                    #
#                                                                               #
#       A two-part framework for (1) estimating eruption/deposition age         #
#  distributions from complex mineral age spectra and (2) subsequently building #
#  a stratigraphic age model based on those distributions. Each step relies on  #
#  a Markov-Chain Monte Carlo model.                                            #
#                                                                               #
#    The first model uses an informative prior distribution to estimate the     #
#  times of first (i.e., saturation) and last  mineral crystallization (i.e.,   #
#  eruption/deposition).                                                        #
#                                                                               #
#    The second model uses the estimated (posterior) eruption/deposition ages   #
#  distributions along with the constraint of stratigraphic superposition to    #
#  produce an age-depth model                                                   #
#                                                                               #
#   Last modified by C. Brenhin Keller 2021-05-05                               #
#                                                                               #
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #

module Chron

    using Reexport
    @reexport using VectorizedStatistics
    @reexport using NaNStatistics
    @reexport using StatGeochemBase

    # Basic statistics and UI resources
    using ProgressMeter: @showprogress, Progress, update!
    using LsqFit: curve_fit
    using KernelDensity: kde
    using DelimitedFiles

    # Bilinear exponential function
    using LoopVectorization
    # using Polyester: @batch
    include("Utilities.jl")
    # Functions for propagating systematic uncertainties
    using Distributions
    include("Systematic.jl")
    # Custom objects for holding Chron age data
    include("Objects.jl")
    # Intcal2013 calibration curve for radiocarbion
    include("Intcal.jl")
    # Functions for estimating extrema of a finite-range distribution
    include("DistMetropolis.jl")
    # Functions for stratigraphic modelling
    include("StratMetropolis.jl")

    using Plots
    include("Fitplot.jl")

    # Structs
    export ChronAgeData, HiatusData, StratAgeModelConfiguration, StratAgeModel

    # High-level functions
    export  StratMetropolis, StratMetropolisDist, StratMetropolis14C,
        tMinDistMetropolis, metropolis_min!, metropolis_min,
        metropolis_minmax!, metropolis_minmax,
        bilinear_exponential, bilinear_exponential_ll,
        plot_rankorder_errorbar, plot_rankorder_errorbar!,
        screen_outliers, BootstrapCrystDistributionKDE


    # Distributions
    export UniformDistribution, TriangularDistribution,
        HalfNormalDistribution, TruncatedNormalDistribution,
        MeltsZirconDistribution, MeltsVolcanicZirconDistribution,
        ExponentialDistribution, EllisDistribution, ArClosureDistribution

end # module