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ADMUR

Ancient Demographic Modelling Using Radiocarbon

Tools to directly model underlying population dynamics using chronological datasets (radiocarbon and other) with a variety of models, including Continuous Piecewise Linear (CPL) model framework. Optional taphonomy. Model comparison framework using BIC. Package also calibrates 14C samples, and generates Summed Probability Distributions (SPD). CPL modelling directly estimates the most likely population trajectory given a dataset, using SPD simulation analysis to generate a Goodness-of-fit test for the best selected model.

Please contact a.timpson@ucl.ac.uk in the first instance to make suggestions, report bugs or request help.

Installation

Install from CRAN, then load

install.packages('ADMUR')
library('ADMUR')

Guide

Refer to the vignette 'guide' for detailed support and examples.

vignette('guide', package = 'ADMUR')

References

This package accompanies the following paper:

Timpson A., Barberena R., Thomas M. G., Mendez C., Manning K. 2020. "Directly modelling population dynamics in the South American Arid Diagonal using 14C dates",Philosophical Transactions B. https://doi.org/10.1098/rstb.2019.0723.

Citations available as follows:

citation(package='ADMUR')

ADMUR was written in collaboration with:

  • University College London
    • Department of Genetics, Evolution and Environment
    • Molecular and Cultural Evolution Laboratory
    • UCL Research Software Development
  • Max Planck Institute for the Science of Human History
    • Department of Archaeology
    • Pan African Evolution ResearchGroup

Special thanks to Yoan Diekmann for his influential inferential input.

Also thanks to the following who have reported bugs, requested additional functionality, offered constructive criticism, or provided other advice:

  • Gregor Seyer
  • Uwe Ligges
  • Prof Brian Ripley
  • Enrico Crema
  • Ricardo Fernandes

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Version

Install

install.packages('ADMUR')

Monthly Downloads

148

Version

1.0.3

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Adrian Timpson

Last Published

March 23rd, 2021

Functions in ADMUR (1.0.3)

data1

Toy radiocarbon dataset
convertPars

Converts parameters to x,y coordinates (date and pdf) that describe a model
checkData

Checks a dataset for obvious clangers
ADMUR

ADMUR R package
loglik

Calculates the log likelihood of a population model, given a calibrated date PD matrix
makeCalArray

Makes a calibration curve probability array
CPLparsToHinges

Converts CPL parameters (0 to 1) into hinge (x,y) coordinates (date and pdf) that describe a model
data3

Toy radiocarbon dataset
sinewavePDF

PDF of a truncated sinusoidal curve
summedCalibrator

Generates a summed probability distribution (SPD) of calibrated dates
data2

Toy radiocarbon dataset
estimateDataDomain

Estimates the calendar date domain of a 14C dataset.
summedCalibratorWrapper

Quick calibration of dates, without the need to choose a date range or generate a CalArray.
summedPhaseCalibrator

Generates a summed probability distribution (SPD) after phasing dates
mcmc

Makes a MCMC chain using the Metropolis-Hastings algorithm.
uncalibrateCalendarDates

Converts calendar dates to 14C dates
toy

Toy population model
phaseCalibrator

Generates an SPD for each phase in a dataset
shcal13

Southern hemisphere 2013 calibration curve
simulateCalendarDates

Converts calendar dates to 14C dates
plotCalArray

Plots a calibration curve probability array
relativeRate

Calculates the relative growth (or decline) rate per generation.
objectiveFunction

Objective function to be minimised in a search. Returns the negative log likelihood.
shcal20

Southern hemisphere 2020 calibration curve
intcal20

Northern hemisphere 2020 calibration curve
intcal13

Northern hemisphere 2013 calibration curve
SAAD

Radiocarbon dataset for South American Arid Diagonal (SAAD)
plotPD

Plots a calibrated PD of a single date, or SPD of multiple dates, or multiple SPDs
SPDsimulationTest

Goodness of Fit test, using SPD simulation
plotSimulationSummary

Plots a summary of the SPD simulation test
bryson1848

Radiocarbon dataset from Bryson et al. 2006
bluhm2421

Radiocarbon dataset from Bluhm and Surovell 2018