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ADMUR

Ancient Demographic Modelling Using Radiocarbon

Provides tools to directly model underlying population dynamics using date datasets (radiocarbon and other) with a Continuous Piecewise Linear (CPL) model framework. Various other model types included. Taphonomic loss included optionally as a power function. Model comparison framework using BIC. Package also calibrates 14C samples, generates Summed Probability Distributions (SPD), and performs SPD simulation analysis to generate a Goodness-of-fit test for the best selected model. Details about the method can be found in Timpson A., Barberena R., Thomas M. G., Mendez C., Manning K. (2020) <doi:10.1098/rstb.2019.0723>.

Functions (32)

ADMUR

ADMUR R package

CPLparsToHinges

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

SAAD

Radiocarbon dataset for South American Arid Diagonal (SAAD)

SPDsimulationTest

Goodness of Fit test, using SPD simulation

bluhm2421

Radiocarbon dataset from Bluhm and Surovell 2018

bryson1848

Radiocarbon dataset from Bryson et al. 2006

checkData

Checks a dataset for obvious clangers

convertPars

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

data1

Toy radiocarbon dataset

data2

Toy radiocarbon dataset

data3

Toy radiocarbon dataset

estimateDataDomain

Estimates the calendar date domain of a 14C dataset.

intcal13

Northern hemisphere 2013 calibration curve

intcal20

Northern hemisphere 2020 calibration curve

loglik

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

makeCalArray

Makes a calibration curve probability array

mcmc

Makes a MCMC chain using the Metropolis-Hastings algorithm.

objectiveFunction

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

phaseCalibrator

Generates an SPD for each phase in a dataset

plotCalArray

Plots a calibration curve probability array

plotPD

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

plotSimulationSummary

Plots a summary of the SPD simulation test

relativeRate

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

shcal13

Southern hemisphere 2020 calibration curve

shcal20

Southern hemisphere 2013 calibration curve

simulateCalendarDates

Converts calendar dates to 14C dates

sinewavePDF

PDF of a truncated sinusoidal curve

summedCalibrator

Generates a summed probability distribution (SPD) of calibrated dates

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

toy

Toy population model

uncalibrateCalendarDates

Converts calendar dates to 14C dates

ADMUR

Ancient Demographic Modelling Using Radiocarbon

v1.0.3
GPL-3
Authors
Adrian Timpson [aut, cre] (<https://orcid.org/0000-0003-0292-8729>)
Initial release
2021-03-19

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