Package: ADMUR 1.0.3.9005

Adrian Timpson

ADMUR: Ancient Demographic Modelling Using Radiocarbon

Statistical tools to directly model underlying population dynamics using date datasets (radiocarbon and other). Various model structures can be tested including Continuous Piecewise Linear (CPL) models that are flexible to estimate any complex population dynamics, Uniform, Exponential, Gaussian, Cauchy, Sinusoidal, Logistic and Power law. Bayesian parameter estimates of population models. 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) <https://royalsocietypublishing.org/doi/10.1098/rstb.2019.0723>.

Authors:Adrian Timpson [aut, cre]

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ADMUR/json (API)
NEWS

# Install 'ADMUR' in R:
install.packages('ADMUR', repos = c('https://ucl.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ucl/admur/issues

Datasets:
  • SAAD - Radiocarbon dataset for South American Arid Diagonal
  • bluhm2421 - Radiocarbon dataset from Bluhm and Surovell 2018
  • bryson1848 - Radiocarbon dataset from Bryson et al. 2006
  • data1 - Toy radiocarbon dataset
  • data2 - Toy radiocarbon dataset
  • data3 - Toy radiocarbon dataset
  • data4 - Toy radiocarbon dataset
  • intcal13 - Northern hemisphere 2013 calibration curve
  • intcal20 - Northern hemisphere 2020 calibration curve
  • shcal13 - Southern hemisphere 2013 calibration curve
  • shcal20 - Southern hemisphere 2020 calibration curve
  • toy - Toy population model

On CRAN:

21 exports 11 stars 1.60 score 1 dependencies 14 scripts 391 downloads

Last updated 1 years agofrom:838f661049. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winOKSep 13 2024
R-4.5-linuxOKSep 13 2024
R-4.4-winOKSep 13 2024
R-4.4-macOKSep 13 2024
R-4.3-winOKSep 13 2024
R-4.3-macOKSep 13 2024

Exports:checkDataconvertParsCPLparsToHingesestimateDataDomaingetModelChoicesloglikmakeCalArraymcmcobjectiveFunctionphaseCalibratorplotCalArrayplotPDplotSimulationSummaryrelativeRaterollmeansimulateCalendarDatesSPDsimulationTestsummedCalibratorsummedCalibratorWrappersummedPhaseCalibratoruncalibrateCalendarDates

Dependencies:mathjaxr

{width=680px} ADMUR: Ancient Demographic Modelling Using Radiocarbon

Adrian Timpson

Rendered fromguide.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2023-09-11
Started: 2020-07-08

{height=0.5in} Replicating published results

Adrian Timpson

Rendered fromreplicating-timpson-rstb.2020.Rmdusingknitr::rmarkdownon Sep 13 2024.

Last update: 2023-09-11
Started: 2020-11-04

Readme and manuals

Help Manual

Help pageTopics
ADMUR R packageADMUR
Radiocarbon dataset from Bluhm and Surovell 2018bluhm2421
Radiocarbon dataset from Bryson et al. 2006bryson1848
Checks a dataset for obvious clangerscheckData
Converts parameters to x,y coordinates (date and pdf) that describe a modelconvertPars
Converts CPL parameters (0 to 1) into hinge (x,y) coordinates (date and pdf) that describe a modelCPLparsToHinges
Toy radiocarbon datasetdata1
Toy radiocarbon datasetdata2
Toy radiocarbon datasetdata3
Toy radiocarbon datasetdata4
Estimates the calendar date domain of a 14C datasetestimateDataDomain
Lists currently available modelsgetModelChoices
Northern hemisphere 2013 calibration curveintcal13
Northern hemisphere 2020 calibration curveintcal20
Calculates the log likelihood of a population model, given a calibrated date PD matrixloglik
Makes a calibration curve probability arraymakeCalArray
Makes a MCMC chain using the Metropolis-Hastings algorithmmcmc
Objective function to be minimised in a search. Returns the negative log likelihoodobjectiveFunction
Generates an SPD for each phase in a datasetphaseCalibrator
Plots a calibration curve probability arrayplotCalArray
Plots a calibrated PD of a single date, or SPD of multiple dates, or multiple SPDsplotPD
Plots a summary of the SPD simulation testplotSimulationSummary
Calculates the relative growth (or decline) rate per generationrelativeRate
Rolling mean of a vector of valuesrollmean
Radiocarbon dataset for South American Arid Diagonal (SAAD)SAAD
Southern hemisphere 2013 calibration curveshcal13
Southern hemisphere 2020 calibration curveshcal20
Converts calendar dates to 14C datessimulateCalendarDates
Goodness of Fit test, using SPD simulationSPDsimulationTest
Generates a summed probability distribution (SPD) of calibrated datessummedCalibrator
Quick calibration of dates, without the need to choose a date range or generate a CalArraysummedCalibratorWrapper
Generates a summed probability distribution (SPD) after phasing datessummedPhaseCalibrator
Toy population modeltoy
Converts calendar dates to 14C datesuncalibrateCalendarDates