Packages and libraries

ADMUR

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, and 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.

adrsm

A tool designed to simulate the paired-end sequencing of a metagenomic community.

allen-relations

Allen relations from Bayesian calibration: R function to compare two indefinite intervals produced by a Bayesian calibration using the Allen algebra.

allen.archaeology

Allen’s Interval Algebra for Archaeologists.

analogue

Analogue and weighted averaging methods for palaeoecology.

anthropmmd

An R package for Smith’s Mean Measure of Divergence (MMD), with a graphical user interface, facilities for trait selection and graphical representations.

aoristAAR

A R package for the aoristic analysis of archaeological data.

aoristic

R package for aoristic analysis; the goal of aoristic is to make sense of temporally vague data.

ArchaeoChron

Bayesian Modeling of Archaeological Chronologies.

archaeodiet

Pipeline for metagenomic identification and authentication of ancient dietary DNA from archaeological samples.

ArchaeoLines

The ArchaeoLines plugin displays any combination of declination arcs most relevant to archaeo- or ethnoastronomical studies.

archaeological-survey-location-collector

An app for use in archaeological field survey to collect high-accurate point locations, photographs, and other data.

archaeology-data-service

An app to collect data on archaeological objects.

archaeology-object-data-collector-app

archaeology-object-data-collector-app

ArchaeoPhases

Tools for the post-processing of the Markov Chain simulated by any software used for the construction of archeological chronologies.

ArchaeoPhases

Post-Processing of the Markov Chain Simulated by ‘ChronoModel’, ‘Oxcal’ or ‘BCal’.

archdata

The archdata package provides several types of data that are typically used in archaeological research

archeofrag

R package for the analysis of the fragmentation of archeological objects.

ArchJobCAD

Tasks for Excavations in AutoCAD

archSeries

Frequency time-series tools for archaeology.

ArkGrid

A QGIS plugin for local site grids.

arkhe

A Collection of R S4 Classes that Represent Archaeological Data.

ArkMatrix

A tool for creating and manipulating Harris Matrices, part of the Archaeological Recording Kit ARK.

ArkSpatial

A QGIS plugin to simplfy digitization of archaeological plans drawn using the Museum of London Single Context Recording methodology.

Arothron

Tools of Virtual Anthropology to build virtual cavities as endocasts, to align two disarticulated models belonging to the same specimen, and functions to import and export format files into another format.

arshm-release

Experimental mobile app demoing cultural heritage documentation tools in augmented reality. Supports capturing and annotating photos in 3D space. Proof-of-concept features in the app include image anchoring and surface drawing tools.

AuthentiCT

Estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded libraries.

baydem

Bayesian tools for reconstructing past demography.

BayLum

An R package for chronological Bayesian models integrated for Optically Stimulated OSL, Luminescence Dating

Bchron

Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling

bioanth

An R package that provides datasets useful for biological and forensic anthropology.

bleiglas

An R package that provides functions for 3D tessellation with Voro++ and subsequent horizontal cutting of the resulting polygons for 2D plotting. It was developed for archaeological spatiotemporal data, but may as well be used for other three dimensional contexts.

c14

R package for tidy radiocarbon data.

c14bazAAR

R package to query different openly accessible radiocarbon date databases, allowing for basic data cleaning, calibration and merging

CAinterprTools

R package to help interpreting Correspondence Analysis' results.

carbon14

The goal of carbon14 is to provide a tidy interface to radiocarbon dating, to promote its inclusion in reproducible manuscripts

CAseriation

R Package for contingency tables seriation via Correspondence Analysis.

cawd

An R package that collects together data for the ancient world

CeraMatch

Visual shape-matching of ceramics profiles.

charcoalhearths

Work with geotifs to detect charcoal hearths

chronochrt

Building chronological charts easily with R.

Chronophage

Applications for obtaining chronograms (quantified chronology diagrams) and time distribution curves of archaeological or historical units from quantified dating indicators treated as inaccuracy intervals.

chronup

NA

cleanc14

Provides some utility functions for cleaning radiocarbon data in R.

cltk

A Python library offering natural language processing (NLP) for pre-modern languages.

clustering_14C

A python implementation of the method of clustering radiocarbon dates in order to determine whether they represent separate events, or phases in time

coenocliner

An R package to simulate species occurences and abundances counts, along gradient.

coproID

CoproID helps you to identify the “true maker” of Illumina sequenced Coprolites/Paleofaeces by checking the microbiome composition and the endogenous DNA.

crp2a

Dose Rate Estimation from In-Situ Gamma-Ray Spectrometry Measurements for Luminescence Dating

cTransmission

An Approximate Bayesian Computation Framework for inferring patterns of cultural transmission from frequency data.

CuneiPainter

An App to recognize cuneiform characters on your Android phone.

cuperdec

R package to generate ‘Cumulative Percent Decay’ curves, with optional filtering functions, for microbial taxonomic profiles.

datplot

Converting date ranges into dating ‘steps’ eases the visualization of changes in e.g. pottery consumption, style and other variables over time. This package provides tools to process and prepare data for visualization.

deeptime

Extends the functionality of other plotting packages like ‘ggplot2’ and ‘lattice’ to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data.

demjanp

Radiocarbon Dating Resolution Calculator.

dimensio

Simple Principal Components Analysis (PCA) and Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation.

distantia

R package to compute dissimilarity between multivariate time series.

DroneSurveyPlanner

This is a LibreOffice Calc spreadsheet designed to help you plan an aerial drone mapping survey mission.

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

ede_interpolation

A QGIS 3 plugin for spatio-temporal interpolation of archaeological settlement evidence.

elemSource

R Package for sourcing elements.

era

R package for year-based time scales

ethnobotanyR

R package for calculating quantitative ethnobotany indices.

Explographe

Application (in LibreOffice Calc) for serializing a graphic matrix from counting tables. The application makes it possible to obtain either a serograph or a graph of the PVI matrograph type (visualization of the differences in independence from the percentages of independence values) which does not favor the vision of the variables over that of the lines and more suitable for non-chronological treatments.

fastmaRching

An R implementation of the Fast Marching Method (FMM), first developed by Sethian (1996), with the modifications of Silva and Steele (2012, 2014). Also included is a spatial wrapper function that makes it easier to model dispersal scenarios in geospatial domains, as originally envisaged for the study and simulation of prehistoric dispersals

field-photographs

Android apps for archaeology that enable photography during field work.

fieldwalkr

Spatial Sampling and Survey Simulation Tools.

FuzzyViewshed

ArcGIS toolbox for fuzzy viewshed calculation.

GeoChronR

An integrated framework that allows scientists to generate state-of-the-art age models for their records, create time-uncertain ensembles of their data, analyze those ensembles with a number of commonly-used techniques, and visualize their results in an intuitive way.

geoCore

Constructs a graphical representation of petrographic drilling profiles.

ggvegan

ggplot-based plots for vegan.

GmAMisc

A collection of functions that built in different points in time. The functions' aim spans from univariate outlier detection, to permutation t test, permutation chi-square test, calculation of Brainerd-Robinson similarity coefficient, validation of logistic regression models, point pattern analysis, and more.

grainsizeR

This package contains all the tools necessary to extract grain sizes from images, digitally sieve grain size measurements, and gather descriptive statistics on sieved data.

hapROH

Software to call ROH from ancient and present-day DNA using reference haplotypes.

harris-matrix

Write Graphviz dot files for archaeological sequence diagrams and Bayesian chronological models.

Harris-matrix-legacy

Create a Harris Matrix from archaeological stratigraphy data using Python and Graphviz.

harris2graph

harris2graph is a script to help migrate data from the LST file format used by the BASP Harris, Stratify and ArchEd packages into modern graph file formats.

HOPS

A pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.

HumanOS

A mobile application for the intuitive recording of human bones from archaeological sites.

iconr

Set of formal methods for studying archaeological iconographic datasets (rock-art, pottery decoration, stelae, etc.) using network and spatial analysis.

idaifieldR

The goal of idaifieldR is to flexibly get data from the idaifield database into R.

input

Makes surveying geospatial data easy by designing your survey project in QGIS with custom forms.

IntCal

The IntCal20 radiocarbon calibration curves are provided here in a single data package, together with previous IntCal curves and postbomb curves.

Iraq_mortar

Enables the creation of a high quality 3D model of an archaeological artefact via process known as photo-masking.

kairos

Analysis of Chronological Patterns from Archaeological Count Data.

khroma

Colour Schemes for Archaeological Data Visualization

kotyle

Calculate the capacity of a ceramic vessel, like an amphora.

Le Stratifiant

Application for creating stratigraphic diagrams and checking the consistency of the chronostratigraphic recording.

leastcostpath

Provides the functionality to calculate Least Cost Paths (LCPs) which are often, but not exclusively, used in archaeological research. This package can be used to apply multiple cost functions when approximating the difficulty of moving across a landscape, as well as taking into account traversing across slope and other costs such as landscape features. This package also provides functionality to validate the accuracy of the computed LCP relative to another path.

lecAAR

Tool for calculating the largest empty circles and estimation of archaeological sites theoretically to be expected in region of interest, an implementation of the method published by Andreas Zimmermann and Karl Peter Wendt (2003).

Lithics3D

An R package for processing and analyzing 3D scans of archaeological lithics.

Luminescence

Development version of the R package ‘Luminescence’. The R package ‘Luminescence’ by the R-Luminescence Group provides a collection of various R functions for luminescence dating data analysis.

LumReader

R package to simulate a Luminescence Reader

magAAR

Analyse geomagnetic data from archaeological context

mapDamage

Tracking and quantifying damage patterns in ancient DNA sequences.

measure3d

A simple qgis plugin that measures the 3d distance between two selected points.

metabit

An integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.

mortAAR

Analysis of Archaeological Mortality Data.

mpvecost

Provides the facility to calculate non-isotropic accumulated cost surface and least-cost paths using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations.

MtreeRing

A tool for automatically measuring tree-ring width using image processing techniques.

mudata

The mudata2 package provides tools to read, write, and document multi-parameter spatiotemporal data.

munsell

Provides easy access to, and manipulation of, the Munsell colours

murature

This Python library was written as an help for the study of stone walls, mainly through the quantitative analysis of spatial dimensions of stones.

neotoma

Programmatic R interface to the Neotoma Paleoecological Database

nexus

Sourcing Archaeological Materials by Chemical Composition.

nimbleCarbon

The nimbleCarbon package provides utility functions and bespoke probability distributions for the Bayesian analyses of radiocarbon dates using the NIMBLE framework. The package is particularly dedicated to demographic inferences based on changing frequencies of radiocarbon dates.

ODK-forms-archaeology

Forms for the Open Data Kit mobile data collection app.

ODKArchForms

Open Data Kit forms and conversion scripts used in archaeology. Including New Mexico LA Forms, photologs, etc

opencontext

An R API client for the Open Context archaeological data repository.

osteoGIS

Plot data on skeletal templates quickly

outlineR

An R package to derive outline shapes from (multiple) artefacts on JPEG images.

outliner

A simple app for tracing outlines of an irregular shape and exporting the coordinates of the outline.

oxcAAR

A collection of functions that can be used to execute OxCal from within R.

p3k14c-data-scrubbing

Scrubbing program for the global archaeological radiocarbon dataset

paleocar

An R package implementing functions to perform spatio-temporal paleoclimate reconstruction from tree-rings using the CAR (Correlation Adjusted corRelation) approach of Zuber and Strimmer.

paleocoreR

R package for interacting with the Paleocore API

paleofire

An R package to analyse sedimentary charcoal records from the Global Charcoal Database to reconstruct past biomass burning

paleoxrf

The goal of paleoxrf is to simplify reading data from Acadia’s paleoenvironmental X-Ray Fluorescence laboratory

pathAAR

R Package to reconstruct paths using archaeological monuments, model parameters of infrastructure and evaluate those parameters, model parameters of infrastructure and evaluate those parameters.

pathPhynder

A workflow for integrating ancient lineages into present-day phylogenies.

piwigo-3dhop

Piwigo plugin for viewing 3D models using 3DHOP.

postAAR

An automated process to detect buildings within large sets of postholes in multi-occupational sites, similar to the obsolete Windows-software “posthole” by Irwin Scollar.

postAAR-python

Python implementation of postAAR.

predictSource

A package to analyze data used to determine whether samples from multiple sources can be separated, to predict the sources of samples from unknown sources, and to evaluation the validity of those predictions. Sample data can include both quantitative and qualitative data. The package includes functions for creating an analysis file from multiple files and exploratory data analysis, as well as multivariate statistical methods to determine source separation, predict sources of unknown samples, and evaluate the validity of the predictions (principal components, classification trees, and random forests).

profileAAR

python qgis plugin of recexcavAAR’s archprofile

pyArchInit

A python plugin for QGIS aimed at managing data from archaeological contexts on the GIS platform

PyXRF

PyXRF is a python-based sophisticated fluorescence analysis package for fitting and visualizing X-ray fluorescence data

QField

A simplified touch optimized interface for QGIS.

QGIS-scripts

Some scripts that could be useful for QGIS users.

QGIS-topographic-networks

Models relationships between elements in a terrain model, connecting pixels according to their height difference.

QGIS-visibility-analysis

Calculates visible surface from a given observer point over a digital elevation model. The plugin is intended for more complex modelling, such as the depth below the visible horizon or generation of intervisibilty networks between groups of points. It is particularly performant for multiple viewshed calculations form a set of fixed points.

quantAAR

R Library for Quantitative Analysis in Archaeology.

Rcarb

The R package ‘RCarb’ provides a collection of various R functions to model dose rates in carbonate-rich samples. The package is a translation of the ‘MATLAB’ program Carb by Roger P. Nathan

rcarbon

Methods for calibrating and analysing radiocarbon dates

rdss

An R package to facilitate the use of Murail et al.’s (1999) approach of sex estimation in past populations.

recexcavAAR

R package for 3D reconstruction of archaeological excavations.

RGPR

RGPR is a free and open-source software package to read, export, analyse, process and visualise ground-penetrating radar (GPR) data

rintchron

rintchron provides an R interface to IntChron, an indexing service and exchange format for chronological data such as radiocarbon dates.

RLumModel

Solving Ordinary Differential Equations to Understand Luminescence

rock-art-transfer-learning

Reconstructing rock art chronology with transfer learning

rpaleoclim

R interface for open paleoclimate data.

rtefact

Brings together a range of methods for analysing the time series, shapes and other properties of archaeological artefacts.

rxylib

R package: wrapper for the C+library xylib

SCEM

Performs the Splitting-Coalescence-Estimation Method to model birth seasonality in studies of herd animals.

sdsanalysis

dsanalysis is the backbone of the sdsbrowser webapp, and can be employed to analyse SDS stone artefact data in R.

senscape

A toolbox for modelling human perception of topography for QGIS, based on QGIS viewshed module.

Seriation

Algorithms, implementations, manuscripts, and test cases for iterative deterministic frequency seriation done by agglomeration.

seriation

R package that provides the infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms (see below for a full list). Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).

Seriographe EPPM

The EPPM serograph is a graphical tool for chronological serialization of archaeological furniture counting tables.

shapAAR

This is an R package for the extraction, analysis and classification of (not only) archaeological objects derived from scanned images. Especially it aims at the analysis of the shapes/profiles of eg. ceramic vessels or arrow heads.

shkrdata

Package for downloading and preparing shkr data for archaeological analysis

signboardr

Extract text from archaeological photos containing a sign board and tag as metadata.

simple-browser-gis-collector

Mobile-oriented browser based application that could be used for data collection.

sindwem

This R package contains exactly one function, that calculates the “sum of individual weighted means” according to a methodology that is quite common among archaeologists and was first published in 1988 by Elisabeth Fentress and Philip Perkins.

sitedefinition

The goal of sitedefinition is to see how feature densities might be used for site definition.

skyscapeR

An R package for data reduction, visualization and analysis in skyscape archaeology, archaeoastronomy and cultural astronomy.

soiltexture

The Soil Texture Wizard is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data

sparch

A set of extra utilities that extend the functionlaity provided by core packages for spatial data management and analysis in R.

SPARSE

Indexes >100,000 reference genomes in public databases in to hierarchical clusters and uses it to predict origins of metagenomic reads.

SPARTAAS

Statistical pattern recognition and dating using archaeological artefacts assemblages.

spDates

Analysis of spatial gradients in radiocarbon dates.

statuAAR

Estimation of human stature from long bone measurements according to several well established estimation formula.

stratigraphr

R package for archaeological stratigraphy and chronological sequences.

tabula

Analysis, Seriation and Visualization of Archaeological Count Data.

Tachy2GIS_arch

QGIS plugin for documentation of archaeological features using Tachy2GIS.

tapas

Evaluate the effectiveness of any short read mapper and its parameters using artificially generated reads.

tdar

R package that allows programmatic access to the Digital Archaeological Record (tDAR), a service of Digital Antiquity.

tfqar

Tools for Quantitative Archaeology - in R.

The Southwestern Taphonomic Protocol

A set of analyses to control for variable taphonomic impacts on archaeological faunal datasets.

tidypaleo

This package simplifies a few workflows when working with multi-proxy paleo-archive data

tipom

TIPOM is based on a methodology that was developed in the 1960s by Bernardino Bagolini. The basic idea is to use the three simple dimensions of length, width and thickness of each lithic artefact to classify them in discrete groups and infer their function.

Tldating

R package for TL dating

totalstation-tools

Tools to use and manipulate total station data

TRANSIT

GIS toolbox for estimating the duration of ancient sail-powered navigation.

TransmissionBias

Includes an agent-based model (ABM) of cultural transmission that simulates the three main forms of transmission bias: content bias, frequency bias, and demonstrator bias.

trenchdrawer

Plugin for drawing trenches.

UniformProbabilityDensityAnalysis

R implementation of the Uniform Probability Density Analysis approach

unstruwwel

Detect and Parse Historic Dates in R.

vegan

R package for community ecologists: popular ordination methods, ecological null models & diversity analysis.

vegan3d

Dynamic and static 3D plotting for vegan.

xrf

The goal of xrf is to provide tools to read, plot, and interpret X-Ray fluorescence spectra

xronos.R

A worldwide database of chronological information from archaeological contexts, including radiocarbon and dendrochronological data.

yada

yada, which stands for Yet Another Demographic Analysis package, supports a variety of demographic tasks, with most applications drawn from forensic anthroplogy and archaeology.

zooaRch

The zooaRch package provides analytical tools to make inferences on zooarchaeological data.

zooaRchGUI

The zooaRchGUI package provides a Graphical User Interface (GUI) to analytical tools for zooarchaeological data in the R package.

zoolog

Manipulate log-ratios (also known as log size index (LSI) values) from measurements obtained on zooarchaeological material.