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An open source radiocarbon (14C) calibration software. Written in Python A radiocarbon calibration software DOI: https://doi.org/10.5281/zenodo.630455 IOSACal is the open source radiocarbon calibration software of the IOSA project. IOSACal includes: a programming library a web-based application a command-line program IOSACal is written in the Python programming language and it can runnatively on any platform where the Python interpreter is available,including all Linux distributions, MacOS X...
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open-archaeo
software

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Program for analysing NGS data. angsd: Program for analysing NGS data. http://www.popgen.dk/angsd Installation: 1) Using a local folder containing htslib git clone https://github.com/samtools/htslib.git; git clone https://github.com/angsd/angsd.git; cd htslib;make;cd ../angsd;make HTSSRC=../htslib 2) Systemwide installation of htslib git clone https://github.com/angsd/angsd.git; cd angsd;make Notes I've switched over to using htslib for parsing single reads (to allow for CRAM reading, while...
Topics: GitHub, code, software, git
open-archaeo
software

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A comprehensive list of literature on Agent Based Models (ABM) in Archaeology. Maintained and created by Iza Romanowska and Lennart Linde. The-ABM-in-Archaeology-Bibliography A selected yet comprehensive list of literature and resources on Agent Based Models (ABM) in Archaeology. Maintained and created by Iza Romanowska and Lennart Linde. Know a missing resource or found a broken link? Put up a pull request ! Our very subjective list of must-reads Axtell, R. L., Epstein, J. M., Dean, J. S. Et...
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open-archaeo
software

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Computer Aided Archaeology - course website repository. smada Statistical methods for archaeological data analysis - course website repository. To restore the repository download the bundle wget https://archive.org/download/github.com-BernCoDALab-caa_-_2021-06-23_13-44-53/BernCoDALab-caa_-_2021-06-23_13-44-53.bundle and run: git clone BernCoDALab-caa_-_2021-06-23_13-44-53.bundle Source: https://github.com/BernCoDALab/caa Uploader: BernCoDALab Upload date: 2021-06-23
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open-archaeo
software

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R package to compute dissimilarity between multivariate time series distantia: an R package to compute the dissimilarity between multivariate time-series Summary The package distantia allows to measure the dissimilarity betweenmultivariate ecological time-series ( METS hereafter). The packageassumes that the target sequences are ordered along a given dimension,being depth and time the most common ones, but others such as latitudeor elevation are also possible. Furthermore, the target METS can...
Topics: GitHub, code, software, git
open-archaeo
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R package for quantitative ethnobotany ethnobotanyR The goal of ethnobotanyR is to provide an easy-to-use platform forethnobotanists to work with quantitative ethnobotany assessments. Itclosely follows Tardio and Pardo-de-Santayana(2008) and Whitney etal. (2018) . Users of ethnobotanyR may find it useful to read the background papersand books on ethnobotany theory. In particular Albuquerque etal. (2019) and Gaoue etal. (2017) offer helpfulguidance to understanding theoretical approaches in...
Topics: GitHub, code, software, git
open-archaeo
software

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None To restore the repository download the bundle wget https://archive.org/download/github.com-Chronomodel-chronomodel_-_2021-02-02_16-41-52/Chronomodel-chronomodel_-_2021-02-02_16-41-52.bundle and run: git clone Chronomodel-chronomodel_-_2021-02-02_16-41-52.bundle Source: https://github.com/Chronomodel/chronomodel Uploader: Chronomodel Upload date: 2021-02-02
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open-archaeo
software

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Core development repository. gitHub: Vsn 6 (2020 - ), Vsn 5 (2018 - 2020), Vsn 4 (2014-2017). Sourceforge: Vsn 3 (2009-2013), Vsn 1 & 2 (2005-2009) HEURIST Core development repository, Vsn 6 (2021 - ), Vsn 5 (2018 - 2020), Vsn 4 (2014-2017). Vsn 1 - 3 on Sourceforge (2005 - 2013) See below the intro for information on code, licensing, installating, contributing and issue tracking Heurist is a mature web-based data management infrastructure that is specifically tailored to the needs of...
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open-archaeo
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Tasks for Excavations in AutoCAD ArchJobCAD This repository comprises three LISP-functions for repeated tasks in archaeological excavations. The aims are efficient work and a homogeneous structure for easy retrieval. This is achieved with standardised named layers for filtering and the extensive use of blocks with attributes including labels of features, finds and profiles. The detailed explanations are in German but the code includes German as well as English comments. The functions are:...
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open-archaeo
software

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R Package - Analyse geomagnetic data from archaeological context magAAR To restore the repository download the bundle wget https://archive.org/download/github.com-ISAAKiel-magAAR_-_2017-06-10_14-34-21/ISAAKiel-magAAR_-_2017-06-10_14-34-21.bundle and run: git clone ISAAKiel-magAAR_-_2017-06-10_14-34-21.bundle Source: https://github.com/ISAAKiel/magAAR Uploader: ISAAKiel Upload date: 2017-06-10
Topics: GitHub, code, software, git
open-archaeo
software

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R Package - Analysis of Archaeological Mortality Data mortAAR With mortAAR you can calculate a life table based on archaeological demographic data. You just need the number of people of a certain age, but you can also use single individual data. mortAAR allows to separate the data according to sex/location/epoch or any other grouping variable. What is a life table [aka discrete time survival analysis]? According to Chamberlain it is a "(...) mathematical device for representing the...
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open-archaeo
software

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R Package - Interaction with Oxcal oxcAAR oxcAAR (previously named roxcal ) is a collection of functions thatcan be used to execute OxCal from within R. Please note that there is a roxcal package package on GitHub,created by Gavin Simpson . If you justneed to import OxCal result files, you may consider using his package. License oxcAAR is released under the GNU General Public License, version2 . Comments and feedback arewelcome, as are code contributions. Installation To install the stable...
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open-archaeo
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Human stature apprixmation according to different conveniant estimation formula. statuAAR Estimation of human stature from long bone measurements according to several well established estimation formula. For a general introduction: Siegmund, F. (2019). Die Körpergröße der Menschen in der Ur- und Frühgeschichte Mitteleuropas und ein Vergleich ihrer anthropologischen Schätzmethoden. (Beiträge zur Archäologie des Lebensstandards, 1). Norderstedt: BoD. Ruff, Chr. B. (ed.) (2018). Skeletal...
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open-archaeo
software

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A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage DamageProfiler This method can be used to calculate damage profiles of mapped ancient DNA reads. Main author: Judith Neukamm judith.neukamm@uzh.ch \Contributor: Alexander Peltzer, James A. Fellows Yates, and Alexander Hübner. Citation If you use the tool, please cite the publication: DamageProfiler Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for...
Topics: GitHub, code, software, git
open-archaeo
by Landesamt-fuer-Archaeologie-Sachsen
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QGIS plugin for documentation of archaeological features using Tachy2GIS Tachy2GIS_arch QGIS plugin for documentation of archaeological features using Tachy2GIS Tachy2GIS arch (T2G arch) is a QGIS plugin that serves as application module for archaeological on-site documentation. It is designed to work with the forked Tachy2GIS plugin. T2g_arch aims to provide functions for an effective workflow with a focus on on-site documentation of geometries using a total station. The plugin is designed to...
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open-archaeo
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Pipelines and tools for the processing of ancient and modern HTS data. To restore the repository download the bundle wget https://archive.org/download/github.com-MikkelSchubert-paleomix_-_2021-06-18_21-33-17/MikkelSchubert-paleomix_-_2021-06-18_21-33-17.bundle and run: git clone MikkelSchubert-paleomix_-_2021-06-18_21-33-17.bundle Source: https://github.com/MikkelSchubert/paleomix Uploader: MikkelSchubert Upload date: 2021-06-18
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open-archaeo
software

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Fluorescence fitting GUI. To restore the repository download the bundle wget https://archive.org/download/github.com-NSLS-II-PyXRF_-_2021-02-03_16-51-52/NSLS-II-PyXRF_-_2021-02-03_16-51-52.bundle and run: git clone NSLS-II-PyXRF_-_2021-02-03_16-51-52.bundle Source: https://github.com/NSLS-II/PyXRF Uploader: NSLS-II Upload date: 2021-02-03
Topics: GitHub, code, software, git
open-archaeo
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An open access digital archive of antique Christian texts Patristic Text Archive: An open access digital archive of antique Christian texts This is the data repository for all texts in the Patristic Text Archive . All texts and metadata are distributed according to Capitains guidelines and encoded according to the Patristic Text Archive Schema . LICENSE: The individual files are licensed by different Creative Commons Licenses. The respective license is mentioned in the header of each file. This...
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open-archaeo
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Development version of the R package 'Luminescence' Luminesence The R package ‘Luminescence’ by the R-Luminescence Group provides acollection of various R functions for luminescence dating data analysis. Social media and other resources Follow us on or visit our R-Luminescence homepage . Installation i. Requirements Windows (32/64bit) : Rtools (providedby CRAN) macOS : Xcode (provided by Apple) Linux : gcc often comes pre-installed inmost distributions. ii. Install the package Install any...
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open-archaeo
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R package 'RCarb' RCarb The R package 'RCarb' provides a collection of various R functionsto model dose rates in carbonate-rich samples. The package is atranslation of the 'MATLAB' program Carb by Roger P. Nathan. Installation of the developer version To install the latest development builds of 'RCarb' directly fromGitHub, run rif(!require("devtools")) install.packages("devtools")devtools::install_github("R-Lum/RCarb@master") To install a developer build other than...
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open-archaeo
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Solving Ordinary Differential Equations to Understand Luminescence RLumModel The R package ‘RLumModel’ by Johannes Friedrich (University ofBayreuth, Germany), Sebastian Kreutzer (IRAMAT-CRP2A, UniversitéBordeaux Montaigne, France) and Christoph Schmidt (University ofBayreuth, Germany) provides a collection of various R functionsmodelling luminescence signals in quartz andAl 2 O 3 , based on energy-band models. For an introduction and further details, visit the RLumModelhomepage ....
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open-archaeo
software

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R package: wrapper for the C++ library `xylib` rxylib The R package rxylib provides and access to the C++ library xylib by wrapping the library usingRcpp. For supported data formats see https://github.com/wojdyr/xylib . Installation i. Requirements Windows (32/64bit) : Rtools (providedby CRAN) macOS : Xcode (provided by Apple) Linux : gcc often comes pre-installed inmost distributions. ii. Install the package (development version) To install the stable version from CRAN, simply run the...
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open-archaeo
software

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alligator - Allen Transformer Alligator - Allen Transformer Prerequisites The code is developed using and tested with: maven 3.5.0 Netbeans 8.2 Apache Tomcat 8.0.27.0 JDK 1.8 Java EE 7 Web Maven The alligator web application is build using maven as WAR-file. For details have a look at pom.xml . Download and install maven and run it. Setup Download and install maven . Run git clone https://github.com/RGZM/alligator.git to create a local copy of this repository. Run mvn install to install all...
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open-archaeo
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Repository containing lists of all published ancient metagenome samples (and related) ----[![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-orange.svg)](https://creativecommons.org/licenses/by/4.0/)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3980833.svg)](https://doi.org/10.5281/zenodo.3980833)![check_dataset](https://github.com/spaam-community/AncientMetagenomeDir/workflows/check_dataset/badge.svg)[![Joins us on...
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open-archaeo
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None 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...
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open-archaeo
software

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A web-based application to assist in geocoding of (mainly historical) datasets. Historical Geocoding Assistant Description The “Historical Geocoding Assistant” is an open-sourced browser-based application for assigning geographic coordinates in a more convenient and faster way than copy-pasting them from services such as Google Maps. The application was designed with historical projects in mind but is suitable for any geocoding work Essential Features works online with a live Google...
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open-archaeo
software

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Proof of concept map for disaster response and archaeology. For Keeping History Above Water conference, 2017 disastermap Demonstration map for disaster response and archaeology. For Keeping History Above Water conference, 2017. This data should not be used for official planning or decision making. Demonstration available at https://aejolene.github.io/disastermap/ Presentation details: Archaeology Disaster Response A demonstration map for Keeping History Above Water Conference, November 1, 2017...
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open-archaeo
software

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Methods for calibrating and analysing radiocarbon dates rcarbon This package enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al...
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open-archaeo
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Package for modelling artefact-scale data rtfact Package for modelling archaeological artefact data To restore the repository download the bundle wget https://archive.org/download/github.com-ahb108-rtfact_-_2021-01-25_09-24-54/ahb108-rtfact_-_2021-01-25_09-24-54.bundle and run: git clone ahb108-rtfact_-_2021-01-25_09-24-54.bundle Source: https://github.com/ahb108/rtfact Uploader: ahb108 Upload date: 2021-01-25
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open-archaeo
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Assorted methods to supplement core spatial packages in R sparch Assorted methods to supplement core spatial packages in R To restore the repository download the bundle wget https://archive.org/download/github.com-ahb108-sparch_-_2021-02-01_09-55-02/ahb108-sparch_-_2021-02-01_09-55-02.bundle and run: git clone ahb108-sparch_-_2021-02-01_09-55-02.bundle Source: https://github.com/ahb108/sparch Uploader: ahb108 Upload date: 2021-02-01
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open-archaeo
software

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A web app and mapping interface for searching and displaying bibliographic information about Anatolian archaeology Anatolia Bibliography Map of Archaeology The goal of this project is to spatially locate bibliographic resources (published articles, books) regarding the archaeology of Anatolia (modern Turkey). This takes the bibliography of archaeology to the next level by showing not only the topics and authors, but where the archaeological research is being done. Note: This web app was...
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open-archaeo
software

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An online space for sharing data, 3d models, etc about archaeological objects to enable the comparison of these objects. Archaoeological Object Sharing The goal of this project is to create a web space for the collaborative sharing of archaeological objects. The users would be able to upload data, photographs, and 3d models of objects from archaeological excavations and surveys. Material could include pottery sherds, stone tools, bones, etc. The ultimate aim is that this forms a place where...
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open-archaeo
software

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R scripts for digitizing, processing, analyzing, and comparing archaeological ceramic Ceramic Computation R scripts for digitizing, processing, analyzing, and comparing archaeological ceramic 2d profile drawings, photographs, and other data Overview This code was written with the goal of being able to automate 2d shape analysis of archaeological ceramics, particularly profile drawings of rim sherds. Much of the work and code was designed to help extract shape data from paper publications about...
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open-archaeo
by andredebuisne
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Archaeological Information System AIS - Archaeological Information System Created by Andre Debuisne - 2017 Written in C++ with Qt library A packaged .exe will be uploaded soon Current state of the AIS Current functionnalities : Create an archaeological site (.archeo) Create a layer (.arcus) Create an object Create a horizon Modify site, horizon, layer or object Delete site, horizon, layer or object I am working on : Harris Matrix Data table view Site sectors To restore the repository download...
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open-archaeo
software

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A Bayesian radiocarbon chronology model with R New: Bchron website Bchron is a Bayesian chronology model implemented in R. The package enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine...
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software

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None Iraq_mortar This application has three files: createTasks.py: for creating the application in PyBossa, and fill it with some tasks. template.html: the view for every task and deal with the data of the answers. tutorial.html: a simple tutorial for the volunteers. Funded Partners Testing the application You need to install the pybossa-client first (use a virtualenv and this needs boto): bash $ pip install -r requirements.txt $ cp s3_settings.py.tmpl s3_settings.py In the settings file, just...
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open-archaeo
software

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Dataset of 10,647 radiocarbon dates from the Near East from the Late Pleistocene until the Late Holocene (ca. 14 - 2 kya BP). NERD (Near East Radiocarbon Dates) Alessio Palmisano, Andrew Bevan, Dan Lawrence & Stephen Shennan The archive NERD provides a collation of 10,647 radiocarbon dates from 999 archaeological sites in the Near East from the Late Pleistocene until the Late Holocene (ca. 14 - 2 kya). These dates have been collected from existing online digital archives, and electronic and...
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open-archaeo
software

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Arches is a web platform for creating, managing, & visualizing geospatial data. Arches was inspired by the needs of the Cultural Heritage community, particularly the widespread need of organizations to build & manage cultural heritage inventories Arches Arches is a web-based, geospatial information system for cultural heritage inventory and management. Arches is purpose-built for the international cultural heritage field, and designed to record all types of immovable heritage, including...
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open-archaeo
software

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Software deliverables for the ArchAIDE project archaide-software Software deliverables for the ArchAIDE project Installation The setup instructions were tested on Linux (Ubuntu 16.04) 64-bits. While theyshould work with minor modifications also on Windows/Mac, this was not tested. Python You will need to use Python >= 3.5.2 Required Python packages To run the code, you will need to have at least the following packages installedin your environment: numpy >= 1.15.1 tensorflow-gpu >=...
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open-archaeo
software

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Datasets used in Binford's 2001 book "Constructing Frames of Reference: An Analytical Method for Archaeological Theory Building Using Ethnographic and Environmental Data Sets" binford This package contains datasets used in: Binford, Lewis R. 2001. Constructing Frames of Reference: An Analytical Method for Archaeological Theory Building Using Ethnographic and Environmental Data Sets University of California Press, Berkeley. This package contains three datasets: LRB : environmental and...
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open-archaeo
software

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CRAN Task View: Archaeological Science CRAN Task View: Archaeological Science Maintainer: Ben Marwick Contact: benmarwick at gmail.com Version: 2020-12-26 This CRAN Task View contains a list of packages useful for scientific work in Archaeology, grouped by topic. Note that this is not an official CRAN Task View, just one I have prepared for my own convenience, so it includes some packages only on GitHub and other non-CRAN resources I find useful. Many of the most highly recommended packages...
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open-archaeo
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None outliner A simple app for tracing outlines of an irregular shape and exporting the coordinates of the outline. Please install ImageMagick before attempting to use. Run the app from GitHub with shiny::runGitHub("benmarwick/outliner") To restore the repository download the bundle wget https://archive.org/download/github.com-benmarwick-outliner_-_2021-01-31_08-26-33/benmarwick-outliner_-_2021-01-31_08-26-33.bundle and run: git clone benmarwick-outliner_-_2021-01-31_08-26-33.bundle...
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open-archaeo
software

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Paleoclimate Reconstruction from Tree Rings using Correlation Adjusted corRelation paleocar paleocar is an R package implementing functions to performspatio-temporal paleoclimate reconstruction from tree-rings using theCAR (Correlation Adjusted corRelation) approach of Zuber and Strimmer asimplemented in the care package for R . It isoptimized for speed and memory use. This is based on the approach used in Bocinsky and Kohler (2014): Bocinsky, R. K. and Kohler, T. A. (2014). A 2,000-year...
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A repository of radiocarbon data for Rapa Nui rapanui-radiocarbon A repository of radiocarbon data for Rapa Nui This repository is intended to provide access to various tables of radiocarbon dates that exist for Rapa Nui. One challenge we have found in doing analyses of radiocarbon samples is that the data are often in tables as appendices but not included in an easy-to-share format (such as CSV). Thus when working on projects involving analyses of dates, one must painfully reenter the data. At...
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open-archaeo
software

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The Classical Language Toolkit To restore the repository download the bundle wget https://archive.org/download/github.com-cltk-cltk_-_2021-07-03_17-12-10/cltk-cltk_-_2021-07-03_17-12-10.bundle and run: git clone cltk-cltk_-_2021-07-03_17-12-10.bundle Source: https://github.com/cltk/cltk Uploader: cltk Upload date: 2021-07-03
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open-archaeo
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OpenAtlas is an open source, web based database system for complex archaeological, historical and prosopographical data. About OpenAtlas is an open source, web based database system forcomplex archaeological, historical and prosopographical data. The information is mapped as a network using classes and properties of the CIDOC CRM . Documentation: Manual , Wiki , Issues Demo versions Demo with data kindly provided by the MEDCON project. Development demo with data kindly provided by the DPP...
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open-archaeo
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Chronological Bayesian models integrated for Optically Stimulated Luminescence (OSL) Dating BayLum An R package for chronological Bay esian models integrated forOptically Stimulated (OSL) Lum inescence Dating Installation To install the latest development builds directly from GitHub, run rif(!require("devtools")) install.packages("devtools")devtools::install_github("crp2a/BayLum@master") To install a developer build other than ‘master’, replace the...
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open-archaeo
software

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:radioactive: Dose Rate Estimation from In-Situ Gamma-Ray Spectrometry Measurements gamma Overview gamma is intended to process in-situ gamma-ray spectrometrymeasurements for luminescence dating. This package allows to import,inspect and (automatically) correct the energy scale of the spectrum. Itprovides methods for estimating the gamma dose rate by the use of acalibration curve. This package only supports Canberra CNF and TKAfiles. The gammaShiny packageprovides an enhanced graphical user...
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open-archaeo
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iDAI.field | Archaeological Field Recording App by the German Archaeological Institute iDAI.field This is a monorepo containing three packages: iDAI.field Desktop : The iDAI.field desktop client based on AngularJS and Electron iDAI.field Mobile : The iDAI.field mobile client based on React Native iDAI.field Core : Shared TypeScript modules Development The repository uses lerna to manage sub-package dependecies.When first checking out the code base, bootstrap the dependencies with: $ npm run...
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open-archaeo
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Code repository of the book by Oliver Nakoinz and Daniel Knitter "Modelling Human Behaviour in Landscapes -- Basic concepts and modelling elements" mhbil Code repository of the book by Oliver Nakoinz and Daniel Knitter "Modelling Human Behaviour in Landscapes -- Basic concepts and modelling elements" published by Springer in 2016. You can get the book here: at Springer Worldcat link What will you find here? the code of the different chapters the data used within the book Why...
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open-archaeo
software

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An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data TKGWV2 An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data Description TKGWV2 is a pipeline to estimate biological relatedness (1st, 2nd, and unrelated degrees) between individuals specifically aimed at ultra-low coverage ancient DNA data obtained from whole genome sequencing.It is a massive update to the original TKrelated method published in 2017 (Fernandes et al.), with ease...
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open-archaeo
software

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Frequency time-series tools for archaeology archSeries Tools for Chronological Uncertainty in Archaeology Overview This package is designed to tackle a common problem in archaeology: the integration of information from multiple entities with varying chronological resolution and overlapping date ranges. It includes functions for constructing overall chronological distributions from tables of start dates, end dates, and weights; and for plotting those distributions in various ways. Distributions...
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open-archaeo
software

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Visual shape-matching of ceramics profiles CeraMatch Shape matching and clustering of ceramic shapes To restore the repository download the bundle wget https://archive.org/download/github.com-demjanp-CeraMatch_-_2021-01-26_21-06-30/demjanp-CeraMatch_-_2021-01-26_21-06-30.bundle and run: git clone demjanp-CeraMatch_-_2021-01-26_21-06-30.bundle Source: https://github.com/demjanp/CeraMatch Uploader: demjanp Upload date: 2021-01-26
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open-archaeo
by dirkseidensticker
software

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Archives des datations radiocarbone d'Afrique centrale aDRAC ( Archive des datations radiocarbones d’Afrique centrale ) Dirk Seidensticker & Wannes Hubau The archive for radiocarbon datings from Central Africa (aDRAC)provides a catalogue of available radiocarbon dates from Central Africa.The data cover published radiocarbon dates and essential metadata foreach date as well as available references. The data cover 1840 radiocarbon dates from 588 sites: Dates are available for the past up to...
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open-archaeo
software

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R package to simulate a Luminescence Reader To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-LumReader_-_2017-01-26_13-55-17/dstreble-LumReader_-_2017-01-26_13-55-17.bundle and run: git clone dstreble-LumReader_-_2017-01-26_13-55-17.bundle Source: https://github.com/dstreble/LumReader Uploader: dstreble Upload date: 2017-01-26
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open-archaeo
software

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R package for TL dating To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-TLdating_-_2017-09-06_14-41-46/dstreble-TLdating_-_2017-09-06_14-41-46.bundle and run: git clone dstreble-TLdating_-_2017-09-06_14-41-46.bundle Source: https://github.com/dstreble/TLdating Uploader: dstreble Upload date: 2017-09-06
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open-archaeo
software

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R package for extracting and analyzing grain sizes within R framework grainsizeR David Tavernini2017-02-12 Introduction This is a package developed by David Tavernini for a term project in GEOB 503. 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. For questions, comments, or issues please refer to the discussion tab or email me at taverninid@gmail.com . Requirements This...
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open-archaeo
software

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Bayesian tools for reconstructing past demography baydem The R package baydem (for bayESIAN demOGRAPHY) provides tools for reconstructing past and present demography. Installation There are three options for installing and using the package: (1) Install on an existing computer with necessary dependencies(2) Build a Docker image using the Dockerfile(3) Use a Docker image from Docker Hub Option 1: Install on an existing computer with necessary dependencies Details will vary based on the machine...
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Open Context Python Code Repository open-context-py Open Context Python Code Repository This project represents the current evolution of Open Context. It's intended to be an easier to maintain code-base,and to make the data published by Open Context easier to maintain. Installation and Deployment See the docs . Licensing: All the source code specific to this project is licensed under a GNU-GPL license (v. 3) All the usual liability waivers and disclaimers about using this code at your own...
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open-archaeo
by emanuelhuber
software

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Ground-penetrating radar (GPR) data processing and visualisation: a free and open-source software package (R language) RGPR : a free and open-source software package for ground-penetrating radar (GPR) data processing If you have any questions, comments or suggestions, feel free to contact me (in english, french or german): emanuel.huber@pm.me I am developing this package on my free time as a gift to the GPR community. Any support will be appreciated! RGPR is a free and open-source software...
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open-archaeo
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Models and Utility Functions for Bayesian Analyses of Radiocarbon Dates with NIMBLE 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 suited for demographic inferences based on changing frequencies of radiocarbon dates and enables parameter estimations and model comparison for the following population growth models (see Crema and Shoda 2021...
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open-archaeo
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R script for analyzing presence/absence data in irregularly distributed archaeological survey units Near-Presence-Analysis R script for analyzing presence/absence data in irregularly distributed archaeological survey units To restore the repository download the bundle wget https://archive.org/download/github.com-eweaverdyck-Near-Presence-Analysis_-_2021-06-11_19-30-34/eweaverdyck-Near-Presence-Analysis_-_2021-06-11_19-30-34.bundle and run: git clone...
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open-archaeo
by frederic-santos
software

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An R package to facilitate the use of Murail et al.’s (1999) approach of sex estimation in past populations rdss rdss is an R-shiny application for making sex estimation somewhat easier. The global approach follows the philosophy of "diagnose sexuelle secondaire", described by Murail et. al (1999) . Feature requests or bug reports are welcome. Documentation Publication This R package has been extensively described and documented in an article published in the International Journal...
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Total Station Online-Surveying with QGIS Dependencies: Tachy2GIS 3D-Viewer requires vtk to run. If you don't have it already (test this by typing import vtk in a python console), see Installation . Alternatively you can use pipenv to handle the dependencies for you, see the section Developer Notes further down for more info on this. You need at least QGIS version 3.10.7. This is because there are issues in previous versions when creating geometry from Well-known text. Your Total Stations Data...
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open-archaeo
software

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ArcGIS toolbox for fuzzy viewshed calculation FuzzyViewshed Short Description The toolbox (built under ArcGIS 10.1 ) provides the facility to calculate the Fuzzy Viewshed as proposed by Ogburn 2006 , which modify the original proposal by Fisher. It produces a Fuzzy Vieshed raster in which, as customary in 'regular' (i.e., binary) viewshed rasters, 0 indicates cells that are not visible, 1 indicates cells that are visible. However, unlike binary viewshed, values between 0 and 1 correspond to a...
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open-archaeo
software

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GIS toolbox for estimating the duration of ancient sail-powered navigation TRANSIT: Toolbox foR ANcient Sailing tIme esTimation Short Description Cost-surface analysis in Geographic Information System environment has been less frequently used in the study of ancient sail navigation than in other studies of the human past. Navigation cost-surface analysis entails the use of GIS tools that are versatile but not very easy to grasp and to put to work. TRANSIT is an ArcGIS toolbox built to...
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open-archaeo
software

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mapDamage: tracking and quantifying damage patterns in ancient DNA sequences mapDamage bioconda installation python3 version 2.2.1 conda install -c bioconda mapdamage2=2.2.1 python3 version 2.2.1 with R and 4 mandatory packages for the Bayesian inference: conda install -c bioconda mapdamage2=2.2.1=pyr40_0 Important From version 2.2.1 the master branch is requiring python3 as python2 is not supported from 2020-01-01. Introduction Complete documentation, instructions, examples, screenshots and...
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open-archaeo
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gargammel is an ancient DNA simulator gargammel: simulations of ancient DNA datasets gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samplesour program can also simulate various levels of present-day human contamination and microbial contamination. The website for gargammel can be found here: https://grenaud.github.io/gargammel/ Questions/bug report/feature requests : If you have Github account, consider creating an issue, you will help others who...
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Bayesian reconstruction of ancient DNA fragments leeHom: Bayesian reconstruction of ancient DNA fragments QUESTIONS: gabriel [dot] reno [ at sign ] gmail.com About leeHom is a program for the Bayesian reconstruction of ancient DNA (the binary is mergeTrimReadsBAM). Downloading: Go to https://github.com/grenaud/leeHom and do one of the following: Clone the repository: git clone --recursive https://github.com/grenaud/leeHom.git Download the ZIP archive and then manually download the submodules...
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open-archaeo
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Software to call ROHs hapROH Software to call ROH from ancient and present-day DNA using reference haplotypes.Author: Harald Ringbauer, September 2020Code released under GNU General Public License v3.0 Development Code behind python package hapROH.See https://pypi.org/project/hapROH/ for detail about the current version and installation. This is the git repository for development, as well as code used in the hapROH publication(Preprint at https://doi.org/10.1101/2020.05.31.126912) This code is...
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open-archaeo
software

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Forms for the Open Data Kit mobile data collection app ODK-forms-archaeology Forms for the Open Data Kit mobile data collection app These are a series of ODK forms I've created for my own archaeological field work. I provide them here, with no guarantees, warranties, support, or instructions, in case they may be useful for you. Most are provided in both the editable Excel spreadsheet form for use with xlsform , as well as the final XML for import into ODK or GeoODX. One or two may only have the...
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open-archaeo
software

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R package for aoristic analysis aoristic The goal of aoristic is to make sense of temporally vague data. It cansometimes be difficult to ascertain when some events (such as propertycrime) occur because the victim is not present when the crime happens Asa result, police databases often record a start (or from ) date andtime, and an end (or to ) date and time. The start datetime usuallyreferences when the victim last saw their stolen property, and the to date-time records when they first...
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open-archaeo
software

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Pipeline for metagenomic identification and authentication of ancient dietary DNA from archaeological samples Pipeline for metagenomic identification of dietary DNA from archaeological samples . Introduction The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. nf-core/archaeodiet performs identification and authentication...
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open-archaeo
software

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R library to generate 'Cumulative Percent Decay' curves for microbial taxonomic profiles cuperdec R package to generate 'Cumulative Percent Decay' curves, with optional filtering functions, for microbial taxonomic profiles. These curves aim to represent the level of 'endogenous' content of microbiome samples, such as ancient dental calculus, to help to identify samples with lowlevels of preservation that should be discarded for downstream analysis. Installation cuperdec is on CRAN. You can...
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open-archaeo
software

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Maya Calendar Tools Tools for converting between Maya and Western calendars. The Classic Maya developed the most sophisticated system for keeping track of time in the New World. In this app, you can convert dates from the Maya Calendar (Long Count and Calendar Round) to the Gregorian or Julian Calendars and vice-versa. You can also check the Maya glyphs for the current date. This is a React-Redux version of the Long Count tool in an older Vanilla app . Go to Web App To restore the repository...
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open-archaeo
software

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Maya Calendar Tools Tools for converting between Maya and Western calendars. The Classic Maya developed the most sophisticated system for keeping track of time in the New World. In this app, you can convert dates from the Maya Calendar (Long Count and Calendar Round) to the Gregorian or Julian Calendars and vice-versa. You can also check the Maya glyphs for the current date. More features will be added in future versions. Go to Web App To restore the repository download the bundle wget...
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open-archaeo
software

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Radiocarbon dates for the spread of farming and ceramics in tropical South America rxpand Radiocarbon dates for the spread of farming and ceramics in tropical South America Jonas Gregorio de Souza This package contains a dataset with 2762 radiocarbon dates from 1023 archaeological sites in lowland South America. In principle, only archaeological cultures related to the spread of polyculture agroforestry (tropical forest farming) and ceramics are represented. The dataset has been compiled and is...
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open-archaeo
software

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Analysis of spatial gradients in radiocarbon dates spDates Analysis of Spatial Gradients in Radiocarbon Dates Jonas Gregorio de Souza jonas.gregorio@gmail.com Tools to perform time-space regressions, an approach often used by archaeologists examining the expansion of cultural phenomena. In essence, one plots the radiocarbon ages of archaeological sites against their distances from a hypothetical origin. If a cultural advance has indeed taken place, the expectation is that radiocarbon dates will...
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open-archaeo
software

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R package for tidy radiocarbon data c14 c14 provides basic classes and functions for radiocarbon data in R.It makes it easier to combine methods from several existing packages(e.g. rcarbon, Bchron, oxcAAR, c14bazAAR, ArchaeoPhases, stratigraphr)together and work with them in a tidy data workflow. It was forked from stratigraphr v0.3.0. Installation You can install the development version of c14 from GitHub: ``` r install.packages("devtools")...
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open-archaeo
software

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R package for clean radiocarbon data cleanc14 cleanc14 provides some utility functions for cleaning radiocarbon data in R. Installation You can install the development version of cleanc14 using the remotes package: rremotes::install_github("joeroe/cleanc14") To restore the repository download the bundle wget https://archive.org/download/github.com-joeroe-cleanc14_-_2021-05-04_08-45-08/joeroe-cleanc14_-_2021-05-04_08-45-08.bundle and run: git clone...
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open-archaeo
software

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R package for years with an era era era is an R package that provides a consistent vector representationof years with an associated calendar era or time scale. It includesbuilt-in definitions of many contemporary and historic calendars; timescales commonly used in archaeology, astronomy, geology, and otherpalaeosciences (e.g. Before Present, SI-prefixed annus ); and supportfor arbitrary user-defined eras. Functions for converting between erasand for type-stable arithmetic with years are also...
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open-archaeo
software

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R Interface to IntChron rintchron: R interface to IntChron rintchron provides an R interface to IntChron , an indexing service and exchangeformat for radiocarbon dates and other chronological data ( Bronk Ramseyet al. 2019 ). It includes a userfriendly interface for querying databases indexed by IntChron, as wellas lower level functions for interacting directly with the IntChronAPI . For an introduction to querying IntChron’s databases see the basicusage vignette . Foradvanced users, low...
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open-archaeo
software

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R package for archaeological stratigraphy and chronological sequences stratigraphr stratigraphr is a tidy framework for working with archaeological stratigraphy and chronology in R.It includes tools for reading, analysing, and visualising stratigraphies (Harris matrices) and sequences as directed graphs;helper functions for using radiocarbon dates in a tidy data analysis; and an R interface to OxCal's Chronological Query Language (CQL). Installation You can install the development version of...
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open-archaeo
software

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Southwest Asian Palaeoarchaeology Data S outh w est A sian P alaeoarchaeology Data A collection of archaeological datasets and tools related to the prehistory of Southwest Asia. Installation You can install the development version of swapdata from GitHub using the remotes package : rremotes::install_github("joeroe/swapdata") To restore the repository download the bundle wget...
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open-archaeo
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None zoolog : Zooarchaeological Analysis with Log-Ratios Jose M Pozo , Silvia Valenzuela-Lamas , Angela Trentacoste , Ariadna Nieto-Espinet and Silvia Guimarães Chiarelli The R package zoolog includes functions and reference data togenerate and manipulate log-ratios (also known as log size index (LSI)values) from measurements obtained on zooarchaeological material. Logratios are used to compare the relative (rather than the absolute)dimensions of animals from archaeological contexts (Meadow...
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open-archaeo
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leastcostpath: Modelling Pathways and Movement Potential Within a Landscape leastcostpath - version 1.7.9 The R library leastcostpath provides the functionality to calculate Cost Surfaces based on multiple cost functions that approximate the difficulty of moving across a landscape. Furthermore, the attraction/repulsion of landscape features can be incorporated into the Cost Surfaces, as well as barriers that inhibit movement. NOTE: The R library leastcostpath requires the use of projected...
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Empirical XRF Calibrations CloudCal This app will allow you to build & apply calibrations for the Tracer & Artax series of XRF devices. It (currently) works with .csv files produced from S1PXRF, PDZ versions 24 and 25, .spx files, Elio spectra (.spt), .mca files, and .csv files of net counts produced from Artax (7.4 or later). How it works It is based on the Lucas-Tooth and Price (1961) algorithm 1 , though I have added modifications to make it more robust (it's really hard to get a...
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open-archaeo
software

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Radiocarbon dating laboratory code Radiocarbon dating laboratory code List of all past and present radiocarbon laboratory codes known to have been used in published references.\* = laboratories that are no longer operating or have changed their code designations. link c14-lab-code.csv c14-lab-code.txt Model |Code|Lab name|Country||---|---|---||A|Arizona|USA||AA|NSF|USA||AAR|University of Aarhus|Denmark||AC|Ingeis|Argentina||AECV |Alberta Environmental Center of Vegreville|Canada||AERIK |Atomic...
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open-archaeo
software

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The ARK v1.1.2 Stable Release ARK 1.1.2 Stable Release This repository is a copy of the ARK v1.1.2 tarball that can be downloaded from the ARK website at http://ark.lparchaeology.com/. Please visit this site for more information and installation instructions. About ARK ARK (The Archaeological Recording Kit) is a web-based ‘toolkit’ for the collection, storage and dissemination of archaeological data. It includes data-editing, data-creation, data-viewing and data-sharing tools, all of which...
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open-archaeo
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Preparation of Object Dating Ranges for Density Plots 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. A rather common problem in archaeology is the fuzzyness of dates assigned to objects. If one wants to visualize overall changes in - let's say - pottery consumption, bar charts often fall short in that regard. If,...
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open-archaeo
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Importing Data from iDAI.field 2 into R idaifieldR idaifieldR imports data from the iDAI.field 2 database into R. The core functions of this package use sofa (available on CRAN) to connect to a running iDAI.field 2-client and store the whole database in a list in R (in memory), avoiding the csv-export that would otherwise be needed and gathering all documents at once, which is not possible with said csv-export. Any R-Script using idaifieldR to import the database can be re-run and updated with...
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open-archaeo
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Survey made easy (Android/iOS/Windows app) Input Platform builds: Other Checks: Input makes surveying of geospatial data easy. You can design your survey project in QGIS with custom forms. Download Click below to download the app on your mobile device: Current Release Beta Release For more information on how to use the app, see Documentation . How to help/contribute? Help with translations, join Input App Transifex Team Write a review of the application on App Store or Android Google Play Test...
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None TransmissionBias Agent-Based Model of Biased Cultural Transmission This package 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. While it was designed to simulate the cultural transmission of birdsong, it is theoretically generalizable to any cultural system where individuals learn a repertoire (or a set) of cultural traits. The ABM is based on Lachlan et al. (2018) ,...
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Ancient DNA Read Simulator for Metagenomic Introduction ADRSM (Ancient DNA Read Simulator for Metagenomics) is a tool designed to simulate the paired-end sequencing of a metagenomic community. ADRSM allows you to control precisely the amount of DNA from each organism in the community, which can be used, for example, to benchmark different metagenomics methods. Requirements Conda Installation conda install -c maxibor adrsm Usage adrsm ./data/short_genome_list.csv Output metagenome.{1,2}.fastq :...
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Infrastructure for Ordering using Seriation - R Package seriation - Infrastructure for Ordering Objects Using Seriation - R package This package provides the infrastructure for ordering objects with an implementation of several seriation /sequencing/ ordination techniques to reorder matrices, dissimilaritymatrices, and dendrograms (see below for a full list). Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, andvisual assessment...
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This is an R implementation of the procedure outlined by John M. Roberts, Jr. et al. (2012) "A method for chronologically apportioning of ceramic assemblages" published in the Journal of Archaeological Science CeramicApportioning This is an R implementation of the procedure outlined by John M. Roberts, Jr. et al. (2012) "A method for chronologically apportioning of ceramic assemblages" published in the Journal of Archaeological Science Roberts, John M., Jr., Barbara J....
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Extract text from sign board and tag as metadata signboardr Utilize Google Vision API to extract text from archaeological photos containing a sign board. Further, the extracted text can be added as searchable XMP metadata tags to photos. Installation You can install signboardr from github with: ``` r install.packages("devtools") devtools::install_github("mrecos/signboardr")``` Description This package is a thin wrapper around the RoogleVision package getGoogleVisionResponse...
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open-archaeo
by msu-anthropology
software

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Digital Encyclopedia of Archaeologists deoa Digital Encyclopedia of Archaeologists To restore the repository download the bundle wget https://archive.org/download/github.com-msu-anthropology-deoa_-_2017-11-29_06-22-59/msu-anthropology-deoa_-_2017-11-29_06-22-59.bundle and run: git clone msu-anthropology-deoa_-_2017-11-29_06-22-59.bundle Source: https://github.com/msu-anthropology/deoa Uploader: msu-anthropology Upload date: 2017-11-29
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None ContamLD ContamLD is a software designed to estimate autosomal contamination in ancient DNA samples. The software requires Python 3 and R (any version should suffice). Citation: Nakatsuka, N.*; Harney, E.*; Mallick, S..; Mah, M.; Patterson, N.; Reich, D. "Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium." BioRxiv. Contact: Nathan Nakatsuka: nathan_nakatsuka@hms.harvard.edu Steps for use: Section 1) Pre-processing steps Part 1) Download...
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R Package - Spatiotemporal Data Interpolation and Visualisation based on 3D Tessellation bleiglas bleiglas is an R package that employs Voro++ for the calculation of threedimensional Voronoi diagrams from input point clouds. This is a specialform of tessellation where each polygon is defined as the area closestto one particular seed point. Voronoi diagrams have useful applicationsin - among others - astronomy, material science or geography andbleiglas provides functions to make 3D tessellation...
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