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open-archaeo
Jul 6, 2021 dainst
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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
Jul 5, 2021 lutraconsulting
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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...
Topics: GitHub, code, software, git
open-archaeo
Jul 5, 2021 ISAAKiel
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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
Jul 3, 2021 nickmckay
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Development repository for GeoChronR geoChronR geoChronR What is it? Quantifying age uncertainties is a critical component of paleoscience (paleoclimatology, paleoecology, paleontology). geoChronR is 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. The code is being developed in...
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open-archaeo
Jul 3, 2021 cltk
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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
Topics: GitHub, code, software, git
open-archaeo
Jul 2, 2021 philriris
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A function for retrieving metrics for resistance-resilience from rcarbon permTest objects. p2pPerm A function for retrieving metrics for resistance-resilience from rcarbon SpdPermTest objects. p2pPerm() is an adaptation of Edinborough et al.'s post-hoc statistical test for demographic events in written and oral history (https://doi.org/10.1073/pnas.1713012114). The original function - p2pTest() in rcarbon - is for use with objects of class SpdModelTest . This function extends the principle to...
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open-archaeo
Jul 2, 2021 parkgayoung
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This repository contains our data and R code for our article on computational text analysis of racism in archaeology. Computational text analysis of archaeological writing about race This repository contains the data and code for our paper. Our pre-printis online here: Park, G., L-Y Wang, B. Marwick, (2020) How do archaeologists write about race? Computational text analysis of 41 years of Society of American Archaeology Annual Meeting Abstracts . , Accessed 21 Jun 2021. Online at...
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open-archaeo
Jul 2, 2021 zheminzhou
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Strain Prediction and Analysis with Representative SEquence Strain Prediction and Analysis using Representative SEquences (SPARSE) SPARSE indexes >100,000 reference genomes in public databases in to hierarchical clusters and uses it to predict origins of metagenomic reads. Installation SPARSE runs on Unix and requires Python version 2.7 (Python 3.x supports are under development) System modules (Ubuntu 16.04) : pip gfortran llvm libncurses5-dev cmake xvfb-run (for malt, optional) 3rd-party...
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open-archaeo
Jul 2, 2021 danimfernandes
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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
Jul 1, 2021 masonyoungblood
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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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open-archaeo
Jun 30, 2021 mhahsler
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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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open-archaeo
Jun 30, 2021 jfy133
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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...
Topics: GitHub, code, software, git
open-archaeo
Jun 29, 2021 stefaneichert
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Presentation frontend for archaeological data from OpenAtlas databases About THANADOS is an open source, web application for the presentation of archaeological data especially for burial studies.It started within the MEDCEM project and actively carries on the development of this application. See examples at THANADOS or MEDCEM The data is based on the OpenAtlas application The information is mapped as a network using classes and properties of the CIDOC CRM . Documentation: Wiki , Issues ,...
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open-archaeo
Jun 29, 2021 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
Jun 26, 2021 lsteinmann
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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
Jun 25, 2021 craws
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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...
Topics: GitHub, code, software, git
open-archaeo
Jun 24, 2021 tesselle
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:hourglass: Analysis of Chronological Patterns from Archaeological Count Data kairos Overview A toolkit for absolute dating and analysis of chronological patterns.This package includes functions for chronological modeling and dating ofarchaeological assemblages from count data. It allows to compute timepoint estimates (e.g. Mean Ceramic Date) and density estimates of theoccupation and duration of an archaeological site. Initial development is in progress. Installation You can install the...
Topics: GitHub, code, software, git
open-archaeo
Jun 23, 2021 ISAAKiel
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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
Jun 23, 2021 BernCoDALab
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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
Jun 23, 2021 hringbauer
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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
Jun 23, 2021 ginolhac
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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
Jun 21, 2021 philriris
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A compilation of anthropogenic radiocarbon dates for the Caribbean region caribbean-14C A compilation of 2147 anthropogenic radiocarbon ( 14 C) dates for the Caribbean region from 504 sites across 57 islands. The information in this repository is largely adapted from the paper "Reevaluating human colonization of the Caribbean using chronometric hygiene and Bayesian modeling" by Napolitano et al. in Science Advances (https://doi.org/10.1126/sciadv.aar7806). It also includes a number of...
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open-archaeo
Jun 18, 2021 MikkelSchubert
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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
Jun 18, 2021 ANGSD
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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...
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open-archaeo
Jun 18, 2021 yesdavid
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An R package to derive outline shapes from (multiple) artefacts on JPEG images. outlineR: An R package to derive outline shapes from (multiple) artefacts on JPEG images This package is a helpful wrapper around functions from mainly the Momocs (Bonhomme et al. 2014), EBImage (Pau et al. 2010), and imager (Barthelme et al. 2020) packages. It is designed for the fast and easy extraction of single outline shapes of, for example, stone tools from images containing multiple thereof, such as the ones...
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open-archaeo
Jun 17, 2021 ercrema
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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
Jun 17, 2021 willismonroe
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Proto-Elamite sign list pe-dictionary Project setup yarn install Compiles and hot-reloads for development yarn serve Compiles and minifies for production yarn build Lints and fixes files yarn lint Customize configuration See Configuration Reference . To restore the repository download the bundle wget https://archive.org/download/github.com-willismonroe-pe-dictionary_-_2021-06-17_05-04-27/willismonroe-pe-dictionary_-_2021-06-17_05-04-27.bundle and run: git clone...
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open-archaeo
Jun 16, 2021 grenaud
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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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open-archaeo
Jun 16, 2021 jgregoriods
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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
Jun 16, 2021 jgregoriods
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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
Jun 14, 2021 stschiff
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None SequenceTools This repository contains some programs that I use for processing sequencing data. Installation Simple Installation via stack and hackage This installation installs the latest version that is up on hackage : Download stack (https://docs.haskellstack.org/en/stable/README/#how-to-install). Run stack install sequenceTools --resolver nightly . You should now have the executables from this package under ~/.local/bin . Add ~/.local/bin to your PATH, for example by adding to your...
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open-archaeo
Jun 11, 2021 eweaverdyck
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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
Jun 4, 2021 RGZM
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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
May 29, 2021 roman-amphitheaters
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A dataset of Roman amphitheaters. About 'roman-amphitheaters' is a digital resource that collects information about Roman amphitheaters with a primary goal being the easy use of its data in a wide variety of computational environments. It is designed to support open-ended inquiry into the place and role of amphitheaters in the Roman Empire. The file 'roman-amphitheaters.geojson' holds the latest information and is the source for other derived files, including 'roman-amphitheaters.csv' and the...
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open-archaeo
May 27, 2021 jgregoriods
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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
May 27, 2021 mpeeples2008
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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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open-archaeo
May 27, 2021 jgregoriods
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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
May 24, 2021 tesselle
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:round_pushpin: Multivariate Data Analysis dimensio Simple Principal Components Analysis (PCA) and Correspondence Analysis(CA) based on the Singular Value Decomposition (SVD). This packageprovides S4 classes and methods to compute, extract, summarize andvisualize results of multivariate data analysis. It also includesmethods for partial bootstrap validation. There are many very good packages for multivariate data analysis (suchas FactoMineR , ade4 or ca , all extended by FactoExtra ). dimensio...
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open-archaeo
May 24, 2021 tesselle
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:closed_book: Datasets for Teaching Archaeology and Palaeontology folio Datasets for teaching quantitative approaches and modeling inarchaeology and paleontology. This package provides several types ofdata related to broad topics (cultural evolution, radiocarbon dating,paleoenvironments, etc.), which can be used to illustrate statisticalmethods in the classroom (multivariate data analysis, compositional dataanalysis, diversity measurement, etc.). This package is for teaching purposes only: some...
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open-archaeo
May 24, 2021 tesselle
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:globe_with_meridians: Sourcing Archaeological Materials by Chemical Composition nexus Exploration and analysis of compositional data in the framework ofAitchison (1986). This package provides tools for chemicalfingerprinting and source tracking of ancient materials. Initial development is in progress. Installation You can install the released version of nexus from CRAN with: rinstall.packages("nexus") And the development version from GitHub with: ``` r...
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open-archaeo
May 20, 2021 dirkseidensticker
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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
May 19, 2021 jfy133
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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
May 7, 2021 willismonroe
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Simple VueJS page generating fake laws of Hammurabi hammurabi-markov Project setup yarn install Compiles and hot-reloads for development yarn serve Compiles and minifies for production yarn build Lints and fixes files yarn lint Customize configuration See Configuration Reference . To restore the repository download the bundle wget https://archive.org/download/github.com-willismonroe-hammurabi-markov_-_2021-05-07_17-40-49/willismonroe-hammurabi-markov_-_2021-05-07_17-40-49.bundle and run: git...
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open-archaeo
May 6, 2021 PatristicTextArchive
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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
May 6, 2021 joeroe
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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
May 4, 2021 joeroe
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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
Apr 26, 2021 Integrative-Transcriptomics
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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...
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open-archaeo
Apr 23, 2021 gbv
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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
Apr 21, 2021 priyamoorjani
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Method for dating admixture in ancient DNA specimens DATES DATES (Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Narasimhan, Patterson et al. 2018 Installation To make the DATES executable, you will need the following libraries: GSL 2.5 (https://www.gnu.org/software/gsl/)OpenBLAS 0.2.20 (www.openblas.net)FFTW 3.3.8 (http://www.fftw.org/download.html)````You will need to edit the file ``Makefile`` and...
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open-archaeo
Apr 20, 2021 maxibor
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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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open-archaeo
Apr 20, 2021 pontussk
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Compute postmortem damage patterns and decontaminate ancient genomes PMDtools Compute postmortem damage patterns and decontaminate ancient genomes. Description PMDtools computes ancient DNA damage patterns, and implements a likelihood framework incorporating postmortem damage (PMD), base quality scores and biological polymorphism to identify degraded DNA sequences that are unlikely to originate from modern contamination. Using the model, each sequence is assigned a PMD score, for which positive...
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open-archaeo
software

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A GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry long-bone-diaphyseal-CSG-Toolkit A GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry The present set of GNU Octave functions provides a novel and robust algorithm foranalyzing the diaphyseal cross-sectional geometric properties of long bones, whichcan be applied to any 3D digital model of a humerus, femur or tibia bone representedas a triangular mesh in a Wavefront OBJ file format. The...
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open-archaeo
Apr 15, 2021 letreiro
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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
Apr 13, 2021 lsteinmann
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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
Apr 10, 2021 nevrome
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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...
Topics: GitHub, code, software, git
open-archaeo
Apr 9, 2021 eehh-stanford
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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-archaeo
Apr 8, 2021 apalmisano82
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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
Mar 31, 2021 clipo
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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
Mar 25, 2021 joeroe
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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...
Topics: GitHub, code, software, git
open-archaeo
Mar 11, 2021 rhuebler
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None HOPS Summary ## HOPS is a java pipeline which focuses on screening MALT data (see Table of Contents) for the presence of a user-specified list of target species. The pipeline essentially exists to make it easier to use MALT and MaltExtract in unison. To use HOPS you will need a config file, which specifies some key parameters for MALT and MaltExtract. You can have multiple config files to quickly redo a previous analysis or archive them to remember parameters you used in an analysis. HOPS...
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open-archaeo
Mar 10, 2021 ISAAKiel
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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:...
Topics: GitHub, code, software, git
open-archaeo
Mar 8, 2021 grenaud
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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...
Topics: GitHub, code, software, git
open-archaeo
Mar 5, 2021 nathan-nakatsuka
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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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open-archaeo
Mar 3, 2021 BlasBenito
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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
Mar 2, 2021 rubenmilla
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Repository of Crop Origins database and Phylo Food phylogeny Crop Origins is a comprehensive ckecklist of crop species cultivated for food. It includes species-level data on diverse continuous and categorical descriptors of antiquity of cultivation, organ harvested for primary use, growth form, and identities, distribution and climate at sites of origin of crops´ wild progenitors. Phylo Food is a time-calibrated and fully resolved phylogenetic tree of the species in Crop Origins. Downloads:...
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open-archaeo
Mar 1, 2021 zoometh
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Formal methods to study Prehistory iconography iconr package modeling Prehistoric iconography Created by Thomas Huet , Jose M Pozo , Craig Alexander The R package iconr is grounded in graph theory and spatial analysis to offer concepts and functions for modeling Prehistoric iconographic compositions and preparing for further analysis (clustering, typology tree, Harris diagram, etc.). The package purpose is to contribute to cross-cultural comparison through a greater normalization of...
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open-archaeo
Mar 1, 2021 HeuristNetwork
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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
Feb 27, 2021 barak-itkin
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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 >=...
Topics: GitHub, code, software, git
open-archaeo
Feb 25, 2021 josempozo
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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
Feb 12, 2021 iggdrasil
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Online archaeological data manager - [website](https://ishtar-archeo.net/) - [tracker](https://tickets.iggdrasil.net/projects/ishtar) - [documentation](http://ishtar.readthedocs.io/) - [forum](https://forum.ishtar-archeo.net/) Ishtar Description Ishtar is a database project for managing archaeological data and documentation (including archaeological finds) from archaeological operations, published as a free software under AGPL 3.0 or any later version license. The aim is to ensure maximum...
Topics: GitLab, code, software, git
open-archaeo
Feb 10, 2021 fcgl
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The GigaMesh Software Framework is a modular software for display, editing and visualization of 3D-data typically acquired with structured light scanning (SLS) or structure from motion (SfM). NAME GigaMesh - GigaMesh Software Framework for processing large meshes. DESCRIPTION The GigaMesh Software Framework is a modular software for display, editing and visualization of 3D-data typically acquired with structured light scanning (SLS) or structure from motion (SfM). It provides numerous functions...
Topics: GitLab, code, software, git
open-archaeo
Feb 9, 2021 poseidon-framework
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A toolset to work with modular genotype databases poseidon-tools A toolset to work with modular genotype databases formatted using Poseidon. The main executable within this package is called trident . Installation Quickstart Guide for the command line utility Poseidon package repositories Analysing your own dataset outside of the main repository Package creation and manipulation commands : init , forge , update Inspection commands : list , summarise , survey , validate Analysis commands :...
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open-archaeo
Feb 8, 2021 emanuelhuber
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 4, 2021 opengisch
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A simplified touch optimized interface for QGIS QField for QGIS A simplified touch optimized interface for QGIS. Perfect for field work on portable touch devices. Get it Check the documentation Contribute QField is an open source project, licensed under the terms of the GPLv2 or later. This means that it is free to use and modify and will stay like that. We are very happy if this app helps you to get your job done or in whatever creative way you may use it. If you found it useful, we will be...
Topics: GitHub, code, software, git
open-archaeo
Feb 4, 2021 bocinsky
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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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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 4, 2021 archesproject
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 4, 2021 ahb108
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 3, 2021 NSLS-II
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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
Feb 2, 2021 Chronomodel
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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
Topics: GitHub, code, software, git
open-archaeo
Feb 2, 2021 scikit-beam
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Data analysis tools for X-Ray, Neutron and Electron sciences MAILING LIST scikit-beam Documentation Examples scikit-beam-examples repository Powder calibration (still needs tilt correction) 1-time correlation dir Jupyter notebook Differential Phase Contrast dir Jupyter notebook Fast conversion to reciprocal space X-Ray Speckle Visibility Spectroscopy Basic Plotting of X-Ray Fluorescence Elemental Lines Quick start install with conda ```conda install scikit-beam -c nsls2forge ``` install...
Topics: GitHub, code, software, git
open-archaeo
Feb 2, 2021 SPAAM-community
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 2, 2021 vegandevs
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R package for community ecologists: popular ordination methods, ecological null models & diversity analysis vegan: an R package for community ecologists Released version Build status To restore the repository download the bundle wget https://archive.org/download/github.com-vegandevs-vegan_-_2021-02-02_10-51-39/vegandevs-vegan_-_2021-02-02_10-51-39.bundle and run: git clone vegandevs-vegan_-_2021-02-02_10-51-39.bundle Source: https://github.com/vegandevs/vegan Uploader: vegandevs Upload...
Topics: GitHub, code, software, git
open-archaeo
Feb 2, 2021 joeroe
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 2, 2021 leedrake5
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 1, 2021 benmarwick
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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
Feb 1, 2021 R-Lum
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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
Feb 1, 2021 andrewcparnell
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 1, 2021 ekansa
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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...
Topics: GitHub, code, software, git
open-archaeo
Feb 1, 2021 ahb108
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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
Jan 31, 2021 benmarwick
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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...
Topics: GitHub, code, software, git
open-archaeo
Jan 31, 2021 jerryratcliffe
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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
Jan 30, 2021 joeroe
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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...
Topics: GitHub, code, software, git
open-archaeo
Jan 29, 2021 zackbatist
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A list of open source archaeological software and resources Open Archaeology Software & Resources A list of open source archaeological software and resources See ToDo.md for a list of tools or resources that are in demand, but which currently do not exist or need to be significantly improved. 3d-ceramics : 3d models of archaeological ceramics. by: sfsheath links: [ GitHub ] * tags: [3D modelling] A Mobile Data-Collection Workflow for Archaeologists : A list of tools and resource for data...
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open-archaeo
Jan 29, 2021 zackbatist
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A database interface designed to facilitate the irregular, iterative, and non-linear workflows that are commonly employed in lithic analysis Queryable Artifact Record Interface [QuARI] QuARI is a database interface designed to facilitate the irregular, iterative, and non-linear workflows that are commonly employed in lithic analysis. Specifically, it is designed to facilitate workflows that tack back and forth between recording assemblage-level and artefact-level data – often beginning with...
Topics: GitHub, code, software, git
open-archaeo
Jan 28, 2021 ropensci
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R Package - Download and Prepare C14 Dates from Different Source Databases c14bazAAR is an R package to query different openly accessible radiocarbon date databases. It allows basic data cleaning, calibration and merging. If you're not familiar with R other tools (such as GoGet ) to search for radiocarbon dates might be better suited for your needs. Installation How to use ( Download , Calibration , Material classification , Country attribution , Duplicates , Conversion , Technical functions ,...
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open-archaeo
Jan 28, 2021 steko
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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...
Topics: Codeberg, code, software, git
open-archaeo
Jan 28, 2021 josephlewis
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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...
Topics: GitHub, code, software, git
open-archaeo
Jan 27, 2021 UCL
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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
Jan 26, 2021 tesselle
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:amphora: A Collection of R S4 Classes that Represent Archaeological Data arkhe Overview A collection of classes that represent archaeological data. This packageprovides a set of S4 classes that represent different special types ofmatrix (absolute/relative frequency, presence/absence data,co-occurrence matrix, etc.) upon which package developers can buildsubclasses. It also provides a set of generic methods (mutators andcoercion mechanisms) and functions (e.g. predicates). In addition, a...
Topics: GitHub, code, software, git