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open-archaeo
Jul 6, 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...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 2021 jgregoriods
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...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 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...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 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...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 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...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 2021 cl379
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R code for Geostatistics in ethnographic contests Geostat R code for Geostatistics in ethnographic contexts Code for executing and plotting kriging analyses in R. To restore the repository download the bundle wget https://archive.org/download/github.com-cl379-Geostat_-_2014-11-10_16-24-57/cl379-Geostat_-_2014-11-10_16-24-57.bundle and run: git clone cl379-Geostat_-_2014-11-10_16-24-57.bundle Source: https://github.com/cl379/Geostat Uploader: cl379 Upload date: 2014-11-10
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 2021 cl379
software

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None kriging Codes for performing kriging for ethnographic and archaeological data. To restore the repository download the bundle wget https://archive.org/download/github.com-cl379-kriging_-_2015-05-04_10-58-32/cl379-kriging_-_2015-05-04_10-58-32.bundle and run: git clone cl379-kriging_-_2015-05-04_10-58-32.bundle Source: https://github.com/cl379/kriging Uploader: cl379 Upload date: 2015-05-04
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 2021 Arothron
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Cross-Sectional Geometry Tool (CSGR) CSGR Cross-Sectional Geometry tool (CSGR extracts and calculates from long bone cross sections (e.g. mesh derived from CT data) cortical thickness maps, and biomechanically pertinent cross-sectional geometric (CSG) properties. Authors Profico Antonio, Damiano Marchi and Paul O'Higgins To restore the repository download the bundle wget https://archive.org/download/github.com-Arothron-CSGR_-_2018-09-12_11-05-11/Arothron-CSGR_-_2018-09-12_11-05-11.bundle and...
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open-archaeo
Jul 6, 2021 AProfico
software

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Tools for Geometric Morphometrics. The package includes tools of Virtual Anthropology to build virtual cavities as endocasts, to align two disarticulated models belonging to the same specimen, and functions to import and export format files into another format. Arothron Tools for Geometric Morphometrics. The package includes tools of Virtual Anthropology to build virtual cavities as endocasts, to align two disarticulated models belonging to the same specimen, and functions to import and export...
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open-archaeo
software

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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
Jul 6, 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 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
Jul 6, 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
software

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A set of GNU Octave functions for biodistance analysis based on non-metric traits To restore the repository download the bundle wget https://archive.org/download/github.com-pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12/pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12.bundle and run: git clone pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12.bundle Source: https://github.com/pr0m1th3as/non-metric-trait-analysis Uploader: pr0m1th3as Upload date: 2018-03-08
Topics: GitHub, code, software, git
open-archaeo
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Data analysis implementation for evaluating a novel sex estimation method based on skullanalyzer data cranial-sex-estimation-code Data analysis implementation for evaluating a novel sex estimation method based on skullanalyzer data To reimplement the analysis grab the morphometric feature dataset from https://zenodo.org/record/3632180 and save the relevant files into the corresponding folders. Keep the current directory structure and from within GNU Octave command window enter the ./analysis...
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open-archaeo
Jul 6, 2021 pr0m1th3as
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Skullanalyzer: a concrete way of extracting cranial morphometric features skullanalyzer a concrete way of extracting cranial mophometric features The skullanalyzer loads a 3D triangular mesh cranial model along with a number of user defined landmarks and extracts a set of cranial morphometric features, which can be used for further analyses. It requires two input files, one Alias Wavefront file (model name.obj) containing a triangular mesh of the cranial model to be analyzed and a Meshlab...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 2021 pr0m1th3as
software

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Tools for osteometric sorting of human remains osteometric-sorting Tools for osteometric sorting of human remains To restore the repository download the bundle wget https://archive.org/download/github.com-pr0m1th3as-osteometric-sorting_-_2020-05-09_00-52-46/pr0m1th3as-osteometric-sorting_-_2020-05-09_00-52-46.bundle and run: git clone pr0m1th3as-osteometric-sorting_-_2020-05-09_00-52-46.bundle Source: https://github.com/pr0m1th3as/osteometric-sorting Uploader: pr0m1th3as Upload date: 2020-05-09
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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
software

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A GNU Octave function for estimating sex from bones of the lower and upper limbs skeletal-sex-estimation A GNU Octave function for skeletal sex estimation The function estimate_sex provides a graphical user interface for estimating sex from various sleletal elements according to the selected classifier saved in the respective .mat files. The required classifier file can be parsed as an input argument to the function or it can be selected through the open file dialog when the function is called...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 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
Jul 6, 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
Jul 6, 2021 bischrob
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R Package for sourcing elements elemSource R Package for sourcing elements Warning: Currently in development: Only works with obsidian data calibrated by Bruker software with data formatted with the artifact/source in the first column the 10 elements from the calibration in the next columns, the source (site name or obsidian source) in the next column, andthe type in the next column (can only be 'Source' or 'Artifact). Example Install Two packages must be installed prior to installing...
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open-archaeo
Jul 6, 2021 bischrob
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Element Sourcing in R ElementSourcing Element Sourcing in R This R script is designed to source archaeological artifacts using elemental composition. It is primarily being designed to source obsidian, but I plan to adapt it for broader uses. To restore the repository download the bundle wget https://archive.org/download/github.com-bischrob-ElementSourcing_-_2018-02-06_20-35-44/bischrob-ElementSourcing_-_2018-02-06_20-35-44.bundle and run: git clone...
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open-archaeo
Jul 6, 2021 lutraconsulting
software

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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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open-archaeo
Jul 6, 2021 apalmisano82
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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
Jul 6, 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
Jul 6, 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 6, 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
Jul 6, 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
Jul 6, 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...
Topics: GitHub, code, software, git
open-archaeo
Jul 6, 2021 ruidlpm
software

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A workflow for integrating ancient lineages into present-day phylogenies. pathPhynder A workflow for ancient DNA placement into reference phylogenies. Description: Ancient DNA data is characterized by deamination and low-coverage sequencing, which results in a high fraction of missing data and erroneous calls. These factors affect the estimation of phylogenetic trees with modern and ancient DNA, especially when dealing with many ancient samples sequenced to lower coverage. Furthermore, most...
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open-archaeo
Jul 6, 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
Jul 6, 2021 StephanePeyregne
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None AuthentiCT is a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded libraries.It estimates contamination using an ancient DNA damage model and assumes that the contaminant is not deaminated. Installation: AuthentiCT requires Python 3.6+ and relies on a number of non-standard libraries. Here is the list of these dependencies with the versions that we used:- numpy (version 1.17.3)- numdifftools (version 0.9.39)-...
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open-archaeo
Jul 6, 2021 BoyanZhou
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SNP calling and genotyping for damaged DNA AntCaller SNP calling and genotyping for damaged ancient DNA Usage This program is built on Python2.7 and can only be used for SAM/BAM files with MD field under Linux system. Copy three .py files to the directory where SAM/BAM files are stored. Print "python AntCaller-1.1.py -help" for detailed usage information. SNP calling can only be performed after extracting damage information and pileuping reads. Examples for BAM file (Require SAMtools...
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 2021 willismonroe
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A digital Babylonian clock babylonian-hours This is a javascript based digital clock which computes your local time in 'seasonal-hours'. It's currently hosted at www.babylonianhours.com . To restore the repository download the bundle wget https://archive.org/download/github.com-willismonroe-babylonian-hours_-_2019-01-05_20-36-50/willismonroe-babylonian-hours_-_2019-01-05_20-36-50.bundle and run: git clone willismonroe-babylonian-hours_-_2019-01-05_20-36-50.bundle Source:...
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open-archaeo
Jul 6, 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
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open-archaeo
Jul 6, 2021 kintigh
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Room Accumulation Simulation ro estimate archaeological population growth rates ReadMe.txt Documentation provided in RoomAccumDocumentation.pdf Licence provided in License.txt Source code RoomAccumXX.dpr Program Source Code KWKStdXE.pas Utility functions called by the program Compiled Windows version RoomAccumXX.exe
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 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
Jul 6, 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
Jul 6, 2021 geanes
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An R package that provides datasets useful for biological and forensic anthropology. In addition, it includes helper functions for working with dataframes. bioanth An R package that provides datasets useful for biological and forensic anthropology. In addition, it includes helper functions for working with dataframes. This package provides the following datasets: howell : Howells Craniometric Data Set howelltest : Howells Craniometric Test Data Set goldman : Goldman Osteometric Data Set Note:...
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 2021 subwaystation
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None TOPAS - TOolkit for Processing and Annotating Sequence data This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules. Example Invocation: java -jar topas.jar -? This lists all available modules. | FASTA Processing Modules | FASTQ Processing Modules | GFF Processing Modules | VCF Processing Modules || ------------- |...
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open-archaeo
Jul 6, 2021 Integrative-Transcriptomics
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None MADAM - iMproving Ancient Dna AsseMbly Dependencies The following software has to be installed in order for the software to run: jdk7+ bwa: http://bio-bwa.sourceforge.net/ samtools: http://samtools.sourceforge.net/ ClipAndMerge: https://github.com/apeltzer/ClipAndMerge sga: https://github.com/jts/sga SOAPdenovo2: https://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/ MEGAHIT: https://github.com/voutcn/megahit qualimap: http://qualimap.bioinfo.cipf.es/ Note: Clip&Merge is...
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open-archaeo
Jul 6, 2021 KHanghoj
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None DamMet, a full probabilistic model for mapping ancient methylomes DamMet is probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.The model is implemented as a two step procedure. The first step recovers a maximum likelihood estimate (MLE) of the position specific deamination rates for methylated and unmethylated cytosine residues. The second step, making use of these deamination rates, returns a MLE of the methylation level in a...
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open-archaeo
software

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Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria mapping-iterative-assembler The basic idea of this program is to align DNA sequencing fragments(shotgun or targeted resequencing) to a reference, then call aconsensus. Then the consensus is used as new reference and the processis repeated until convergence. Since it was originally designed to beused on ancient DNA, it supports a position specific substitutionmatrix, which improves both alignment and...
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open-archaeo
Jul 6, 2021 jlapaijmans
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Consensify method for error reduction in ancient DNA pseudohaploidisation Consensify Documentation for Consensify v0.1 The manuscript accompanying this source is available on BioRxiv: https://www.biorxiv.org/content/early/2018/12/18/498915?rss=1 Axel Barlow and Johanna L. A. Paijmans, December 2018 emails: axel.barlow.ab@gmail.com, paijmans.jla@gmail.com Introduction Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to...
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open-archaeo
Jul 6, 2021 mpieva
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The ANFO ancient DNA mapper Where to start? Get the prerequisites, compile, create documentation, test. Also see the Github Wiki. Prerequisites are... Not too ancient G++; 4.0 and later work fine, 3.x might cause somedifficulties. Also make, a shell, and so on. protobuf. Find it at http://code.google.com/p/protobuf popt. You might already have it, else ask your admin or grab it athttp://rpm5.org/files/popt Doxygen, if you want the documentation. Can be found at http://doxygen.org zlib from...
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open-archaeo
Jul 6, 2021 grenaud
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Joint estimate of demography and contamination for nuclear ancient DNA Readme for DICE DICE is a Bayesian method to jointly estimate error rates, demographic parameters and the rate of contamination from present-day humans in ancient DNA (aDNA) samples from modern or archaic humans. Our approach is based on an MCMC sampler, and is applicable to nuclear autosomal aDNA data. It can also serve to infer the most probable ancestry of the individual(s) that contaminated the sample. Contact Fernando...
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open-archaeo
Jul 6, 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
Jul 6, 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...
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 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
Jul 6, 2021 alexherbig
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None MultiVCFAnalyzer Table of Contents Description Citation Usage Example Output FAQs Description MultiVCFAnalyzer is a SNP filtering and SNP alignment generation tool, designed around (but not limited to) low coverage ancient DNA data. MultiVCFanalyzer reads multiple VCF files as produced by GATK UnifiedGenotyper, performs filtering based on a number of criteria, and provides the combined genotype calls in a number of formats that are suitable for follow-up analyses such as phylogenetic...
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open-archaeo
Jul 6, 2021 TCLamnidis
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A python script to calculate the relative coverage of X and Y chromosomes, and their associated error bars, from the depth of coverage at specified SNPs. Sex.DetERRmine A python script to calculate the relative coverage of X and Y chromosomes, and their associated error bars, from the depth of coverage at specified SNPs. Mathematical equations added to README using this tool . Instructions The python script takes a modified output from samtools depth as input, via stdin. The samtools depth file...
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 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 6, 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
Jul 6, 2021 apeltzer
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The EAGER Pipeline DEPRECATED Please instead use https://github.com/nf-core/eager as EAGERv1 won't be developed any further. EAGER-GUI This is the main project for the EAGER project, with links to some tutorials, subsequent tools and HowTos and a FAQ which will be updated once we get feedback from end users. Please use the different bug trackers for other tools than the actual pipeline, e.g. the Clip&Merge issue tracking if you encounter issues with the Clip&Merge application. There is...
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open-archaeo
Jul 6, 2021 KHanghoj
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None epiPALEOMIX Pipeline Recently moved from BITBUCKET. A Fast, Accurate, and Automatic pipeline for generating nucleosome and methylation maps from high throughput sequencing data underlying ancient samples. Recent developments in ancient DNA research have shown that not only ancient genomes but ancient epigenomes can be recovered from high-throughput DNA sequence data. Although direct methods, such as bisulfite DNA treatment (Llamas et al. 2012) and target enrichment for methylated...
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open-archaeo
Jul 6, 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
Jul 6, 2021 survey2gis
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None survey2gis It is a little tool that can process survey data, suchas produced by a GPS or total station, and export it as topologicallycleaned data fit for use in GIS. For more information, seehttp://survey-tools.org and the user manual that came withthis software. Important links Official Website: http://survey-tools.org.Bugtracker: https://github.com/survey2gis/survey-tools/issuesMailinglist: https://groups.io/g/survey2gis/topics FAQs How do I install this software? Look into the folder...
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open-archaeo
Jul 6, 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
Jul 6, 2021 izaromanowska
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A collection of tutorial on agent-based modelling for archaeologists To restore the repository download the bundle wget https://archive.org/download/github.com-izaromanowska-ABM_tutorials_-_2019-06-21_13-17-40/izaromanowska-ABM_tutorials_-_2019-06-21_13-17-40.bundle and run: git clone izaromanowska-ABM_tutorials_-_2019-06-21_13-17-40.bundle Source: https://github.com/izaromanowska/ABM_tutorials Uploader: izaromanowska Upload date: 2019-06-21
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open-archaeo
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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
Jul 6, 2021 bocinsky
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Bindings to the tDAR API tdar This package allows programmatic access to the Digital ArchaeologicalRecord (tDAR) , a service of DigitalAntiquity . Installation You can install tdar from github with: # install.packages("devtools")devtools::install_github("bocinsky/tdar") Please note that this project is released with a Contributor Code ofConduct . By participating in this project you agree toabide by its terms. Basic usage Authentication tDAR authentication is handled through...
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open-archaeo
Jul 6, 2021 bocinsky
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The Southwest Taphonomic Protocol swtp This repository contains the data and code for our paper: Bocinsky, R. Kyle, Tiffany Clark, and Katherine A. Spielmann, (2020). The Southwestern Taphonomic Protocol . In review. How to cite Please cite this compendium as: Bocinsky, R. Kyle, Tiffany Clark, and Katherine A. Spielmann, (2020). Compendium of R code and data for ‘The Southwestern Taphonomic Protocol’ . Accessed 10 Dec 2020. Contents The :file_folder: paper directory contains:...
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open-archaeo
Jul 6, 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
Jul 6, 2021 eehh-stanford
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Yet Another Demographic Analysis package yada yada , which stands for Yet Another Demographic Analysis package,supports a variety of demographic tasks, with most applications drawnfrom forensic anthroplogy and archaeology. Installation You can install yada with: rdevtools::install_github("eehh-stanford/yada") Contributing Please note that the ‘yada’ project is released with a Contributor Codeof Conduct . By contributing to thisproject, you agree to abide by its terms. To restore...
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 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:...
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open-archaeo
Jul 6, 2021 ISAAKiel
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Largest Empty Circles after Andreas Zimmermann Largest Empty Circles (LEC) after Zimmermann and Wendt. Tool for calculating the largest empty circles and estimation of archaeological sites theoretically to be expected in region of interest. This package is an implementation of the method published by Andreas Zimmermann and Karl Peter Wendt (Zimmermann/Wendt 2003). Method to do Installation if(!require('devtools')) install.packages('devtools')devtools::install_github("ISAAKiel/lecAAR")...
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open-archaeo
Jul 6, 2021 ISAAKiel
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Exchange data format (XML) for NoNeK (Nordmitteleuropäische Neolithische Keramik) nonekXML In order to simplify an exchange of data included in NoNeK (Nordmitteleuropäische Neolithische Keramik), an XML schema for this purpose is presented here(http://www.uf.uni-erlangen.de/projekte-der-juengeren-urgeschichte/nonek-nordmitteleuropaeische-neolithische-keramik/) To restore the repository download the bundle wget...
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open-archaeo
Jul 6, 2021 ISAAKiel
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None postAAR The goal is to develop an automated process to detect buildings within large sets of postholes in multi-occupational sites, similar to the obsolete Windows-software "posthole" (http://www.uni-koeln.de/~al001/posthole.html) by Irwin Scollar. We start off with the original fortran-code by Karel Segeth. The first idea is to write a wrapper for R, perhaps moving to Python (with a QGIS-Plugin as final solution) at a later stage. To restore the repository download the bundle...
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open-archaeo
Jul 6, 2021 ISAAKiel
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Python implementation for https://github.com/ISAAKiel/postAAR postAAR-python Python Implementation for https://github.com/ISAAKiel/postAAR Current algorithm for finding rectangles Previous algorithm for finding rectangles Commit https://github.com/ISAAKiel/postAAR-python/commit/b914c0a86412de4d88c57111c344c41d3f9503ff and before To restore the repository download the bundle wget...
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open-archaeo
Jul 6, 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
Jul 6, 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...
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open-archaeo
Jul 6, 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...
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open-archaeo
Jul 6, 2021 clipo
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Iterative Deterministic Seriation Solution Seriation Algorithms, implementations, manuscripts, and test cases for iterative deterministic frequency seriation done by agglomeration. These algorithms are intended to automate and extend the initial, mainly manual implementation of IDSS in Lipo (2001). commandline: python ./IDSS.py --inputfile=../testdata/pfg.txt --xyfile=../testdata/pfgXY.txt --largestonly=1 --mst=1 --screen=1 as a module: import IDSSseriation= IDSS() args={}args['inputfile']...
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open-archaeo
Jul 6, 2021 aksel-blaise
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Peer reviewed and indexed articles published on Caddo archaeology since 2000. caddonet Peer reviewed and indexed articles published on Caddo archaeology since 2000. To restore the repository download the bundle wget https://archive.org/download/github.com-aksel-blaise-caddonet_-_2020-04-03_11-10-46/aksel-blaise-caddonet_-_2020-04-03_11-10-46.bundle and run: git clone aksel-blaise-caddonet_-_2020-04-03_11-10-46.bundle Source: https://github.com/aksel-blaise/caddonet Uploader: aksel-blaise Upload...
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open-archaeo
Jul 6, 2021 aksel-blaise
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Learn Git and Contribute to Texas Archaeology Git-to-the-Point: Learn Git and Contribute to Texas Archaeology Contributors: Robert Z. Selden, Jr.; Juanita D. Garcia; and David Foxe Diagnostic artifacts comprise the basis for archaeological interpretations; however, as our taxonomic definitions evolve, artifacts that were previously assigned to a type generally retain that designation, potentially confounding future research efforts and interpretations. For this exercise, the original type...
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open-archaeo
Jul 6, 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
Jul 6, 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
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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
Jul 6, 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
Jul 6, 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...
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open-archaeo
Jul 6, 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...
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open-archaeo
Jul 6, 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
Jul 6, 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
Jul 6, 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...
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open-archaeo
Jul 6, 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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