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Archive of open-archaeo, a list of open source archaeological software and resources.



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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...
Topics: GitHub, code, software, git
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A Distant Reading of the Day of Archaeology A Distant Reading of the Day of Archaeology Introduction The Day of Archaeology is an event where archaeologists write about their acitivities on a group blog . The event started in 2011 and aims to 'provide a window into the daily lives of archaeologists from all over the world'. Currently there are over 1000 posts on the blog, rather a lot to read in one sitting. Rather than closely read each post, we can do a distant reading to get some insights...
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Tidy Radiocarbon Dating Tools carbon14 The goal of carbon14 is to provide a tidy interface to radiocarbon dating, to promote its inclusion in reproducible manuscripts. Installation You can install carbon14 from github with: ``` r install.packages("devtools") devtools::install_github("paleolimbot/carbon14")``` Example Radiocarbon ages from Long Lake, Nova Scotia, Canada : #> # A tibble: 5 x 4#> sample_id depth age_14C age_error#> #> 1 LL082011-C2-39 94.0 9148...
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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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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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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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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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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...
Topics: GitHub, code, software, git
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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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An R package for the extraction, analysis and classification of (not only) archaeological objects from scanned images shapAAR This is an R package for the extraction, analysis and classification of (not only) archaeological objects derived from scanned images. Especially it aims at the analysis of the shapes/profiles of eg. ceramic vessels or arrow heads. Currently the extraction is implemented using active contour to identify and extract the shape informations. You can get an idea about its...
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QGIS plugin to transforms profile control points for fotogrammetric rectification from archaeological excavations. profileAAR A python PluginThe plugin profileAAR transforms profile control points for fotogrammetric rectification of profile images of archaeological excavations How to use profileAAR After installing and opening the plugin there is a "?"-Button in the Plugin. There you will find additional informations. QGIS 3 Install Qgis3 >3.6.0 You will find the Plugin in the...
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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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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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Interface for 14C-Database CalPal CalPal-Database CalPal 14C-Database created by Bernhard Weninger (Universität zu Köln) as part of the CalPal software package. This repository serves as an interface to access the data more easily. To restore the repository download the bundle wget https://archive.org/download/github.com-nevrome-CalPal-Database_-_2020-08-30_12-27-59/nevrome-CalPal-Database_-_2020-08-30_12-27-59.bundle and run: git clone nevrome-CalPal-Database_-_2020-08-30_12-27-59.bundle...
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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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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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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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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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R Shiny App - Search engine for radiocarbon dates from different source databases WebGIS-App and Search Engine neolithicRC Shiny app to search and filter radiocarbon dates from various source databases. neolithicRC is based on the R package c14bazAAR . You'll find more information there about the included databases and how to cite (!) them the meaning of the variables in the output table the methods to compile the data You can run this app on your own system by forking and cloning this...
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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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A web app and mapping interface for searching and displaying bibliographic information about Anatolian archaeology Anatolia Bibliography Map of Archaeology The goal of this project is to spatially locate bibliographic resources (published articles, books) regarding the archaeology of Anatolia (modern Turkey). This takes the bibliography of archaeology to the next level by showing not only the topics and authors, but where the archaeological research is being done. Note: This web app was...
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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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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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R interface for PaleoClim paleoclimate data rpaleoclim: an R interface for PaleoClim paleoclimate data PaleoClim \ < http://paleoclim.org > is a database of free, highresolution paleoclimate surfaces covering the whole globe. It includesthe standard bioclimatic variables commonly used in ecologicalmodelling, downscaled from the HadCM3 general circulation model for keytime periods, at up to 2.5 minute spatial resolution. This package provides a simple interface for downloading PaleoClim...
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A collection of time-stratigraphic publications Strativerse (source) This is the source of the Strativerse , as a Hugo site. Changes to this repository areautomatically synced to https://strativerse.org using Netlify . If you are interested in contributing, Isuggest opening anissue . Youcan browse the Strativerse at https://strativerse.org/ , or clone thisrepository, open in RStudio and use thehacked-together R toolbox to work with objects in tabular form. ``` r these functions are in the...
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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
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A Data Package specification for archaeological stratigraphy data following the Harris Matrix convention. Harris Matrix Data Package This repository contains archaeological stratigraphic datasets in CSVformat, following the table schema developed by Thomas S. Dye for the hm Lisp package ,together with a Python command-line tool that can check consistency ofdata with the format. Each dataset contains various tables and a data package descriptor( datapackage.json ) that enables consistency checks...
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munsell colour system for R munsell The munsell package provides easy access to, and manipulation of, the Munsell colours. The munsell package provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal sRGB strings suitable for use directly in R graphics. The package also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes. Munsell devised his system of colour notation to match the...
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ArcGIS toolbox for fuzzy viewshed calculation FuzzyViewshed Short Description The toolbox (built under ArcGIS 10.1 ) provides the facility to calculate the Fuzzy Viewshed as proposed by Ogburn 2006 , which modify the original proposal by Fisher. It produces a Fuzzy Vieshed raster in which, as customary in 'regular' (i.e., binary) viewshed rasters, 0 indicates cells that are not visible, 1 indicates cells that are visible. However, unlike binary viewshed, values between 0 and 1 correspond to a...
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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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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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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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by 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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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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Software deliverables for the ArchAIDE project archaide-software Software deliverables for the ArchAIDE project Installation The setup instructions were tested on Linux (Ubuntu 16.04) 64-bits. While theyshould work with minor modifications also on Windows/Mac, this was not tested. Python You will need to use Python >= 3.5.2 Required Python packages To run the code, you will need to have at least the following packages installedin your environment: numpy >= 1.15.1 tensorflow-gpu >=...
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by 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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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 Context Python Code Repository open-context-py Open Context Python Code Repository This project represents the current evolution of Open Context. It's intended to be an easier to maintain code-base,and to make the data published by Open Context easier to maintain. Installation and Deployment See the docs . Licensing: All the source code specific to this project is licensed under a GNU-GPL license (v. 3) All the usual liability waivers and disclaimers about using this code at your own...
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open-archaeo
by emanuelhuber
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Ground-penetrating radar (GPR) data processing and visualisation: a free and open-source software package (R language) RGPR : a free and open-source software package for ground-penetrating radar (GPR) data processing If you have any questions, comments or suggestions, feel free to contact me (in english, french or german): emanuel.huber@pm.me I am developing this package on my free time as a gift to the GPR community. Any support will be appreciated! RGPR is a free and open-source software...
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Experimenting with the opencontext.org API using R To restore the repository download the bundle wget https://archive.org/download/gist.github.com-50aa4c39b7d955d0ec40_-_2016-09-16_22-55-57/50aa4c39b7d955d0ec40_-_2016-09-16_22-55-57.bundle and run: git clone 50aa4c39b7d955d0ec40_-_2016-09-16_22-55-57.bundle Source: https://gist.github.com/50aa4c39b7d955d0ec40 Uploader: benmarwick Upload date: 2016-09-16
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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
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R package for years with an era era era is an R package that provides a consistent vector representationof years with an associated calendar era or time scale. It includesbuilt-in definitions of many contemporary and historic calendars; timescales commonly used in archaeology, astronomy, geology, and otherpalaeosciences (e.g. Before Present, SI-prefixed annus ); and supportfor arbitrary user-defined eras. Functions for converting between erasand for type-stable arithmetic with years are also...
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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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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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Configurable data entry program for archaeology E5 (Beta Version) E5 is a generalized data entry program intended for archaeologists but likely useful for others as well. It works with a configuration file where the data entry fields are defined. Importantly, E5 makes it simple to make entry in one field conditional on values previously entered for other fields. The goal is to make data entry fast, efficient and error free. E5 is a complete, from scratch re-write of E4. It is backwards...
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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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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...
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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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R Package - Explore SDS datasets (Systematic and digital documentation of stone artefacts) sdsanalysis sdsanalysis is the backbone of the sdsbrowser webapp. To learn more about it's role for this webapp please check the For developers section in the README over there. Beyond that sdsanalysis can be employed to analysis SDS stone artefact data in R. It offers two major functionalities for this purpose: Download available SDS datasets ?sdsdownload sdsanalysis offers functions to access openly...
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open-archaeo
by Landesamt-fuer-Archaeologie-Sachsen
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QGIS plugin for documentation of archaeological features using Tachy2GIS Tachy2GIS_arch QGIS plugin for documentation of archaeological features using Tachy2GIS Tachy2GIS arch (T2G arch) is a QGIS plugin that serves as application module for archaeological on-site documentation. It is designed to work with the forked Tachy2GIS plugin. T2g_arch aims to provide functions for an effective workflow with a focus on on-site documentation of geometries using a total station. The plugin is designed to...
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Data from Uerpmann 1987, The Ancient Distribution of Ungulate Mammals in the Middle East, TAVO A27 Uerpmann 1987, The Ancient Distribution of Ungulate Mammals in the Middle East , TAVO A27 This repository contains data from Uerpmann’s (1987), The AncientDistribution of Ungulate Mammals in the MiddleEast ,volume 27 of the Tübinger Atlas des Vorderen Orients (TAVO), Series A. Uerpmann catalogued the occurrence of ungulate taxa in animal boneassemblages from 196 sites across the Middle East,...
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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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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
by msu-anthropology
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Digital Encyclopedia of Archaeologists deoa Digital Encyclopedia of Archaeologists To restore the repository download the bundle wget https://archive.org/download/github.com-msu-anthropology-deoa_-_2017-11-29_06-22-59/msu-anthropology-deoa_-_2017-11-29_06-22-59.bundle and run: git clone msu-anthropology-deoa_-_2017-11-29_06-22-59.bundle Source: https://github.com/msu-anthropology/deoa Uploader: msu-anthropology Upload date: 2017-11-29
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open-archaeo
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Collection of 250+ datasets for photogrammetry Photogrammetry Datasets This is a collection of datasets for photogrammetry. A csv-table with 350+ datasets can be downloaded from this repository: datasets.csv . Contents Dataset,Camera,Category,Author,Organisation/Project,Source,Dataset link,Images,Size in GB,Ground Truth,License,License link,SampleImage,Image Format,DOI,Masks,Description The list includes a large variety of image sets and sizes.From small (
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open-archaeo
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Southwest Asian Palaeoarchaeology Data S outh w est A sian P alaeoarchaeology Data A collection of archaeological datasets and tools related to the prehistory of Southwest Asia. Installation You can install the development version of swapdata from GitHub using the remotes package : rremotes::install_github("joeroe/swapdata") To restore the repository download the bundle wget...
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open-archaeo
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R Package - Spatiotemporal Data Interpolation and Visualisation based on 3D Tessellation bleiglas bleiglas is an R package that employs Voro++ for the calculation of threedimensional Voronoi diagrams from input point clouds. This is a specialform of tessellation where each polygon is defined as the area closestto one particular seed point. Voronoi diagrams have useful applicationsin - among others - astronomy, material science or geography andbleiglas provides functions to make 3D tessellation...
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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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Bayesian reconstruction of ancient DNA fragments leeHom: Bayesian reconstruction of ancient DNA fragments QUESTIONS: gabriel [dot] reno [ at sign ] gmail.com About leeHom is a program for the Bayesian reconstruction of ancient DNA (the binary is mergeTrimReadsBAM). Downloading: Go to https://github.com/grenaud/leeHom and do one of the following: Clone the repository: git clone --recursive https://github.com/grenaud/leeHom.git Download the ZIP archive and then manually download the submodules...
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open-archaeo
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http://orbis.stanford.edu data as an R package rorbium http://orbis.stanford.edu data as an R package. Very little here yet. The source of the nodes and edges is http://github.com/sfsheath/gorbit . See that repository for links to Orbis related pages as ultimate source. To restore the repository download the bundle wget https://archive.org/download/github.com-sfsheath-rorbium_-_2014-12-25_21-10-56/sfsheath-rorbium_-_2014-12-25_21-10-56.bundle and run: git clone...
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open-archaeo
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This R Function creates a simple Ford diagram for archaeological seriation with error bars determined based on sample size where count data are given. Ford-Diagram This R Function creates a simple Ford diagram for archaeological seriation with error bars determined based on sample size where count data are given. To restore the repository download the bundle wget...
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open-archaeo
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The ARK v1.1.2 Stable Release ARK 1.1.2 Stable Release This repository is a copy of the ARK v1.1.2 tarball that can be downloaded from the ARK website at http://ark.lparchaeology.com/. Please visit this site for more information and installation instructions. About ARK ARK (The Archaeological Recording Kit) is a web-based ‘toolkit’ for the collection, storage and dissemination of archaeological data. It includes data-editing, data-creation, data-viewing and data-sharing tools, all of which...
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open-archaeo
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R package to simulate a Luminescence Reader To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-LumReader_-_2017-01-26_13-55-17/dstreble-LumReader_-_2017-01-26_13-55-17.bundle and run: git clone dstreble-LumReader_-_2017-01-26_13-55-17.bundle Source: https://github.com/dstreble/LumReader Uploader: dstreble Upload date: 2017-01-26
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open-archaeo
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Scripts to create QR-Code images for storage boxes. Each box has an associated web page describing its content, and the QR-Code serves as a short-link from the physical object to the web page. To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-qrcode-storage_-_2020-06-22_14-11-12/steko-qrcode-storage_-_2020-06-22_14-11-12.bundle and run: git clone steko-qrcode-storage_-_2020-06-22_14-11-12.bundle Source: https://codeberg.org/steko/qrcode-storage...
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open-archaeo
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Analogue and weighted averaging methods for palaeoecology analogue Released version Build status | Linux | Windows | Codecov || ----- | ------- | ------- || | | | What is analogue? analogue is an R package for use with palaeoecological data. Originally, analogue was intended as an R implementation of analogue methods such as analogue matching, ROC curves, and MAT transfer function models, and the computation of dissimilarity coefficients. Since then the scope of the package has grown to include...
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open-archaeo
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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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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
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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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R Package - Reconstruct Paths using Archaeological Monuments & Model Parameters of Infrastructure pathAAR R Package to reconstruct paths using archaeological monuments, model parameters of infrastructure and evaluate those parameters Archaeological remains of roads or infrastructure are rarely found, especially in earlier epochs. Usually, most premodern paths have been country lanes, which might be paved when needed. Hence, their preservation is linked to specific conditions, like...
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Installer files for Cherish software Installer files for Cherish software Requirements Windows platform. Qt Installer Framework (can be installed through Qt Maintenance Tool). Installer generation First, make sure the packages contains the latest archive of the software distribution. Use archivegen to create and place the *.7z file, e.g.: archivegen.exe cheris.7z cherish_directory The archive file has to be placed in \packages\...\data folder. Second, once the cherish software is updated and...
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open-archaeo
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A tool for creating and manipulating Harris Matrices, part of the Archaeological Recording Kit (ARK) by L ~ P : Archaeology ARK Matrix A tool for creating and manipulating Harris Matrices.Part of the Archaeological Recording Kit by L-P : Archaeology http://ark.lparchaeology.com NOTE: Primary development occurs on GitLab at https://gitlab.com/arklab/ArkMatrix . This repo is mirrored on GitHub for legacy links only. Features The following features are currently supported by the command line tool...
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open-archaeo
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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
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Radiocarbon Dating Resolution Calculator Res14C Radiocarbon Dating Resolution Calculator Overview A python implementation of the method of calculating radiocarbon dating resolution. For an overview of the method see: Svetlik, I., A. J. T. Jull, M. Molnár, P. P. Povinec, T. Kolář, P. Demján, K. Pachnerova Brabcova, et al. “The Best Possible Time Resolution: How Precise Could a Radiocarbon Dating Method Be?” Radiocarbon 61, no. 6 (December 2019): 1729–40....
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open-archaeo
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This is an R implementation of the Fast Marching Method (FMM), first developed by Sethian (1996), with the modifications of Silva and Steele (2012, 2014). fastmaRching This package is an R implementation of the Fast Marching Method (FMM) first developed by Sethian (1996). Although developed to model evolving boundaries, FMM can and has been used widely in fluid dynamics, image segmentation, to construct Voronoi diagrams, simulate diffusion processes, and calculate shortest-paths. This algorithm...
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open-archaeo
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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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