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open-archaeo
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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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open-archaeo
by Landesamt-fuer-Archaeologie-Sachsen
software

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QGIS plugin for documentation of archaeological features using Tachy2GIS Tachy2GIS_arch QGIS plugin for documentation of archaeological features using Tachy2GIS Tachy2GIS arch (T2G arch) is a QGIS plugin that serves as application module for archaeological on-site documentation. It is designed to work with the forked Tachy2GIS plugin. T2g_arch aims to provide functions for an effective workflow with a focus on on-site documentation of geometries using a total station. The plugin is designed to...
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open-archaeo
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Routines to read and analyze LA-ICP-MS data from the Field Museum's Elemental Analysis Facility LA ICP MS-Routines_FMNH Routines to read and analyze LA-ICP-MS data from the Field Museum's Elemental Analysis Facility Significant contributions include:- Reading in large amounts of cleaned LA-ICP-MS data from xlsx files with each day as a separate sheet- Tidying the LA-ICP-MS data into a tidy data frame- Functions for converting elements calculated as % oxide to ppm- Writing the file to a csv in...
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open-archaeo
software

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R Package - Quantitative Analysis in Archaeology quantAAR quantAAR contains tidy wrappers and useful utility function for common applications of exploratory statistics in archaeology: Wrapper functions: Correspondence Analysis : ca.ca_ca ( ca::ca ), ca.vegan_cca ( vegan::cca ) Principal Components Analysis : pca.stats_prcomp ( stats::prcomp ), pca.vegan_rda ( vegan::rda ) Seriation : seriation.seriation_seriate ( seriation::seriate ), seriation.tabula_seriate ( tabula::seriate ) Principal...
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open-archaeo
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CharTool is a macro tool for quantifying charcoal particles for paleoecological research applications. The Charcoal Quantification Tool (CharTool): A suite of open-source tools for quantifying charcoal fragments in archaeological and paleoecological analysis 2020 CharTool is a suite of macro tools for quantifying charcoal fragment metrics and sediment attributes in archaeological, paleoecological, and paleo-fire science contexts. This folder contains ImageJ version 1.52 with CharTool installed...
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open-archaeo
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Software to call ROHs hapROH Software to call ROH from ancient and present-day DNA using reference haplotypes.Author: Harald Ringbauer, September 2020Code released under GNU General Public License v3.0 Development Code behind python package hapROH.See https://pypi.org/project/hapROH/ for detail about the current version and installation. This is the git repository for development, as well as code used in the hapROH publication(Preprint at https://doi.org/10.1101/2020.05.31.126912) This code is...
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open-archaeo
software

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Piwigo plugin for viewing 3D models using 3DHOP piwigo-3dhop piwigo-3dhop is a plugin for Piwigo that allows 3D models to be added to galleries and viewed using 3DHOP . 3DHOP currently supports models in .ply and .nxs format. Other files may be added to Piwigo using the "multiple formats" functionality but cannot be viewed directly. Installation From Piwigo The easiest way to install the plugin is from within Piwigo. Search for '3dhop' in the plugin manager, click 'install', and then...
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open-archaeo
software

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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
software

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

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Dashboard showing ceramic EDA and interaction network construction in the Late Prehistoric CIRV Ceramic_Dashboard Dashboard showing ceramic EDA and interaction network construction in the Late Prehistoric Central Illinois River Valley (CIRV). To learn more about the Late Prehistoric CIRV, take a look at The Mississippian Period and The Late Mississippian Period in this pdf document. This flexdashboard is a companion to Chapter 6 of the recently completed dissertation by Andrew Upton at Michigan...
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open-archaeo
software

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Management system for physical storage of archaeological finds (ARCHIVED) To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-nervia_-_2020-06-22_07-37-06/steko-nervia_-_2020-06-22_07-37-06.bundle and run: git clone steko-nervia_-_2020-06-22_07-37-06.bundle Source: https://codeberg.org/steko/nervia Uploader: steko Upload date: 2020-06-22
Topics: Codeberg, code, software, git
open-archaeo
software

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

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A page for video tutorials on R, specifically for archaeology To restore the repository download the bundle wget https://archive.org/download/github.com-MartinHinz-vitutr_-_2019-07-10_07-18-25/MartinHinz-vitutr_-_2019-07-10_07-18-25.bundle and run: git clone MartinHinz-vitutr_-_2019-07-10_07-18-25.bundle Source: https://github.com/MartinHinz/vitutr Uploader: MartinHinz Upload date: 2019-07-10
Topics: GitHub, code, software, git
open-archaeo
software

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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
software

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Map of the Roman Empire made with vector tiles Roman Empire Roman Empire Map made with vector tiles :globe with meridians: Browse the map Edit online Blog posts: http://commons.pelagios.org/2017/11/building-the-roman-empire-vector-tile-map/ http://commons.pelagios.org/2017/09/rdg-update-the-roman-empire-vector-map-project/ More information at: Source: Digital Atlas of the Roman Empire Further information at OpenMapTiles.org To restore the repository download the bundle wget...
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open-archaeo
software

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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:...
Topics: GitHub, code, software, git
open-archaeo
software

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R package for spatial sampling and survey simulation fieldwalkr fieldwalkr is a tool for designing and evaluating sampling strategies in spatial survey ( fieldwalking in archaeological jargon).It contains functions for simulating the effect of different survey units, sampling methods and detection functions on the estimation of randomly generated or observed point processes. Installation {r}devtools::install_github("joeroe/fieldwalkr") Demo An introduction to and short demonstration...
Topics: GitHub, code, software, git
open-archaeo
by msu-anthropology
software

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Digital Encyclopedia of Archaeologists deoa Digital Encyclopedia of Archaeologists To restore the repository download the bundle wget https://archive.org/download/github.com-msu-anthropology-deoa_-_2017-11-29_06-22-59/msu-anthropology-deoa_-_2017-11-29_06-22-59.bundle and run: git clone msu-anthropology-deoa_-_2017-11-29_06-22-59.bundle Source: https://github.com/msu-anthropology/deoa Uploader: msu-anthropology Upload date: 2017-11-29
Topics: GitHub, code, software, git
open-archaeo
software

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Plugin for drawing trenches To restore the repository download the bundle wget https://archive.org/download/github.com-MikeJJohnson-trenchdrawer_-_2016-05-10_08-42-06/MikeJJohnson-trenchdrawer_-_2016-05-10_08-42-06.bundle and run: git clone MikeJJohnson-trenchdrawer_-_2016-05-10_08-42-06.bundle Source: https://github.com/MikeJJohnson/trenchdrawer Uploader: MikeJJohnson Upload date: 2016-05-10
Topics: GitHub, code, software, git
open-archaeo
software

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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
software

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An R package to simulate species occurences and abundances (counts) along gradients coenocliner Released version Build status What is coenocliner? An R package to simulate species abundances (counts) along gradients One of the key ways quantitative ecologists attempt to understand the properties and behaviour of the methods they use or dream up is through the use of simulated data. There are a number of computer programmes for simulating ecological data along gradients, such as Peter Minchin's...
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open-archaeo
software

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None zoolog : Zooarchaeological Analysis with Log-Ratios Jose M Pozo , Silvia Valenzuela-Lamas , Angela Trentacoste , Ariadna Nieto-Espinet and Silvia Guimarães Chiarelli The R package zoolog includes functions and reference data togenerate and manipulate log-ratios (also known as log size index (LSI)values) from measurements obtained on zooarchaeological material. Logratios are used to compare the relative (rather than the absolute)dimensions of animals from archaeological contexts (Meadow...
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open-archaeo
software

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Quantum GIS plugin for visibility analysis Advanced viewshed analysis for QGIS Version: 1.2 Supported QGIS version: 3.x Licence: GNU GPLv3 Documentation : zoran-cuckovic.github.io/QGIS-visibility-analysis/ Author: Zoran Čučković ( web page ) Introduction: Viewshed analysis plugin for QGIS calculates visible surface from a given observer point over a digital elevation model. The plugin is intended for more complex modelling, such as the depth below the visible horizon or generation of...
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open-archaeo
software

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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
software

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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
software

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Synthetic Categories for Archaeological Vessel Comparison synthkat Synthetic Categories for Archaeological Vessel Comparison Synthkat is a computational initiative to construct flexible, synthetic categories of established ceramic and glass vessel classifications and typologies of the ancient Roman world. It will take a collection of different vessel-types, expressed as a set of attributes, and recategorize them to allow for cross-project comparison of assemblages. Project files and algorithms...
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open-archaeo
software

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R-script for conducting and evaluating bootstrapped correspondence analyses following methods published by Peeples and Schachner (2012) in the Journal of Archaeological Science Bootstrap-Correspondence-Analysis R-script for conducting and evaluating bootstrapped correspondence analyses following methods published by Peeples and Schachner (2012) in the Journal of Archaeological Science This code relates to the following article: Peeples, Matthew A. and Gregson Schachner2012 Refining...
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open-archaeo
software

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Script for conducting K-means cluster analysis using R. This script provides output designed to help the user select an appropriate cluster solution. Kmeans Script for conducting K-means cluster analysis using R. This script provides output designed to help the user select an appropriate cluster solution. K-means Cluster Analysis:K-means analysis is a divisive, non-hierarchical method of defining clusters. This is an iterative process, which means that at each step the membership of each...
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open-archaeo
software

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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
software

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3d models of archaeological ceramics. I work on Roman pottery so that's what's here for now. 3d-ceramics 3d models of archaeological ceramics. I work on Roman pottery so that's what's here for now. Here's an X3dom version of an African Red Slip plate. Click on the labels for links to further information: http://sfsheath.github.com/3d-ceramics/african red slip/hayes/ars hayes 61b.xhtml To restore the repository download the bundle wget...
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open-archaeo
software

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a light-weight database application designed to standardize and simplify data entry of archaeological or historical artifacts. ARCHIE An open source digitial inventory system designed for field and lab use byarchelogists. Branch | Build Status------ | ------------ Master | Development | Contents License Contact Info Dependencies License This Application falls under the Standard GPL v2. See Licence included with this tar file. Credit for code is listed in the changelog, or in the respective...
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open-archaeo
software

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Information and guidelines for a workshop about managing archaeological databases archaeo-db-workshop [homepage] [github] [etherpad] [.zip] Description Databases are crucial components of the archaeological toolbox that facilitate with the storage, organization and retrieval of information across a project. However, designing and implementing archaeological databases can be challenging due to the technical learning curve involved, the unique needs of archaeological projects, and lack of support...
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open-archaeo
software

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DIYFieldworkDatabase Overview of the system I put together a little DIY fieldwork database server using nearly entirely open source tools and software. It consists of a Raspberry Pi operating on a local network, which contains a MariaDB server, a SMB file sharing server, an R Shiny server, and automatic scheduled backups, but can be configured or extended to suit whatever situation you're in. This is a more collaborative and distributed setup than a typical Microsoft Access setup (or even...
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open-archaeo
software

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These scrapers, when ready, will make it possible to aggregate severalexisting databases into one (giant) metadatabase of radiocarbon dates. They're written in Javascript with Node.js and the scraperjs library. You can do cool stuff with many thousand radiocarbon dates: Reconstructing regional population fluctuations in the European Neolithic using radiocarbon dates: a new case-study using an improved method To restore the repository download the bundle wget...
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open-archaeo
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Analytical Dashboard for conducting various analysis to group and assess groupings for Neutron Activation Analytical chemical compositional data NAA analytical dashboard Analytical Dashboard for conducting various analysis to group and assess groupings for Neutron Activation Analytical chemical compositional data Very much a work in progress at this point but includes scripts to assess group membership probabilities using Mahalanobis distances (following Neff 2002) and a procedure for selecting...
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open-archaeo
software

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Tools to use and manipulate total station data totalstation-tools Tools to use and manipulate total station data Installation Requires a setup with python2.7. You can setup a virtualenv or conda env for this. Clone repository ``` clone repository from Github git clone https://github.com/WiseLabCMU/totalstation-tools.git clone totalopenstation as a submodule (if you do not want to set this up yourself, you should skip the submodule initialization) git submodule update --init``` Install...
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open-archaeo
software

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Programmatic R interface to the Neotoma Paleoecological Database. neotoma NOTE The Neotoma R package accesses the Windows-based API for the database. This API is being deprecated, but is still available. Due to changes in the database servers, the API Help is no longer functioning. Links to API help have been left, but do not resolve. The neotoma package is a programmatic R interface to the Neotoma Paleoecological Database . The package is intended to both allow users to search for sites and to...
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open-archaeo
software

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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
software

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R Package - Interaction with Oxcal oxcAAR oxcAAR (previously named roxcal ) is a collection of functions thatcan be used to execute OxCal from within R. Please note that there is a roxcal package package on GitHub,created by Gavin Simpson . If you justneed to import OxCal result files, you may consider using his package. License oxcAAR is released under the GNU General Public License, version2 . Comments and feedback arewelcome, as are code contributions. Installation To install the stable...
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open-archaeo
software

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An app for use in archaeological field survey to collect high-accurate point locations, photographs, and other data, using affordable differential GNSS equipment. Archaeology Survey - Android App This Android app is designed to support data collection during archaeological fieldwork. Specifically, this app can be modified to fit the data structures and infrastructure of a field surface survey project that involves fieldwalking. The main goal of this app is to geolocate field observations,...
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open-archaeo
software

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

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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
software

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The next generation archaeological data manager - O.I.A. code enhancements Siponto Medievale This repo contains the code running under www.sipontomedievale.it , an interactive website based on solid open source software (Bootstrap, OpenLayers, ThingiView) created to illustrate historical background, findings and data of the Siponto excavation site (Manfredonia, FG -- Italy). Folders sip-site contains the whole website and libraries ark-guide contains an old version of the GIS tool used to...
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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...
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open-archaeo
software

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:radioactive: Dose Rate Estimation from In-Situ Gamma-Ray Spectrometry Measurements gamma Overview gamma is intended to process in-situ gamma-ray spectrometrymeasurements for luminescence dating. This package allows to import,inspect and (automatically) correct the energy scale of the spectrum. Itprovides methods for estimating the gamma dose rate by the use of acalibration curve. This package only supports Canberra CNF and TKAfiles. The gammaShiny packageprovides an enhanced graphical user...
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open-archaeo
software

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Empirical XRF Calibrations CloudCal This app will allow you to build & apply calibrations for the Tracer & Artax series of XRF devices. It (currently) works with .csv files produced from S1PXRF, PDZ versions 24 and 25, .spx files, Elio spectra (.spt), .mca files, and .csv files of net counts produced from Artax (7.4 or later). How it works It is based on the Lucas-Tooth and Price (1961) algorithm 1 , though I have added modifications to make it more robust (it's really hard to get a...
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open-archaeo
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Tools for Quantitative Archaeology – in R. A list of R equivalents of TFQA (http://tfqa.com) programs. Tools for Quantitative Archaeology – in R 2020-11-06 Tools for Quantitative Archaeology (TFQA) is acollection of DOS programs developed by Keith Kintigh to performstatistical analyses used in archaeology. TFQA includes 50 programs andso gives a good representation of the range of analyses used byarchaeologists. The purpose of this document is to track which of theseanalyses are currently...
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open-archaeo
software

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Proto-Elamite sign list pe-dictionary Project setup yarn install Compiles and hot-reloads for development yarn serve Compiles and minifies for production yarn build Lints and fixes files yarn lint Customize configuration See Configuration Reference . To restore the repository download the bundle wget https://archive.org/download/github.com-willismonroe-pe-dictionary_-_2021-06-17_05-04-27/willismonroe-pe-dictionary_-_2021-06-17_05-04-27.bundle and run: git clone...
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open-archaeo
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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
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Pipeline for metagenomic identification and authentication of ancient dietary DNA from archaeological samples Pipeline for metagenomic identification of dietary DNA from archaeological samples . Introduction The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. nf-core/archaeodiet performs identification and authentication...
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open-archaeo
software

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Ahiny app for TL dating To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-shiny_TLdating_-_2016-11-02_16-04-05/dstreble-shiny_TLdating_-_2016-11-02_16-04-05.bundle and run: git clone dstreble-shiny_TLdating_-_2016-11-02_16-04-05.bundle Source: https://github.com/dstreble/shiny_TLdating Uploader: dstreble Upload date: 2016-11-02
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What’s the correlation between the exposure time of your photographs and the time of the day? expotime What's the correlation between the exposure time of your photographs and the time of the day? Good question. With clever use of GExiv2 via Python, it's easy to extract the data from EXIF tags. I used R to plot the data. To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-expotime_-_2020-08-08_08-20-45/steko-expotime_-_2020-08-08_08-20-45.bundle...
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open-archaeo
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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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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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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
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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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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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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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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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Geospatial analysis for neolithic settlements and archaeological data management To restore the repository download the bundle wget https://archive.org/download/github.com-fradeve-ark-addons_-_2014-10-30_23-48-58/fradeve-ark-addons_-_2014-10-30_23-48-58.bundle and run: git clone fradeve-ark-addons_-_2014-10-30_23-48-58.bundle Source: https://github.com/fradeve/ark-addons Uploader: fradeve Upload date: 2014-10-30
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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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source code for ODATE textbook draft ODATE Logo by LogoMakr.com To restore the repository download the bundle wget https://archive.org/download/github.com-o-date-draft_-_2020-07-11_17-25-37/o-date-draft_-_2020-07-11_17-25-37.bundle and run: git clone o-date-draft_-_2020-07-11_17-25-37.bundle Source: https://github.com/o-date/draft Uploader: o-date Upload date: 2020-07-11
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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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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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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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XRF tools for R xrftools The goal of xrftools is to provide tools to read, plot, and interpretX-Ray fluorescence spectra. Installation You can install xrftools from github with: ``` r install.packages("remotes") remotes::install_github("paleolimbot/xrftools")``` Example Read in a Panalytical XRF spectrum and plot it. ``` rlibrary(tidyverse)library(xrftools) > > Attaching package: 'xrftools' > The following object is masked from 'package:stats': > > filter pan...
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Database of roman construction materials, includes shapefiles, primary sources, and archaeological evidence. # Roman-material-database ABSTRACT: The Historic Materials Database is an interactive database of construction materials used in antiquity. This is the first step of my larger PhD project that will enable a wider audience to create 3D and virtual reality (VR) models of historic structures. By helping a user build accurate models, my project will provide new perspectives of historic...
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Allen's Interval Algebra for Archaeologists To restore the repository download the bundle wget https://archive.org/download/github.com-tsdye-allen.archaeology_-_2021-01-08_18-37-11/tsdye-allen.archaeology_-_2021-01-08_18-37-11.bundle and run: git clone tsdye-allen.archaeology_-_2021-01-08_18-37-11.bundle Source: https://github.com/tsdye/allen.archaeology Uploader: tsdye Upload date: 2021-01-08
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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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putting this in a separate repo, since it's a million files and many of them go on the android rather than the pi ScannerApp Created for the very-specific purpose of communicating via android with a raspberry pi running a scanner. "theApp" repository includes the android-side code, and the server code (server cam long_test.py) for the pi, and the code to automatically run the agisoft software on a model (agisoft-automation.py). To test the server without running the cameras or motor,...
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Plot data on skeletal templates quickly To restore the repository download the bundle wget https://archive.org/download/github.com-davidcorton-osteoGIS_-_2016-11-30_23-04-56/davidcorton-osteoGIS_-_2016-11-30_23-04-56.bundle and run: git clone davidcorton-osteoGIS_-_2016-11-30_23-04-56.bundle Source: https://github.com/davidcorton/osteoGIS Uploader: davidcorton Upload date: 2016-11-30
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by frederic-santos
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An R package to facilitate the use of Murail et al.’s (1999) approach of sex estimation in past populations rdss rdss is an R-shiny application for making sex estimation somewhat easier. The global approach follows the philosophy of "diagnose sexuelle secondaire", described by Murail et. al (1999) . Feature requests or bug reports are welcome. Documentation Publication This R package has been extensively described and documented in an article published in the International Journal...
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R package 'RCarb' RCarb The R package 'RCarb' provides a collection of various R functionsto model dose rates in carbonate-rich samples. The package is atranslation of the 'MATLAB' program Carb by Roger P. Nathan. Installation of the developer version To install the latest development builds of 'RCarb' directly fromGitHub, run rif(!require("devtools")) install.packages("devtools")devtools::install_github("R-Lum/RCarb@master") To install a developer build other than...
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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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Assorted methods to supplement core spatial packages in R sparch Assorted methods to supplement core spatial packages in R To restore the repository download the bundle wget https://archive.org/download/github.com-ahb108-sparch_-_2021-02-01_09-55-02/ahb108-sparch_-_2021-02-01_09-55-02.bundle and run: git clone ahb108-sparch_-_2021-02-01_09-55-02.bundle Source: https://github.com/ahb108/sparch Uploader: ahb108 Upload date: 2021-02-01
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R package for TL dating To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-TLdating_-_2017-09-06_14-41-46/dstreble-TLdating_-_2017-09-06_14-41-46.bundle and run: git clone dstreble-TLdating_-_2017-09-06_14-41-46.bundle Source: https://github.com/dstreble/TLdating Uploader: dstreble Upload date: 2017-09-06
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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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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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A tool for measuring tree-ring width MtreeRing Authors: Jingning Shi , Wei Xiang License: GPL3 MtreeRing is a tool for automatically measuring tree-ring width using image processing techniques. Installation Install the stable version from CRAN rinstall.packages("MtreeRing") or the development version from GitHub ```r install.packages("devtools") devtools::install_github("ropensci/MtreeRing")``` Ring-width measurement 1. Read an image ```rlibrary(MtreeRing) Read and...
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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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A database interface designed to facilitate the irregular, iterative, and non-linear workflows that are commonly employed in lithic analysis Queryable Artifact Record Interface [QuARI] QuARI is a database interface designed to facilitate the irregular, iterative, and non-linear workflows that are commonly employed in lithic analysis. Specifically, it is designed to facilitate workflows that tack back and forth between recording assemblage-level and artefact-level data – often beginning with...
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GeoJSON files for ceramic kilns of the ancient world, no chronological/spatial boundaries. An experiment, feel free to submit your pull requests! Ceramic kilns and workshops in the ancient world This repository contains GeoJSON map files about ceramic kilns and workshops ( ateliers ) in the ancient world: Classical antiquity, Eastern civilizations, pre-Columbian Americas, etc.. if it is an archaeological feature, it will be good for this repository. How to contribute You will need a GitHub...
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Faked GIS-Datasets, simulating an island in the Atlantic for educational purposes in using GIS in archaeology AtlantGIS Faked GIS-Datasets, simulating an island in the Atlantic for educational purposes in using GIS in archaeology. All AtlantGIS data are published under a CC-BY-SA 4.0 license. The idea is to create artificial data creatively referring to the story of Atlantis as told by Platon.We believe that simple datasets with a narrative are most qualified to impart knowledge and skills to...
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open-archaeo
by Big-Ancient-Mediterranean
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A tool for the geospatial analysis, literary network visualization, and plot mapping of ancient texts To restore the repository download the bundle wget https://archive.org/download/github.com-Big-Ancient-Mediterranean-BAM_-_2018-09-16_12-29-16/Big-Ancient-Mediterranean-BAM_-_2018-09-16_12-29-16.bundle and run: git clone Big-Ancient-Mediterranean-BAM_-_2018-09-16_12-29-16.bundle Source: https://github.com/Big-Ancient-Mediterranean/BAM Uploader: Big-Ancient-Mediterranean Upload date: 2018-09-16
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Bayesian Modeling of Archaeological Chronologies ArchaeoChron Bayesian Modeling of Archaeological Chronologies ArchaeoChron provides a list of functions for the Bayesian modeling of archaeological chronologies. The Bayesian models are implemented in 'JAGS' ('JAGS' stands for Just Another Gibbs Sampler. It is a program for the analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. See http://mcmc-jags.sourceforge.net/ and "JAGS Version 4.3.0 user...
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Gianmarco Alberti Miscellaneous GmAMisc (Gianmarco Alberti Miscellaneous) vers 0.24 GmAMisc is a collection of functions that I have built in different points in time. The functions' aim spans from univariate outlier detection, to permutation t test, permutation chi-square test, calculation of Brainerd-Robinson similarity coefficient, validation of logistic regression models, point pattern analysis, and more. The package comes with some toy datasets: assemblage : distribution of 7...
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Script for calculating mean ceramic dates based on tabular data. This script also estimates sampling error using a bootstrapping procedure. Mean-Ceramic-Date-and-Error-Estimation Script for calculating mean ceramic dates based on tabular data. This script also estimates sampling error using a bootstrapping procedure. Mean Ceramic Dates:The mean ceramic date (MCD) of an assemblage is a point estimate of the occupation of a site calculated based on the frequency and date range of types present,...
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graphical interface for DRAC To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-shiny_DRAC_-_2016-11-02_16-04-27/dstreble-shiny_DRAC_-_2016-11-02_16-04-27.bundle and run: git clone dstreble-shiny_DRAC_-_2016-11-02_16-04-27.bundle Source: https://github.com/dstreble/shiny_DRAC Uploader: dstreble Upload date: 2016-11-02
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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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Models and Utility Functions for Bayesian Analyses of Radiocarbon Dates with NIMBLE nimbleCarbon The nimbleCarbon package provides utility functions and bespoke probability distributions for the Bayesian analyses of radiocarbon dates using the NIMBLE framework. The package is particularly suited for demographic inferences based on changing frequencies of radiocarbon dates and enables parameter estimations and model comparison for the following population growth models (see Crema and Shoda 2021...
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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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The R-script implements a means for statistically assessing the degree of co-occurrence between classes within a dataset based on an idea origially suggested by James Allison at BYU and published by Keith Kintigh in 2006. Binomial-Co-occurrence-Assessment The R-script implements a means for statistically assessing the degree of co-occurrence between classes within a dataset based on an idea origially suggested by James Allison at BYU and published by Keith Kintigh in 2006. I have implemented...
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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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None Introduction to Analysing Archaeological Radiocabon Ages Using R Ben Marwick, July 2020 Overview In this workshop we will practice some techniques for analysingarchaeological radiocabon ages using R. Here are the slides . Here’s the outline of keytopics: Calibrate and plot a single age Calibrate and plot multiple ages Combine and plot multiple ages using non-parametric phase estimation Age-depth modelling Summed probability density plots Hypothesis testing with SPDs You can download the...
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Code repository of the book by Oliver Nakoinz and Daniel Knitter "Modelling Human Behaviour in Landscapes -- Basic concepts and modelling elements" mhbil Code repository of the book by Oliver Nakoinz and Daniel Knitter "Modelling Human Behaviour in Landscapes -- Basic concepts and modelling elements" published by Springer in 2016. You can get the book here: at Springer Worldcat link What will you find here? the code of the different chapters the data used within the book Why...
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None R-Scripts This contains a set of data about human mobility, subsistance, population, and environmental productivity derived from the Standard Cross Cultural Sample . Missing cases have been filled in via Multiple Imputation. It also contains a suite of R scripts for processing these data. Included routines are cluster analyses, Multidimentional Scaling, and Canonical Correspondence analysis. Plotting commands are also included. These data and analyses were used in my article "Towards...
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paleofire package paleofire paleofire: an R package to analyse sedimentary charcoal records from the Global Charcoal Database to reconstruct past biomass burning The paleofire package provides tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database (see http://gpwg.paleofire.org for details). Main functionalities includes data extraction and sites selection, transformation and homogenization of the charcoal records as well as regional to global compositing....
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open-archaeo
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iDAI.field | Archaeological Field Recording App by the German Archaeological Institute iDAI.field This is a monorepo containing three packages: iDAI.field Desktop : The iDAI.field desktop client based on AngularJS and Electron iDAI.field Mobile : The iDAI.field mobile client based on React Native iDAI.field Core : Shared TypeScript modules Development The repository uses lerna to manage sub-package dependecies.When first checking out the code base, bootstrap the dependencies with: $ npm run...
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open-archaeo
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Manuals for total stations total-station-manuals Manuals for total stations To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-total-station-manuals_-_2020-04-18_22-50-09/steko-total-station-manuals_-_2020-04-18_22-50-09.bundle and run: git clone steko-total-station-manuals_-_2020-04-18_22-50-09.bundle Source: https://codeberg.org/steko/total-station-manuals Uploader: steko Upload date: 2020-04-18
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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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