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open-archaeo
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Dynamic and static 3D plotting for vegan What is vegan3d? vegan3d is an R package of 3D plotting routines split apart from vegan . It can be used for dynamic plots based on rgl package,and for static 3D plots based on scatterplot3d package. The package contains the following functions: ordirgl with its support functions orglpoints , orgltext , orglsegments , orglellipse , orglspider , orglcluster and orglspantree . Theserequire rgl package and provide dynamic ordination graphics.See a simple...
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open-archaeo
by andredebuisne
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Archaeological Information System AIS - Archaeological Information System Created by Andre Debuisne - 2017 Written in C++ with Qt library A packaged .exe will be uploaded soon Current state of the AIS Current functionnalities : Create an archaeological site (.archeo) Create a layer (.arcus) Create an object Create a horizon Modify site, horizon, layer or object Delete site, horizon, layer or object I am working on : Harris Matrix Data table view Site sectors To restore the repository download...
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open-archaeo
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Android apps for archaeology that enable photography during field work, with resulting photographs named and located on the filesystem based on information from a relational database. Disclaimer: This application was coded by an inexpensive freelance company. It was written quickly and for a very specific purpose, and it has fulfilled this purpose during multiple archaeological field seasons. However, the quality of the code leaves much to be desired and the application could be more robust....
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open-archaeo
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R Shiny Document - Visualizing model functions in Neimans 'Stylistic variation in evolutionary perspective' with an interactive document The interactive document neiman1995.Rmd aims to visualize the model functions in Neiman, F. (1995). Stylistic Variation in Evolutionary Perspective: Inferences from Decorative Diversity and Interassemblage Distance in Illinois Woodland Ceramic Assemblages. American Antiquity, 60(1), 7-36. doi:10.2307/282074 For study and teaching purposes. To restore the...
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open-archaeo
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None A collection of texts, 3d models, and maybe other resources useful for teaching about the Roman Empire. gh-pages versions: http://sebastianheath.com/teaching-rome/open-university-intro http://sebastianheath.com/teaching-rome/identify-imperial-portraits/ To restore the repository download the bundle wget https://archive.org/download/github.com-sfsheath-teaching-rome_-_2017-09-21_03-53-33/sfsheath-teaching-rome_-_2017-09-21_03-53-33.bundle and run: git clone...
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open-archaeo
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Total Open Station downloads and exports survey data from your total station To restore the repository download the bundle wget https://archive.org/download/github.com-steko-totalopenstation_-_2020-11-18_11-12-29/steko-totalopenstation_-_2020-11-18_11-12-29.bundle and run: git clone steko-totalopenstation_-_2020-11-18_11-12-29.bundle Source: https://github.com/steko/totalopenstation Uploader: steko Upload date: 2020-11-18
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open-archaeo
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This R script produces a exploratory visual for assessing site date ranges originally suggested to me by Wesley Bernardini (Redlands University). The plot consits of horizontal bars on an x-axis reprenting time with the width determined based on the production span for that type and with the height of each box determined based on the relative frequency of that type with types sorted vertically by start date. The script reads in csv files in the formatted of the example dataset here and produces...
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open-archaeo
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A web app and mapping interface for searching and displaying bibliographic information about Anatolian archaeology Anatolia Bibliography Map of Archaeology The goal of this project is to spatially locate bibliographic resources (published articles, books) regarding the archaeology of Anatolia (modern Turkey). This takes the bibliography of archaeology to the next level by showing not only the topics and authors, but where the archaeological research is being done. Note: This web app was...
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open-archaeo
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A collection of tutorial on agent-based modelling for archaeologists To restore the repository download the bundle wget https://archive.org/download/github.com-izaromanowska-ABM_tutorials_-_2019-06-21_13-17-40/izaromanowska-ABM_tutorials_-_2019-06-21_13-17-40.bundle and run: git clone izaromanowska-ABM_tutorials_-_2019-06-21_13-17-40.bundle Source: https://github.com/izaromanowska/ABM_tutorials Uploader: izaromanowska Upload date: 2019-06-21
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open-archaeo
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A simple gui app to simplify scanning single context plans. To restore the repository download the bundle wget https://archive.org/download/github.com-lparchaeology-ArkScan_-_2015-07-28_08-06-46/lparchaeology-ArkScan_-_2015-07-28_08-06-46.bundle and run: git clone lparchaeology-ArkScan_-_2015-07-28_08-06-46.bundle Source: https://github.com/lparchaeology/ArkScan Uploader: lparchaeology Upload date: 2015-07-28
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open-archaeo
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A git mirror of the tridas SVN repository from https://sourceforge.net/projects/tridas/ To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-tridas_-_2020-02-10_16-10-11/steko-tridas_-_2020-02-10_16-10-11.bundle and run: git clone steko-tridas_-_2020-02-10_16-10-11.bundle Source: https://codeberg.org/steko/tridas Uploader: steko Upload date: 2020-02-10
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open-archaeo
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Fluorescence fitting GUI. To restore the repository download the bundle wget https://archive.org/download/github.com-NSLS-II-PyXRF_-_2021-02-03_16-51-52/NSLS-II-PyXRF_-_2021-02-03_16-51-52.bundle and run: git clone NSLS-II-PyXRF_-_2021-02-03_16-51-52.bundle Source: https://github.com/NSLS-II/PyXRF Uploader: NSLS-II Upload date: 2021-02-03
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open-archaeo
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Proof of concept map for disaster response and archaeology. For Keeping History Above Water conference, 2017 disastermap Demonstration map for disaster response and archaeology. For Keeping History Above Water conference, 2017. This data should not be used for official planning or decision making. Demonstration available at https://aejolene.github.io/disastermap/ Presentation details: Archaeology Disaster Response A demonstration map for Keeping History Above Water Conference, November 1, 2017...
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None HOPS Summary ## HOPS is a java pipeline which focuses on screening MALT data (see Table of Contents) for the presence of a user-specified list of target species. The pipeline essentially exists to make it easier to use MALT and MaltExtract in unison. To use HOPS you will need a config file, which specifies some key parameters for MALT and MaltExtract. You can have multiple config files to quickly redo a previous analysis or archive them to remember parameters you used in an analysis. HOPS...
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open-archaeo
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None predictSource The package predictSource provides functions to verify that data can beused to separate sources of samples, to predict the sources ofadditional samples, and to create plots that evaluate the validity ofthe predictions. Data can be both quantitative and qualitative. Aproposed analysis strategy is to use random forests to evaluate whetherthe data can separate the sources and to identify the most importantpredictors if there are many, use a classification tree to understandhow...
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None To restore the repository download the bundle wget https://archive.org/download/github.com-Chronomodel-chronomodel_-_2021-02-02_16-41-52/Chronomodel-chronomodel_-_2021-02-02_16-41-52.bundle and run: git clone Chronomodel-chronomodel_-_2021-02-02_16-41-52.bundle Source: https://github.com/Chronomodel/chronomodel Uploader: Chronomodel Upload date: 2021-02-02
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open-archaeo
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downloads and prepares shkr data for analysis shkrdata Package for downloading and preparing shkr data for archaeological analysis. The database contains archaeological information from the Early Iron Age in South-West Germany. This package is intended to simplify the data access as well as some basic steps of the preparation of the data. For this purpose shkrdata comprises function for accessing the data as well as function wrapping functionality from our package moin...
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open-archaeo
software

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R Package - Download and Prepare C14 Dates from Different Source Databases c14bazAAR is an R package to query different openly accessible radiocarbon date databases. It allows basic data cleaning, calibration and merging. If you're not familiar with R other tools (such as GoGet ) to search for radiocarbon dates might be better suited for your needs. Installation How to use ( Download , Calibration , Material classification , Country attribution , Duplicates , Conversion , Technical functions ,...
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open-archaeo
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None Iraq_mortar This application has three files: createTasks.py: for creating the application in PyBossa, and fill it with some tasks. template.html: the view for every task and deal with the data of the answers. tutorial.html: a simple tutorial for the volunteers. Funded Partners Testing the application You need to install the pybossa-client first (use a virtualenv and this needs boto): bash $ pip install -r requirements.txt $ cp s3_settings.py.tmpl s3_settings.py In the settings file, just...
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open-archaeo
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An R package that provides datasets useful for biological and forensic anthropology. In addition, it includes helper functions for working with dataframes. bioanth An R package that provides datasets useful for biological and forensic anthropology. In addition, it includes helper functions for working with dataframes. This package provides the following datasets: howell : Howells Craniometric Data Set howelltest : Howells Craniometric Test Data Set goldman : Goldman Osteometric Data Set Note:...
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open-archaeo
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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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R package for quantitative ethnobotany ethnobotanyR The goal of ethnobotanyR is to provide an easy-to-use platform forethnobotanists to work with quantitative ethnobotany assessments. Itclosely follows Tardio and Pardo-de-Santayana(2008) and Whitney etal. (2018) . Users of ethnobotanyR may find it useful to read the background papersand books on ethnobotany theory. In particular Albuquerque etal. (2019) and Gaoue etal. (2017) offer helpfulguidance to understanding theoretical approaches in...
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open-archaeo
software

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.obj slicing for lithic 3d morphometrics To restore the repository download the bundle wget https://archive.org/download/github.com-kotdijian-lithic3dslicer_-_2019-06-23_01-39-40/kotdijian-lithic3dslicer_-_2019-06-23_01-39-40.bundle and run: git clone kotdijian-lithic3dslicer_-_2019-06-23_01-39-40.bundle Source: https://github.com/kotdijian/lithic3dslicer Uploader: kotdijian Upload date: 2019-06-23
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open-archaeo
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A toolset to work with modular genotype databases poseidon-tools A toolset to work with modular genotype databases formatted using Poseidon. The main executable within this package is called trident . Installation Quickstart Guide for the command line utility Poseidon package repositories Analysing your own dataset outside of the main repository Package creation and manipulation commands : init , forge , update Inspection commands : list , summarise , survey , validate Analysis commands :...
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open-archaeo
software

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A set of GNU Octave functions for biodistance analysis based on non-metric traits To restore the repository download the bundle wget https://archive.org/download/github.com-pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12/pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12.bundle and run: git clone pr0m1th3as-non-metric-trait-analysis_-_2018-03-08_14-05-12.bundle Source: https://github.com/pr0m1th3as/non-metric-trait-analysis Uploader: pr0m1th3as Upload date: 2018-03-08
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Skullanalyzer: a concrete way of extracting cranial morphometric features skullanalyzer a concrete way of extracting cranial mophometric features The skullanalyzer loads a 3D triangular mesh cranial model along with a number of user defined landmarks and extracts a set of cranial morphometric features, which can be used for further analyses. It requires two input files, one Alias Wavefront file (model name.obj) containing a triangular mesh of the cranial model to be analyzed and a Meshlab...
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open-archaeo
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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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None Photogrammetry - Data Collection https://leadr-msu.github.io/photogrammetry-data-collection This tutorial was prepared by Jack A. Biggs and is maintained by LEADR staff. Here are the usage rights associated with this tutorial. Find all our tutorials at https://leadr-msu.github.io . To restore the repository download the bundle wget...
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An open source radiocarbon (14C) calibration software. Written in Python A radiocarbon calibration software DOI: https://doi.org/10.5281/zenodo.630455 IOSACal is the open source radiocarbon calibration software of the IOSA project. IOSACal includes: a programming library a web-based application a command-line program IOSACal is written in the Python programming language and it can runnatively on any platform where the Python interpreter is available,including all Linux distributions, MacOS X...
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software

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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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open-archaeo
software

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A simple algorithm to find local maxima/minima in sequential data findPeaks A repo for a function I posted as part of my answer to a quesiton about peak detection on StackExchange. The function takes an ordered sequence (vector) of values x and a number m and returns a vector of indices of local peaks in x . A (local) peak is defined as a point such that m points either side of it has a lower or equal value to it. Thus, m can be used adjust the sensitivity of the peak detection procedure:...
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open-archaeo
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None survey2gis It is a little tool that can process survey data, suchas produced by a GPS or total station, and export it as topologicallycleaned data fit for use in GIS. For more information, seehttp://survey-tools.org and the user manual that came withthis software. Important links Official Website: http://survey-tools.org.Bugtracker: https://github.com/survey2gis/survey-tools/issuesMailinglist: https://groups.io/g/survey2gis/topics FAQs How do I install this software? Look into the folder...
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open-archaeo
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:closed_book: Datasets for Teaching Archaeology and Palaeontology folio Datasets for teaching quantitative approaches and modeling inarchaeology and paleontology. This package provides several types ofdata related to broad topics (cultural evolution, radiocarbon dating,paleoenvironments, etc.), which can be used to illustrate statisticalmethods in the classroom (multivariate data analysis, compositional dataanalysis, diversity measurement, etc.). This package is for teaching purposes only: some...
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open-archaeo
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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...
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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
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A digital Babylonian clock babylonian-hours This is a javascript based digital clock which computes your local time in 'seasonal-hours'. It's currently hosted at www.babylonianhours.com . To restore the repository download the bundle wget https://archive.org/download/github.com-willismonroe-babylonian-hours_-_2019-01-05_20-36-50/willismonroe-babylonian-hours_-_2019-01-05_20-36-50.bundle and run: git clone willismonroe-babylonian-hours_-_2019-01-05_20-36-50.bundle Source:...
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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
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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
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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
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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
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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
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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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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
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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
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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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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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
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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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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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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: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...
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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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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
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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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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
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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
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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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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
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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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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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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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How does wikipedia see archaeology? To restore the repository download the bundle wget https://archive.org/download/gist.github.com-0d5e6526604e755b556f_-_2015-09-22_16-54-45/0d5e6526604e755b556f_-_2015-09-22_16-54-45.bundle and run: git clone 0d5e6526604e755b556f_-_2015-09-22_16-54-45.bundle Source: https://gist.github.com/0d5e6526604e755b556f Uploader: benmarwick Upload date: 2015-09-22
Topics: Gist, GitHub, code, software, git
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osl_calibration To restore the repository download the bundle wget https://archive.org/download/gist.github.com-5f996a0f52ba1d92f76968119f941bd8_-_2016-05-10_07-53-04/5f996a0f52ba1d92f76968119f941bd8_-_2016-05-10_07-53-04.bundle and run: git clone 5f996a0f52ba1d92f76968119f941bd8_-_2016-05-10_07-53-04.bundle Source: https://gist.github.com/5f996a0f52ba1d92f76968119f941bd8 Uploader: benmarwick Upload date: 2016-05-10
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open-archaeo
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R package to help interpreting Correspondence Analysis’ results CAinterprTools vers 0.24 A number of interesting packages are available to perform Correspondence Analysis in R. At the best of my knowledge, however, they lack some tools to help users to eyeball some critical CA aspects (e.g., contribution of rows/cols categories to the principal axes, quality of the display,correlation of rows/cols categories with dimensions, etc). Besides providing those facilities, this package allows...
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open-archaeo
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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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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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Table of faunal analyses from archaeological sites in the Levant levant-zooarch Table of faunal analyses from archaeological sites in the Levant To restore the repository download the bundle wget https://archive.org/download/github.com-sarahkansa-levant-zooarch_-_2015-01-15_06-52-11/sarahkansa-levant-zooarch_-_2015-01-15_06-52-11.bundle and run: git clone sarahkansa-levant-zooarch_-_2015-01-15_06-52-11.bundle Source: https://github.com/sarahkansa/levant-zooarch Uploader: sarahkansa Upload date:...
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None DamMet, a full probabilistic model for mapping ancient methylomes DamMet is probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.The model is implemented as a two step procedure. The first step recovers a maximum likelihood estimate (MLE) of the position specific deamination rates for methylated and unmethylated cytosine residues. The second step, making use of these deamination rates, returns a MLE of the methylation level in a...
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A set of best practices, how-tos and implementations for publishing pottery drawings on the Web as SVG To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-svg-pottery_-_2020-04-05_22-34-18/steko-svg-pottery_-_2020-04-05_22-34-18.bundle and run: git clone steko-svg-pottery_-_2020-04-05_22-34-18.bundle Source: https://codeberg.org/steko/svg-pottery Uploader: steko Upload date: 2020-04-05
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A simple adventure game in Unity2D. Revolves around being an archaeologist exploring some ruin and digging up treasure/fossils. ArchaeologyAdventure A simple adventure game in Unity2D. Revolves around being an archaeologist exploring some ruin and digging up treasure/fossils. To restore the repository download the bundle wget https://archive.org/download/github.com-Camology-ArchaeologyAdventure_-_2018-06-06_19-54-37/Camology-ArchaeologyAdventure_-_2018-06-06_19-54-37.bundle and run: git clone...
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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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open-archaeo
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Datasets from studies of cultural evolution in Archaeology evoarchdata The goal of evoarchdata is to make easily available some importantartefact datasets from archaeological studies of cultural evolution. Themotivation for this package is to make it easier to teach and studycultural evolution in the archaeological record. Installation You can install the development version of evoarchdata from GitHub with: rif (!require(devtools))...
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Package for modelling artefact-scale data rtfact Package for modelling archaeological artefact data To restore the repository download the bundle wget https://archive.org/download/github.com-ahb108-rtfact_-_2021-01-25_09-24-54/ahb108-rtfact_-_2021-01-25_09-24-54.bundle and run: git clone ahb108-rtfact_-_2021-01-25_09-24-54.bundle Source: https://github.com/ahb108/rtfact Uploader: ahb108 Upload date: 2021-01-25
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open-archaeo
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A simple qgis plugin that measures the 3d distance between two selected points. Measure 3d - Qgis plugin A simple plugin that measure the 3d distance between two selected points. A field of the attribute table or the geometry (PointZ, PointZM) can be used to get the 3th dimension information. How to use Clone or Download the repository Rename the main folder to measure3d Copy measure3d to Qgis's plugin folder Run Qgis and activate the plugin Screenshot To restore the repository download the...
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open-archaeo
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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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None SequenceTools This repository contains some programs that I use for processing sequencing data. Installation Simple Installation via stack and hackage This installation installs the latest version that is up on hackage : Download stack (https://docs.haskellstack.org/en/stable/README/#how-to-install). Run stack install sequenceTools --resolver nightly . You should now have the executables from this package under ~/.local/bin . Add ~/.local/bin to your PATH, for example by adding to your...
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open-archaeo
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Small command line tool for 14C calibration calibrator Calibrator is a small c++ command line tool to calibrate 14C dates. In can process inputs in csv, json or as cli parameters, and it outputs csv or json, that can be piped into a file. Usage Allowed arguments: -h [ --help ] Produce this help message. -i [ --input-file ] arg Specifies input file. -b [ --bp ] arg The BP Value. -s [ --std ] arg The standard deviation. -j [ --json-string ] arg Input as as JSON string. Format: {"bp":...
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None QGIS-scripts Random scripts that could be useful for QGIS users... Installing QGIS scripts Simply go to Processing Toolbox -> Scripts -> Tools -> Create new script and paste the code. Or use "Add from file" option (which doesn'talways work) To restore the repository download the bundle wget https://archive.org/download/github.com-zoran-cuckovic-QGIS-scripts_-_2018-07-21_22-11-13/zoran-cuckovic-QGIS-scripts_-_2018-07-21_22-11-13.bundle and run: git clone...
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open-archaeo
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Online archaeological data manager - [website](https://ishtar-archeo.net/) - [tracker](https://tickets.iggdrasil.net/projects/ishtar) - [documentation](http://ishtar.readthedocs.io/) - [forum](https://forum.ishtar-archeo.net/) Ishtar Description Ishtar is a database project for managing archaeological data and documentation (including archaeological finds) from archaeological operations, published as a free software under AGPL 3.0 or any later version license. The aim is to ensure maximum...
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open-archaeo
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This is a R-Project which uses transect data to define site sizes sitedefinition The goal of sitedefinition is to see, how feature densities might beused for site definition. To be published in “PraehistorischeZeitschrift” in 2019. Citation Please cite this compendium as: Authors, (2018). Title of compendium . Accessed 25 Jun 2018. Online at https://doi.org/xxx/xxx Installation You can install sitedefinition from github with: ``` r install.packages("devtools")...
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open-archaeo
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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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open-archaeo
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Software deliverables for the ArchAIDE project archaide-software Software deliverables for the ArchAIDE project Installation The setup instructions were tested on Linux (Ubuntu 16.04) 64-bits. While theyshould work with minor modifications also on Windows/Mac, this was not tested. Python You will need to use Python >= 3.5.2 Required Python packages To run the code, you will need to have at least the following packages installedin your environment: numpy >= 1.15.1 tensorflow-gpu >=...
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open-archaeo
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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Consensify method for error reduction in ancient DNA pseudohaploidisation Consensify Documentation for Consensify v0.1 The manuscript accompanying this source is available on BioRxiv: https://www.biorxiv.org/content/early/2018/12/18/498915?rss=1 Axel Barlow and Johanna L. A. Paijmans, December 2018 emails: axel.barlow.ab@gmail.com, paijmans.jla@gmail.com Introduction Consensify is a method for generating a consensus pseudohaploid genome sequence with greatly reduced error rates compared to...
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The ANFO ancient DNA mapper Where to start? Get the prerequisites, compile, create documentation, test. Also see the Github Wiki. Prerequisites are... Not too ancient G++; 4.0 and later work fine, 3.x might cause somedifficulties. Also make, a shell, and so on. protobuf. Find it at http://code.google.com/p/protobuf popt. You might already have it, else ask your admin or grab it athttp://rpm5.org/files/popt Doxygen, if you want the documentation. Can be found at http://doxygen.org zlib from...
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A library for X-ray matter interaction cross sections for X-ray fluorescence applications xraylib: a library for interactions of X-rays with matter Welcome to the xraylib Github project page! For all information, consult the official documentation Get in touch using Gitter To restore the repository download the bundle wget https://archive.org/download/github.com-tschoonj-xraylib_-_2021-01-06_18-55-17/tschoonj-xraylib_-_2021-01-06_18-55-17.bundle and run: git clone...
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open-archaeo
software

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Core development repository. gitHub: Vsn 6 (2020 - ), Vsn 5 (2018 - 2020), Vsn 4 (2014-2017). Sourceforge: Vsn 3 (2009-2013), Vsn 1 & 2 (2005-2009) HEURIST Core development repository, Vsn 6 (2021 - ), Vsn 5 (2018 - 2020), Vsn 4 (2014-2017). Vsn 1 - 3 on Sourceforge (2005 - 2013) See below the intro for information on code, licensing, installating, contributing and issue tracking Heurist is a mature web-based data management infrastructure that is specifically tailored to the needs of...
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open-archaeo
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This repository contains our data and R code for our article on computational text analysis of racism in archaeology. Computational text analysis of archaeological writing about race This repository contains the data and code for our paper. Our pre-printis online here: Park, G., L-Y Wang, B. Marwick, (2020) How do archaeologists write about race? Computational text analysis of 41 years of Society of American Archaeology Annual Meeting Abstracts . , Accessed 21 Jun 2021. Online at...
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open-archaeo
software

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Platform for crowdsourcing the digital recreation of lost heritage Rekrei Platform About Rekrei Rekrei (founded as Project Mosul, we changed our name in late 2015) is a volunteer project that crowdsources the digital reconstruction of lost heritage. The project was founded by Matthew Vincent and Chance Coughenour in March 2015. You can read more about the project on our about page Core Team Rekrei is a community of people who actively contribute towards the preservation of cultural heritage...
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open-archaeo
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ARCSCore is a metadata scheme developed as part of the Archaeological Resource Cataloging System (ARCS: http://arcs.matrix.msu.edu/) project. ARCSCore ARCSCore is a metadata standard developed as part of the Archaeological Resource Cataloging System (ARCS: http://arcs.matrix.msu.edu/) project. Funded by the National Endowment for the Humanities and developed at Michigan State University’s MATRIX: The Center for Digital Humanities and Social Sciences, ARCS is an open source, web-based platform...
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open-archaeo
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Imaging software utilities for RTI imaging You can sort out a stream of images using Phil's RTI Card Importer (best to copy from camera first). You can run ptmfitter on the rti tree using his RTI Processor. (Which uses John's fast PTM fitter) To restore the repository download the bundle wget https://archive.org/download/github.com-kmartinez-rti_-_2019-05-29_15-38-12/kmartinez-rti_-_2019-05-29_15-38-12.bundle and run: git clone kmartinez-rti_-_2019-05-29_15-38-12.bundle Source:...
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open-archaeo
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An App to recognize cuneiform characters on your Android phone CuneiPainter An App to recognize cuneiform characters on your Android phone CuneiPainter enables you to paint cuneiform characters using your fingers on the touchscreen of your smartphone.The app recognizes the four stroke types of cuneiform as defined by the Gottstein System :* left to right (A)* up to down (B)* down right to up left (C)* down left to up right (D) Wedges are recognized as class C and not as class E as also...
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open-archaeo
software

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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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open-archaeo
software

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None opencontext: An R API client for the Open Context archaeological data repository This packages enables browsing and downloading data from Open Context using R. Open Context reviews, edits, and publishes archaeological research data and archives data with university-backed repositories, including the California Digital Library. Installation Install opencontext rinstall.packages("devtools")devtools::install_github("ropensci/opencontext") rlibrary("opencontext")...
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R package for community ecologists: popular ordination methods, ecological null models & diversity analysis vegan: an R package for community ecologists Released version Build status To restore the repository download the bundle wget https://archive.org/download/github.com-vegandevs-vegan_-_2021-02-02_10-51-39/vegandevs-vegan_-_2021-02-02_10-51-39.bundle and run: git clone vegandevs-vegan_-_2021-02-02_10-51-39.bundle Source: https://github.com/vegandevs/vegan Uploader: vegandevs Upload...
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open-archaeo
software

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ArcGIS toolbox for fuzzy viewshed calculation FuzzyViewshed Short Description The toolbox (built under ArcGIS 10.1 ) provides the facility to calculate the Fuzzy Viewshed as proposed by Ogburn 2006 , which modify the original proposal by Fisher. It produces a Fuzzy Vieshed raster in which, as customary in 'regular' (i.e., binary) viewshed rasters, 0 indicates cells that are not visible, 1 indicates cells that are visible. However, unlike binary viewshed, values between 0 and 1 correspond to a...
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open-archaeo
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An Approximate Bayesian Computation Framework for inferring patterns of cultural transmission from frequency data cTransmission An Approximate Bayesian Computation Framework for inferring patterns of cultural transmission from frequency data To restore the repository download the bundle wget https://archive.org/download/github.com-ercrema-cTransmission_-_2020-05-14_17-43-37/ercrema-cTransmission_-_2020-05-14_17-43-37.bundle and run: git clone ercrema-cTransmission_-_2020-05-14_17-43-37.bundle...
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open-archaeo
software

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R Package - Aoristic analysis of archaeological data aoristAAR A R package for the aoristic analysis of archaeological data Installation aoristAAR is currently not on CRAN , but you can use devtools to install the development version. To do so: if(!require('devtools')) install.packages('devtools')library(devtools)install_github('ISAAKiel/aoristAAR') Licence aoristAAR is released under the GNU General Public Licence, version 3 . Comments and feedback are welcome, as are code contributions. To...
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open-archaeo
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Repository containing lists of all published ancient metagenome samples (and related) ----[![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-orange.svg)](https://creativecommons.org/licenses/by/4.0/)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3980833.svg)](https://doi.org/10.5281/zenodo.3980833)![check_dataset](https://github.com/spaam-community/AncientMetagenomeDir/workflows/check_dataset/badge.svg)[![Joins us on...
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