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Archive of open-archaeo, a list of open source archaeological software and resources.
Topics: Archaeology, open source, research software, digital archaeology
open-archaeo
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A list of open source archaeological software and resources Open Archaeology Software & Resources A list of open source archaeological software and resources See ToDo.md for a list of tools or resources that are in demand, but which currently do not exist or need to be significantly improved. 3d-ceramics : 3d models of archaeological ceramics. by: sfsheath links: [ GitHub ] * tags: [3D modelling] A Mobile Data-Collection Workflow for Archaeologists : A list of tools and resource for data...
Topics: GitHub, code, software, git
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...
Topics: GitHub, code, software, git
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Empirical XRF Calibrations CloudCal This app will allow you to build & apply calibrations for the Tracer & Artax series of XRF devices. It (currently) works with .csv files produced from S1PXRF, PDZ versions 24 and 25, .spx files, Elio spectra (.spt), .mca files, and .csv files of net counts produced from Artax (7.4 or later). How it works It is based on the Lucas-Tooth and Price (1961) algorithm 1 , though I have added modifications to make it more robust (it's really hard to get a...
Topics: GitHub, code, software, git
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ggplot-based plots for vegan ggvegan; ggplot2-based plots for vegan What is ggvegan? ggvegan is a package for the R statistical software and environment. It aims to implement ggplot -based versions of the plots produced by the vegan package. Initially, ggvegan will provide fortify and autoplot methods for objects created in vegan, with the aim of providing full replacement plots via autoplot . The fortify methods allow the data contained within objects created by vegan to be converted into a...
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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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:art: Colour Schemes for Scientific Data Visualization khroma Overview Color blindness affects a large number of individuals. Whencommunicating scientific results colour palettes must therefore becarefully chosen to be accessible to all readers. This R package provides an implementation of Paul Tol[1] and Okabe andIto[2] colour schemes. These schemes are ready for each type of data(qualitative, diverging or sequential), with colours that are distinctfor all people, including colour-blind...
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Largest Empty Circles after Andreas Zimmermann Largest Empty Circles (LEC) after Zimmermann and Wendt. Tool for calculating the largest empty circles and estimation of archaeological sites theoretically to be expected in region of interest. This package is an implementation of the method published by Andreas Zimmermann and Karl Peter Wendt (Zimmermann/Wendt 2003). Method to do Installation if(!require('devtools')) install.packages('devtools')devtools::install_github("ISAAKiel/lecAAR")...
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Compute postmortem damage patterns and decontaminate ancient genomes PMDtools Compute postmortem damage patterns and decontaminate ancient genomes. Description PMDtools computes ancient DNA damage patterns, and implements a likelihood framework incorporating postmortem damage (PMD), base quality scores and biological polymorphism to identify degraded DNA sequences that are unlikely to originate from modern contamination. Using the model, each sequence is assigned a PMD score, for which positive...
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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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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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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
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...
Topics: GitHub, code, software, git
A Distant Reading of the Day of Archaeology Brainerd-Robinson-Similarity-Coefficient-and-Sampling-Error-Assessment Script for calculating Brainerd-Robinson coefficients based on tabular count or percent data. This script also estimates the probability that a given difference between two samples is the product of sampling error. Brainerd Robinson Coefficient of Similarity: The Brainerd-Robinson (BR) coefficient is a similarity measure that was developed within archaeology specifically for...
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Learn Git and Contribute to Texas Archaeology Git-to-the-Point: Learn Git and Contribute to Texas Archaeology Contributors: Robert Z. Selden, Jr.; Juanita D. Garcia; and David Foxe Diagnostic artifacts comprise the basis for archaeological interpretations; however, as our taxonomic definitions evolve, artifacts that were previously assigned to a type generally retain that designation, potentially confounding future research efforts and interpretations. For this exercise, the original type...
Topics: GitHub, code, software, git
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Infrastructure for Ordering using Seriation - R Package seriation - Infrastructure for Ordering Objects Using Seriation - R package This package provides the infrastructure for ordering objects with an implementation of several seriation /sequencing/ ordination techniques to reorder matrices, dissimilaritymatrices, and dendrograms (see below for a full list). Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, andvisual assessment...
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Maya Calendar Tools Tools for converting between Maya and Western calendars. The Classic Maya developed the most sophisticated system for keeping track of time in the New World. In this app, you can convert dates from the Maya Calendar (Long Count and Calendar Round) to the Gregorian or Julian Calendars and vice-versa. You can also check the Maya glyphs for the current date. This is a React-Redux version of the Long Count tool in an older Vanilla app . Go to Web App To restore the repository...
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Room Accumulation Simulation ro estimate archaeological population growth rates ReadMe.txt Documentation provided in RoomAccumDocumentation.pdf Licence provided in License.txt Source code RoomAccumXX.dpr Program Source Code KWKStdXE.pas Utility functions called by the program Compiled Windows version RoomAccumXX.exe
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This R Function creates a simple Ford diagram for archaeological seriation with error bars determined based on sample size where count data are given. Ford-Diagram This R Function creates a simple Ford diagram for archaeological seriation with error bars determined based on sample size where count data are given. To restore the repository download the bundle wget...
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A GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry long-bone-diaphyseal-CSG-Toolkit A GNU Octave toolkit for analyzing diaphyseal long bone cross sectional geometry The present set of GNU Octave functions provides a novel and robust algorithm foranalyzing the diaphyseal cross-sectional geometric properties of long bones, whichcan be applied to any 3D digital model of a humerus, femur or tibia bone representedas a triangular mesh in a Wavefront OBJ file format. The...
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Repository of Crop Origins database and Phylo Food phylogeny Crop Origins is a comprehensive ckecklist of crop species cultivated for food. It includes species-level data on diverse continuous and categorical descriptors of antiquity of cultivation, organ harvested for primary use, growth form, and identities, distribution and climate at sites of origin of crops´ wild progenitors. Phylo Food is a time-calibrated and fully resolved phylogenetic tree of the species in Crop Origins. Downloads:...
Topics: GitHub, code, software, git
open-archaeo
by Johanna-Mestorf-Academy
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R Shiny App - Exploration and visualization of SDS datasets (Systematic and digital documentation of stone artefacts) sdsbrowser: sds.ufg.uni-kiel.de What is SDS? SDS ( Systematic and Digital Documentation of Stone Artefacts ) [1] is a recording system for stone artefacts. It was created as an uniform coding and standardized listing system of conventional attributes recorded at lithic inventories to enable well structured, quantitative, and comparative analysis. The variable collection in SDS...
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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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A tool for creating and manipulating Harris Matrices, part of the Archaeological Recording Kit (ARK) by L ~ P : Archaeology ARK Matrix A tool for creating and manipulating Harris Matrices.Part of the Archaeological Recording Kit by L-P : Archaeology http://ark.lparchaeology.com NOTE: Primary development occurs on GitLab at https://gitlab.com/arklab/ArkMatrix . This repo is mirrored on GitHub for legacy links only. Features The following features are currently supported by the command line tool...
Topics: GitLab, code, software, git
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Radiocarbon Dating Resolution Calculator Res14C Radiocarbon Dating Resolution Calculator Overview A python implementation of the method of calculating radiocarbon dating resolution. For an overview of the method see: Svetlik, I., A. J. T. Jull, M. Molnár, P. P. Povinec, T. Kolář, P. Demján, K. Pachnerova Brabcova, et al. “The Best Possible Time Resolution: How Precise Could a Radiocarbon Dating Method Be?” Radiocarbon 61, no. 6 (December 2019): 1729–40....
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None MultiVCFAnalyzer Table of Contents Description Citation Usage Example Output FAQs Description MultiVCFAnalyzer is a SNP filtering and SNP alignment generation tool, designed around (but not limited to) low coverage ancient DNA data. MultiVCFanalyzer reads multiple VCF files as produced by GATK UnifiedGenotyper, performs filtering based on a number of criteria, and provides the combined genotype calls in a number of formats that are suitable for follow-up analyses such as phylogenetic...
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R library to generate 'Cumulative Percent Decay' curves for microbial taxonomic profiles cuperdec R package to generate 'Cumulative Percent Decay' curves, with optional filtering functions, for microbial taxonomic profiles. These curves aim to represent the level of 'endogenous' content of microbiome samples, such as ancient dental calculus, to help to identify samples with lowlevels of preservation that should be discarded for downstream analysis. Installation cuperdec is on CRAN. You can...
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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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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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Fluorescence fitting GUI. To restore the repository download the bundle wget https://archive.org/download/github.com-NSLS-II-PyXRF_-_2021-02-03_16-51-52/NSLS-II-PyXRF_-_2021-02-03_16-51-52.bundle and run: git clone NSLS-II-PyXRF_-_2021-02-03_16-51-52.bundle Source: https://github.com/NSLS-II/PyXRF Uploader: NSLS-II Upload date: 2021-02-03
Topics: GitHub, code, software, git
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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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Sketch of a look at the 'grand challenges' of Kintigh et al. 2014 (http://www.pnas.org/content/111/3/879.full) in five archaeology journals To restore the repository download the bundle wget https://archive.org/download/gist.github.com-d3eb3167ccb2116197ca_-_2015-08-29_14-00-53/d3eb3167ccb2116197ca_-_2015-08-29_14-00-53.bundle and run: git clone d3eb3167ccb2116197ca_-_2015-08-29_14-00-53.bundle Source: https://gist.github.com/d3eb3167ccb2116197ca Uploader: benmarwick Upload date: 2015-08-29
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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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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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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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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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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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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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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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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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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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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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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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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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A LaTeX textbook devoted to explain how archaeologists can work with GRASS GIS grass-arch A LaTeX textbook devoted to explain how archaeologists can work with GRASS GIS.See the INSTALL.txt files for code issues. Slides The repository fradeve/slides contains slides from my talks about this project. See 2011 gnuarch grass . To restore the repository download the bundle wget...
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Analysis of spatial gradients in radiocarbon dates spDates Analysis of Spatial Gradients in Radiocarbon Dates Jonas Gregorio de Souza jonas.gregorio@gmail.com Tools to perform time-space regressions, an approach often used by archaeologists examining the expansion of cultural phenomena. In essence, one plots the radiocarbon ages of archaeological sites against their distances from a hypothetical origin. If a cultural advance has indeed taken place, the expectation is that radiocarbon dates will...
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known pyramids of Ancient Egypt using python + OpenStreetMap OpenStreetMap of Pyramids of Ancient Egypt Man fears time, but time fears the Pyramids. Probably all of you saw maps of Ancient Egyptian sites (I had school workbook) in stylized way like this below: I wished to recreate this kind of map using Python and OpenStreetMap but the problem I faced was the absolute absence of some dataset or even list with coordinates of egyptian pyramids. So I took different historical sources, Google Maps,...
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SNP calling and genotyping for damaged DNA AntCaller SNP calling and genotyping for damaged ancient DNA Usage This program is built on Python2.7 and can only be used for SAM/BAM files with MD field under Linux system. Copy three .py files to the directory where SAM/BAM files are stored. Print "python AntCaller-1.1.py -help" for detailed usage information. SNP calling can only be performed after extracting damage information and pileuping reads. Examples for BAM file (Require SAMtools...
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R scripts for digitizing, processing, analyzing, and comparing archaeological ceramic Ceramic Computation R scripts for digitizing, processing, analyzing, and comparing archaeological ceramic 2d profile drawings, photographs, and other data Overview This code was written with the goal of being able to automate 2d shape analysis of archaeological ceramics, particularly profile drawings of rim sherds. Much of the work and code was designed to help extract shape data from paper publications about...
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library for reading files with x-y data from powder diffraction, spectroscopy, or other experimental methods To restore the repository download the bundle wget https://archive.org/download/github.com-wojdyr-xylib_-_2021-01-19_22-48-51/wojdyr-xylib_-_2021-01-19_22-48-51.bundle and run: git clone wojdyr-xylib_-_2021-01-19_22-48-51.bundle Source: https://github.com/wojdyr/xylib Uploader: wojdyr Upload date: 2021-01-19
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This is an R implementation of the procedure outlined by John M. Roberts, Jr. et al. (2012) "A method for chronologically apportioning of ceramic assemblages" published in the Journal of Archaeological Science CeramicApportioning This is an R implementation of the procedure outlined by John M. Roberts, Jr. et al. (2012) "A method for chronologically apportioning of ceramic assemblages" published in the Journal of Archaeological Science Roberts, John M., Jr., Barbara J....
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None ContamLD ContamLD is a software designed to estimate autosomal contamination in ancient DNA samples. The software requires Python 3 and R (any version should suffice). Citation: Nakatsuka, N.*; Harney, E.*; Mallick, S..; Mah, M.; Patterson, N.; Reich, D. "Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium." BioRxiv. Contact: Nathan Nakatsuka: nathan_nakatsuka@hms.harvard.edu Steps for use: Section 1) Pre-processing steps Part 1) Download...
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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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INSIGHT has written several tools for Paolo Cignoni's Meshlab; these tools are meant to help you render orthographic views of 3D models for archaeological publication by simplifying, segmenting, cleaning and rendering 3D meshes. Meshlab Tools for Epigraphers These tools are meant to help you render orthographic views of 3D models for archaeological publication by simplifying, segmenting, cleaning and rendering 3D meshes. Before producing final plates for publication from 3D models, we find it...
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Bayesian reconstruction of ancient DNA fragments leeHom: Bayesian reconstruction of ancient DNA fragments QUESTIONS: gabriel [dot] reno [ at sign ] gmail.com About leeHom is a program for the Bayesian reconstruction of ancient DNA (the binary is mergeTrimReadsBAM). Downloading: Go to https://github.com/grenaud/leeHom and do one of the following: Clone the repository: git clone --recursive https://github.com/grenaud/leeHom.git Download the ZIP archive and then manually download the submodules...
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Importing Data from iDAI.field 2 into R idaifieldR idaifieldR imports data from the iDAI.field 2 database into R. The core functions of this package use sofa (available on CRAN) to connect to a running iDAI.field 2-client and store the whole database in a list in R (in memory), avoiding the csv-export that would otherwise be needed and gathering all documents at once, which is not possible with said csv-export. Any R-Script using idaifieldR to import the database can be re-run and updated with...
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Dédalo: Cultural Heritage & Oral History Management System To restore the repository download the bundle wget https://archive.org/download/github.com-renderpci-dedalo_-_2021-01-16_08-50-03/renderpci-dedalo_-_2021-01-16_08-50-03.bundle and run: git clone renderpci-dedalo_-_2021-01-16_08-50-03.bundle Source: https://github.com/renderpci/dedalo Uploader: renderpci Upload date: 2021-01-16
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A repository listing Museums active on GitHub, written in Rstats Museums on Github This repository provides CSV raw data for museums active on Github. The following files are included from the GitHub api (accessed via authenticated requests): A list of museums with basic info A list of museum github api urls A list of museum extended github data (bio, repo numbers etc) To restore the repository download the bundle wget...
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Development version of the R package 'Luminescence' Luminesence The R package ‘Luminescence’ by the R-Luminescence Group provides acollection of various R functions for luminescence dating data analysis. Social media and other resources Follow us on or visit our R-Luminescence homepage . Installation i. Requirements Windows (32/64bit) : Rtools (providedby CRAN) macOS : Xcode (provided by Apple) Linux : gcc often comes pre-installed inmost distributions. ii. Install the package Install any...
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R package for aoristic analysis aoristic The goal of aoristic is to make sense of temporally vague data. It cansometimes be difficult to ascertain when some events (such as propertycrime) occur because the victim is not present when the crime happens Asa result, police databases often record a start (or from ) date andtime, and an end (or to ) date and time. The start datetime usuallyreferences when the victim last saw their stolen property, and the to date-time records when they first...
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None outliner A simple app for tracing outlines of an irregular shape and exporting the coordinates of the outline. Please install ImageMagick before attempting to use. Run the app from GitHub with shiny::runGitHub("benmarwick/outliner") To restore the repository download the bundle wget https://archive.org/download/github.com-benmarwick-outliner_-_2021-01-31_08-26-33/benmarwick-outliner_-_2021-01-31_08-26-33.bundle and run: git clone benmarwick-outliner_-_2021-01-31_08-26-33.bundle...
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Paleoclimate Reconstruction from Tree Rings using Correlation Adjusted corRelation paleocar paleocar is an R package implementing functions to performspatio-temporal paleoclimate reconstruction from tree-rings using theCAR (Correlation Adjusted corRelation) approach of Zuber and Strimmer asimplemented in the care package for R . It isoptimized for speed and memory use. This is based on the approach used in Bocinsky and Kohler (2014): Bocinsky, R. K. and Kohler, T. A. (2014). A 2,000-year...
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Geometrical 2D analysis of archaeological walls. To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-murature_-_2020-06-22_14-12-21/steko-murature_-_2020-06-22_14-12-21.bundle and run: git clone steko-murature_-_2020-06-22_14-12-21.bundle Source: https://codeberg.org/steko/murature Uploader: steko Upload date: 2020-06-22
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PaleoView is a visualization tool for paleoclimatic modeling data. To restore the repository download the bundle wget https://archive.org/download/github.com-GlobalEcologyLab-PaleoView_-_2020-03-06_02-42-12/GlobalEcologyLab-PaleoView_-_2020-03-06_02-42-12.bundle and run: git clone GlobalEcologyLab-PaleoView_-_2020-03-06_02-42-12.bundle Source: https://github.com/GlobalEcologyLab/PaleoView Uploader: GlobalEcologyLab Upload date: 2020-03-06
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R package for clean radiocarbon data cleanc14 cleanc14 provides some utility functions for cleaning radiocarbon data in R. Installation You can install the development version of cleanc14 using the remotes package: rremotes::install_github("joeroe/cleanc14") To restore the repository download the bundle wget https://archive.org/download/github.com-joeroe-cleanc14_-_2021-05-04_08-45-08/joeroe-cleanc14_-_2021-05-04_08-45-08.bundle and run: git clone...
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An R package for processing and analyzing 3D scans of archaeological lithics Lithics3D Lithics3D provides a toolbox for working with 3D scans of archaeological lithicswithin the R environment. The functions included herein are designed towork with clean triangular meshes and existing landmarks. For the time being atleast, mesh generation, pre-processing (e.g. cleaning), and landmarking must bedone with different tools (e.g. Meshlab and Landmark Editor ) The included functions can be divided...
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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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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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Solving Ordinary Differential Equations to Understand Luminescence RLumModel The R package ‘RLumModel’ by Johannes Friedrich (University ofBayreuth, Germany), Sebastian Kreutzer (IRAMAT-CRP2A, UniversitéBordeaux Montaigne, France) and Christoph Schmidt (University ofBayreuth, Germany) provides a collection of various R functionsmodelling luminescence signals in quartz andAl 2 O 3 , based on energy-band models. For an introduction and further details, visit the RLumModelhomepage ....
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Climate Response and Virginia Archaeology: Maps from Different Points of View Climate Response and Virginia Archaeology: Maps from Different Points of View Jolene Smith, Virginia Department of Historic Resources A Paper for the 48th Annual Middle Atlantic Archaeology Conference in Virginia Beach, VA. March 17, 2018. In Geospatial Studies in Middle Atlantic ArchaeologySession Organizer: Yvonne French (Northern Virginia Chapter, Archeological Society of Virginia) Introduction: Expectations for...
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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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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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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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A function for retrieving metrics for resistance-resilience from rcarbon permTest objects. p2pPerm A function for retrieving metrics for resistance-resilience from rcarbon SpdPermTest objects. p2pPerm() is an adaptation of Edinborough et al.'s post-hoc statistical test for demographic events in written and oral history (https://doi.org/10.1073/pnas.1713012114). The original function - p2pTest() in rcarbon - is for use with objects of class SpdModelTest . This function extends the principle to...
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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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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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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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None paleoxrf The goal of paleoxrf is to simplify reading data from Acadia's paleoenvironmental X-Ray Fluorescence laboratory. Installation You can install paleoxrf from GitHub using the following code: ``` r install.packages("remotes") remotes::install_github("paleolimbot/paleoxrf")``` If all is well, you should be able to load the package: rlibrary(paleoxrf) The examples below use dplyr to manipulate the output of the read functions. rlibrary(dplyr) Reading XRF Data The...
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Scripts to create QR-Code images for storage boxes. Each box has an associated web page describing its content, and the QR-Code serves as a short-link from the physical object to the web page. To restore the repository download the bundle wget https://archive.org/download/codeberg.org-steko-qrcode-storage_-_2020-06-22_14-11-12/steko-qrcode-storage_-_2020-06-22_14-11-12.bundle and run: git clone steko-qrcode-storage_-_2020-06-22_14-11-12.bundle Source: https://codeberg.org/steko/qrcode-storage...
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R package to simulate a Luminescence Reader To restore the repository download the bundle wget https://archive.org/download/github.com-dstreble-LumReader_-_2017-01-26_13-55-17/dstreble-LumReader_-_2017-01-26_13-55-17.bundle and run: git clone dstreble-LumReader_-_2017-01-26_13-55-17.bundle Source: https://github.com/dstreble/LumReader Uploader: dstreble Upload date: 2017-01-26
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R Interface to IntChron rintchron: R interface to IntChron rintchron provides an R interface to IntChron , an indexing service and exchangeformat for radiocarbon dates and other chronological data ( Bronk Ramseyet al. 2019 ). It includes a userfriendly interface for querying databases indexed by IntChron, as wellas lower level functions for interacting directly with the IntChronAPI . For an introduction to querying IntChron’s databases see the basicusage vignette . Foradvanced users, low...
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The GigaMesh Software Framework is a modular software for display, editing and visualization of 3D-data typically acquired with structured light scanning (SLS) or structure from motion (SfM). NAME GigaMesh - GigaMesh Software Framework for processing large meshes. DESCRIPTION The GigaMesh Software Framework is a modular software for display, editing and visualization of 3D-data typically acquired with structured light scanning (SLS) or structure from motion (SfM). It provides numerous functions...
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Analogue and weighted averaging methods for palaeoecology analogue Released version Build status | Linux | Windows | Codecov || ----- | ------- | ------- || | | | What is analogue? analogue is an R package for use with palaeoecological data. Originally, analogue was intended as an R implementation of analogue methods such as analogue matching, ROC curves, and MAT transfer function models, and the computation of dissimilarity coefficients. Since then the scope of the package has grown to include...
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None Senscape Senscape is a toolbox for modelling human perception of topography for QGIS, based on QGIS viewshed module . It is a subclass of QGIS processing framework and can be readily used in custom models or scripts. The plugin is in experimental phase. To install: 1. Search for “Senscape” in QGIS plugin manager (make sure experimental plugins are allowed)2. In Processing menu, under Options, allow Senscape provider For manual instalation see QGIS viewshed module . Files should be...
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R Package - Reconstruct Paths using Archaeological Monuments & Model Parameters of Infrastructure pathAAR R Package to reconstruct paths using archaeological monuments, model parameters of infrastructure and evaluate those parameters Archaeological remains of roads or infrastructure are rarely found, especially in earlier epochs. Usually, most premodern paths have been country lanes, which might be paved when needed. Hence, their preservation is linked to specific conditions, like...
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QGIS plugin to transforms profile control points for fotogrammetric rectification from archaeological excavations. profileAAR A python PluginThe plugin profileAAR transforms profile control points for fotogrammetric rectification of profile images of archaeological excavations How to use profileAAR After installing and opening the plugin there is a "?"-Button in the Plugin. There you will find additional informations. QGIS 3 Install Qgis3 >3.6.0 You will find the Plugin in the...
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Modelling and feature detection in palaeoenvironmental time series using additive models Modelling and feature detection in palaeoenvironmental time series using additive models Code and text for manuscript describing my additive modelling approach to modelling palaeoenvironmental time series and detecting periods of significant change in palaeo data. To restore the repository download the bundle wget...
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Data analysis tools for X-Ray, Neutron and Electron sciences MAILING LIST scikit-beam Documentation Examples scikit-beam-examples repository Powder calibration (still needs tilt correction) 1-time correlation dir Jupyter notebook Differential Phase Contrast dir Jupyter notebook Fast conversion to reciprocal space X-Ray Speckle Visibility Spectroscopy Basic Plotting of X-Ray Fluorescence Elemental Lines Quick start install with conda ```conda install scikit-beam -c nsls2forge ``` install...
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Floor plan app using augmented reality. Used for Heritage Structures Lab. ARFloorPlanApp Floor plan app using augmented reality. Used for Heritage Structures Lab.See the Developer Guide for full details. To restore the repository download the bundle wget https://archive.org/download/github.com-carlsun98-ARFloorPlanApp_-_2018-07-27_22-02-36/carlsun98-ARFloorPlanApp_-_2018-07-27_22-02-36.bundle and run: git clone carlsun98-ARFloorPlanApp_-_2018-07-27_22-02-36.bundle Source:...
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leastcostpath: Modelling Pathways and Movement Potential Within a Landscape leastcostpath - version 1.7.9 The R library leastcostpath provides the functionality to calculate Cost Surfaces based on multiple cost functions that approximate the difficulty of moving across a landscape. Furthermore, the attraction/repulsion of landscape features can be incorporated into the Cost Surfaces, as well as barriers that inhibit movement. NOTE: The R library leastcostpath requires the use of projected...
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Roman amphitheater data as R package. See http://github.com/sfsheath/roman-amphitheaters ramphs Roman amphitheater data as R package. See http://github.com/sfsheath/roman-amphitheaters Install with: install_github('sfsheath/ramphs') # requires devtools package. Then: data(ramphs, package = 'ramphs')ramphs$title # for example / to confirm it worked To restore the repository download the bundle wget...
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Presentation frontend for archaeological data from OpenAtlas databases About THANADOS is an open source, web application for the presentation of archaeological data especially for burial studies.It started within the MEDCEM project and actively carries on the development of this application. See examples at THANADOS or MEDCEM The data is based on the OpenAtlas application The information is mapped as a network using classes and properties of the CIDOC CRM . Documentation: Wiki , Issues ,...
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A comprehensive list of literature on Agent Based Models (ABM) in Archaeology. Maintained and created by Iza Romanowska and Lennart Linde. The-ABM-in-Archaeology-Bibliography A selected yet comprehensive list of literature and resources on Agent Based Models (ABM) in Archaeology. Maintained and created by Iza Romanowska and Lennart Linde. Know a missing resource or found a broken link? Put up a pull request ! Our very subjective list of must-reads Axtell, R. L., Epstein, J. M., Dean, J. S. Et...
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Clustering of calibrated radiocarbon dates Clustering of calibrated radiocarbon dates Overview A python implementation of the method of clustering radiocarbon dates in order to determine whether they represent separate events, or phases in time. For an overview of the method see: [upcoming paper] Demján, P., Pavúk, P. Clustering of calibrated radiocarbon dates: Site-specific chronological sequences identified by dense radiocarbon sampling. How to run Find optimal number of clusters: python...
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None Topographic network analysis for QGIS Terrain can be represented as a collection of objects - terrain features such as valleys, ridges, hills etc. One possible approach to arrive at such a model is modelling relationships between elements in a terrain model, most commonly pixels in an elevation model. Here, pixels are connected according to their height difference. Such a network, in it's simplest form identical to the one used for watershed modelling, can then be analysed for further...
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