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@CABAH

Centre of Excellence for Australian Biodiversity and Heritage

We aim to tell a culturally inclusive, globally significant human and environmental history of Australia. We like to call it, Australia’s Epic Story.
Readme.md

Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH)

This is the shared Github code and data repository for members of CABAH. Curated by @cjabradshaw & @fredsaltre (please contact for membership).

Example content:

Databases

  • Atlas of Living Australia: Free and open source IT infrastructure for the aggregation and delivery of biodiversity data (links to Github organisation page)
  • FosSahul: A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates (a CABAH product)
  • IPPD: An evolving, open-access database of the largest collection of palaecological information in the Indo-Pacific region (a CABAH product)
  • MorphoSource: Find, view, and download 3D data representing the world's natural history, cultural heritage, and scientific collections (links to Github organisation page)
  • Neotoma: This R package pulls data from the Neotoma Palaeoecology Database, an online hub for data, research, education, and discussion about palaeoenvironments
  • OCTOPUS: Open Cosmogenic Isotope and Luminescence Database (a CABAH product)
  • SahulArch: Database of published radiocarbon ages for archaeological records from Sahul (a CABAH product)
  • WorldClim: a database of high spatial resolution global weather and climate data (see here for instructions on how to access the data directly from R)

Scripts

  • holoflow: Bioinformatics pipeline for hologenomics data generation and analysis
  • Inferring-networks-and-modelling-trophic-cascades: Scripts and data associated with the paper: Sahul’s megafauna species were vulnerable to plant-community changes due to their position in the trophic network
  • MegafaunaSusceptibility: R code for building stochastic demographic models of extinct megafauna of Sahul
  • Predator-prey-ABM: code and simulation data for agent-based model in paper: Habitat features and performance interact to determine the outcomes of terrestrial predator–prey pursuits
  • SahulHumanSpread: Code and data files necessary for reproducing cellular-automaton model of human spread across Sahul
  • SEOZ_megafauna_extirpation: Inferring spatio-temporal trajectories of megafauna extirpations (local extinction) and initial human colonisation in southeastern Australia

Learning resources

  • assignDOI: Assign a digital object identifier (DOI) to your Github repository
  • FAIR_Workshop_github: A repository for practising the basic use of Github
  • learningRresources: Various online & other resources for learning and improving skills in the R programming language
  • learningPythonResources: Various online & other resources for learning and improving skills in the Python programming language

Software/utilities

  • QGIS: A free, open source, cross platform (lin/win/mac) geographical information system (GIS)


Centre of Excellence for Australian Biodiversity and Heritage Australian Research Council

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  1. learningRresources learningRresources Public

    Various online & other resources for learning and improving skills in the R programming language

    14 8

  2. FosSahul FosSahul Public

    Forked from GlobalEcologyFlinders/FosSahul

    A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates

    R

  3. Inferring-networks-and-modelling-trophic-cascades Inferring-networks-and-modelling-trophic-cascades Public

    Forked from JohnLlewelyn/Inferring-networks-and-modelling-trophic-cascades

    Scripts and data associated with the paper: Sahul’s megafauna species were vulnerable to plant-community changes due to their position in the trophic network

    R 1

  4. SahulHumanSpread SahulHumanSpread Public

    Forked from cjabradshaw/SahulHumanSpread

    Code and data files necessary for reproducing cellular-automaton model of human spread across Sahul

    R

  5. SEOZ_megafauna_extirpation SEOZ_megafauna_extirpation Public

    Forked from FredSaltre/SEOZ_megafauna_extirpation

    Inferring spatio-temporal trajectories of megafauna extirpations (local extinction) and initial human colonisation in southeastern Australia

    R

  6. holoflow holoflow Public

    Forked from EisenRa/holoflow

    Bioinformatics pipeline for hologenomics data generation and analysis

    Python

Repositories

Showing 10 of 36 repositories
  • .github Public
    CABAH/.github’s past year of commit activity
    0 0 0 0 Updated Sep 23, 2024
  • CyprusHippoElephant Public Forked from cjabradshaw/CyprusHippoElephant

    Demographic models predicting the effect of human hunting on now-extinct dwarf hippopotamus and dwarf elephant in Cyprus

    CABAH/CyprusHippoElephant’s past year of commit activity
    R 0 MIT 3 0 0 Updated Sep 23, 2024
  • AusIndigN Public Forked from cjabradshaw/AusIndigN

    Estimating the pre-colonial size of the Indigenous population in Australia

    CABAH/AusIndigN’s past year of commit activity
    R 0 MIT 3 0 0 Updated Aug 29, 2024
  • globalHumanPopSwitch Public Forked from cjabradshaw/globalHumanPopSwitch

    Global human population ended self-facilitation in the 1950s

    CABAH/globalHumanPopSwitch’s past year of commit activity
    R 0 MIT 3 0 0 Updated Jul 31, 2024
  • CyprusHumanPleistocene Public Forked from cjabradshaw/CyprusHumanPleistocene

    Demographic models of initial human arrival and spread in Cyprus at the end of the Pleistocene

    CABAH/CyprusHumanPleistocene’s past year of commit activity
    R 0 MIT 3 0 0 Updated Apr 10, 2024
  • IndoAustralianMonsoon Public Forked from cjabradshaw/IndoAustralianMonsoon

    A continuous, absolute-dated, 150,000-year record of monsoon hydroclimate dynamics from a permanent lagoon in the core monsoon region of northern Australia, compared to global circulation model hindcasts

    CABAH/IndoAustralianMonsoon’s past year of commit activity
    R 0 MIT 2 0 0 Updated Apr 8, 2024
  • SavannaCorridors Public Forked from cjabradshaw/SavannaCorridors

    Analysis of palaeoecological records across South-East Asia to determine the evidence for regime shifts between open savannas and dense tropical forests occurred since the Last Glacial Maximum

    CABAH/SavannaCorridors’s past year of commit activity
    R 0 MIT 2 0 0 Updated Nov 28, 2023
  • OCTOPUS Public

    The Open Cosmogenic Isotope and Luminescence Database

    CABAH/OCTOPUS’s past year of commit activity
    0 Apache-2.0 1 0 0 Updated Sep 13, 2023
  • learningRresources Public

    Various online & other resources for learning and improving skills in the R programming language

    CABAH/learningRresources’s past year of commit activity
    14 8 0 0 Updated Jun 5, 2023
  • SuperhighwaysSpreadModel Public Forked from cjabradshaw/SuperhighwaysSpreadModel

    ‘Superhighways’ of human movement in Sahul combined with a demographic cellular automaton

    CABAH/SuperhighwaysSpreadModel’s past year of commit activity
    R 0 MIT 2 0 0 Updated Mar 14, 2023
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