ticktack
ticktack: A Python package for carbon box modelling - Published in JOSS (2023)
Science Score: 93.0%
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
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Published in Journal of Open Source Software
Scientific Fields
Repository
An open-source carbon box model implementation built on JAX.
Basic Info
- Host: GitHub
- Owner: SharmaLlama
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://sharmallama.github.io/ticktack
- Size: 112 MB
Statistics
- Stars: 11
- Watchers: 4
- Forks: 3
- Open Issues: 4
- Releases: 2
Metadata Files
README.md
ticktack
A lightweight, open-source carbon box modelling library in Python, adapted for modelling tree ring radiocarbon time series.
Contributors
Utkarsh Sharma, Qingyuan Zhang, Jordan Dennis, Benjamin Pope
Overview
Radiocarbon measurements from tree rings allow us to recover measurements of cosmic radiation from the distant past, and exquisitely calibrate carbon dating of archaeological sites. But in order to infer cosmic production rates from raw ΔC14 data, we need to model the entire global carbon cycle, from the production of radiocarbon in the stratosphere and troposphere to its uptake by the oceans and biosphere. Many such competing models exist, in which the Earth system is partitioned into 'boxes' with reservoirs of C12, C14, and coefficients of flow between them.
ticktack is the first open-source package for carbon box modelling, allowing you to specify your own model or load a model with the same parameters as several leading closed-source models. Built in Python on Google Jax, it solves the carbon box ordinary differential equations using the Runge-Kutta method, on arbitrarily fine time grids and with arbitrary production rates. This forwards model is connected via a simple API to Bayesian inference using MCMC: currently we support only emcee, but implementations are in progress of HMC and nested sampling.
Installation
The easiest way to install is from PyPI: just use
pip install ticktack
To install from source: clone this git repo, enter the directory, and run
python setup.py install
License
We invite anyone interested to use and modify this code under a MIT license.
Name
The 'little boxes' in Malvina Reynolds' famous song are all made of ticky-tacky, and they all look just the same. Here we provide an open-source toolkit for reproducing and extending carbon box models for radiocarbon analysis, and we expect they will be as interchangeable as Malvina Reynolds' boxes!
Owner
- Name: Utkarsh Sharma
- Login: SharmaLlama
- Kind: user
- Repositories: 1
- Profile: https://github.com/SharmaLlama
3rd year Computer Science and Mathematics Student @ UQ, UQ Computer Science Society Committee.
JOSS Publication
ticktack: A Python package for carbon box modelling
Authors
School of Mathematics and Physics, The University of Queensland, St Lucia, QLD 4072, Australia
School of Mathematics and Physics, The University of Queensland, St Lucia, QLD 4072, Australia
School of Mathematics and Physics, The University of Queensland, St Lucia, QLD 4072, Australia
School of Mathematics and Physics, The University of Queensland, St Lucia, QLD 4072, Australia, Centre for Astrophysics, University of Southern Queensland, West Street, Toowoomba, QLD 4350, Australia
Editor
Dan Foreman-Mackey
Tags
Radiocarbon Miyake Events Carbon Box ModelsCodeMeta (codemeta.json)
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"@type": "Person",
"email": "j.dennis@uq.edu.au",
"name": "Jordan Dennis",
"affiliation": "University of Queensland"
},
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"@id": "0000-0002-0906-8533",
"@type": "Person",
"email": "qingyuan.zhang@uq.edu.au",
"name": "qingyuanzhang3",
"affiliation": "University of Queensland"
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"email": "u.sharma@uq.net.au",
"name": "Utkarsh Sharma",
"affiliation": "University of Queensland"
},
{
"@id": "0000-0003-2595-9114",
"@type": "Person",
"email": "b.pope@uq.edu.au",
"name": "Benjamin Pope",
"affiliation": "University of Queensland"
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],
"identifier": "",
"codeRepository": "https://github.com/sharmaLlama/ticktack",
"datePublished": "2022-10-26",
"dateModified": "2022-10-26",
"dateCreated": "2022-10-26",
"description": "A Python/Jax based open source package for carbon box modelling of radiocarbon time series.",
"keywords": "radiocarbon, Miyake Events, carbon cycle, atmospheric carbon, solar flares",
"license": "MIT",
"title": "ticktack",
"version": "v1.0.0"
}GitHub Events
Total
Last Year
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jordan Dennis | j****5@g****m | 321 |
| qingyuanzhang3 | z****3@i****m | 142 |
| Utkarsh Sharma | 7****a | 128 |
| benjaminpope | b****e@g****m | 114 |
| Dan F-M | f****y@g****m | 3 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 32
- Total pull requests: 18
- Average time to close issues: about 1 month
- Average time to close pull requests: 1 day
- Total issue authors: 4
- Total pull request authors: 4
- Average comments per issue: 1.47
- Average comments per pull request: 0.28
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- benjaminpope (13)
- dfm (11)
- Jordan-Dennis (7)
- ahessl (1)
Pull Request Authors
- benjaminpope (8)
- SharmaLlama (6)
- dfm (3)
- qingyuanzhang3 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 31 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 19
- Total maintainers: 2
pypi.org: ticktack
Python package to build a carbon box model.
- Homepage: https://github.com/SharmaLlama/ticktack
- Documentation: https://ticktack.readthedocs.io/
- License: MIT
-
Latest release: 1.1.4
published almost 2 years ago
Rankings
Maintainers (2)
Dependencies
- astropy *
- celerite2 *
- chainconsumer *
- emcee *
- h5py ==3.3.0
- hdfdict *
- jax >=0.3.13
- jax-cosmo *
- jaxlib >=0.3.7
- jaxns *
- matplotlib *
- numpy *
- pandas *
- scipy *
- seaborn *
- tinygp *
- tqdm *
- actions/checkout v2 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite
- actions/checkout master composite
- actions/setup-python v1 composite