https://github.com/tillahoffmann/coaloracle

Repository for simulated genetic data presented by Nunes and Balding (2010).
https://github.com/tillahoffmann/coaloracle

likelihood-free-inference open-data summary-statistics

Last synced: 27 days ago
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Repository for simulated genetic data presented by Nunes and Balding (2010).

• Host: GitHub
• URL: https://github.com/tillahoffmann/coaloracle
• Owner: tillahoffmann
• License: mit
• Created: 2022-06-13T19:07:29.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-06-28T19:38:08.000Z (over 2 years ago)
• Last Synced: 2024-03-23T13:31:21.973Z (8 months ago)
• Topics: likelihood-free-inference, open-data, summary-statistics
• Language: Makefile
• Homepage: https://paperswithcode.com/dataset/summaries-of-genetic-variation
• Size: 9.77 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Summaries of Genetic Variation

Repository for simulated genetic data presented by [Nunes and Balding (2010)](https://doi.org/10.2202/1544-6115.1576). See https://paperswithcode.com/dataset/summaries-of-genetic-variation for details.

The data comprise

- `csv/coal.csv`: 100,000 simulations with  $\theta\sim\mathrm{Uniform}\left(2,10\right) $ and  $\rho\sim\mathrm{Uniform}\left(0,10\right) $, where  $\theta $ is the scaled mutation rate and  $\rho $ is the scaled recombination rate.

- `csv/coalobs.csv`: 100 simulations with the same prior distribution as for `csv/coal.csv`.

- `csv/coaloracle.csv`: 1,000,000 simulations with  $\theta\sim\mathrm{Uniform}\left(0,10\right) $ and  $\rho\sim\mathrm{Uniform}\left(0,10\right) $.

## Getting the data from scratch

Run

- `make csv` to download data and regenerate the CSV files (`Rscript` and `curl` must be installed).

- `make rda.shasum` to regenerate the checksum file to validate the integrity of the input data (`shasum` and `curl` must be installed).

- `make rda/validate` to validate the `rda` input files checksums (`shasum` and `curl` must be installed).

[comment]: <> (there are some math rendering issues that can be resolved by funky formatting above; see https://github.com/github-community/community/discussions/19480 for details)