Skip to content

Add preprint citation to README #492

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
nspope wants to merge 2 commits into
base: main
Choose a base branch
from
+13 −8
Open

Add preprint citation to README #492

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7db16d1
Add preprint citation to readme
nspope Jan 26, 2026
70b8bd0
update citation in docs
nspope Jan 29, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,11 @@ Please refer to the documentation ([stable](https://tskit.dev/tsdate/docs/stable
python -m pip install tsdate
```

The algorithms for the original `inside_outside` and `maximization` [methods](https://tskit.dev/tsdate/docs/stable/methods.html) are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (citation below, preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2), evaluations in [another repository](https://github.com/awohns/unified_genealogy_paper)). The new `variational_gamma` method, the default from version 0.2 onwards, has not yet been described in print. For the moment, please cite this github repository if you need a citable reference.
If using the `variational_gamma` algorithm (the default from version 0.2 onwards), please cite the [preprint](https://www.biorxiv.org/content/10.64898/2026.01.07.698223v1):

> Nathaniel S. Pope, Sam Tallman, Ben Jeffery, Duncan Robertson, Yan Wong, Savita Karthikeyan, Peter L. Ralph, and Jerome Kelleher (2026) _Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs_. bioRxiv: 2026.01.07.698223; doi: https://doi.org/10.64898/2026.01.07.698223
The algorithms for the original `inside_outside` and `maximization` [methods](https://tskit.dev/tsdate/docs/stable/methods.html) (the default prior to version 0.2) are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (citation below, preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2), evaluations in [another repository](https://github.com/awohns/unified_genealogy_paper)).

The citation to use for the original tsdate algorithms is:

Expand Down
15 changes: 8 additions & 7 deletions docs/citation.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,16 +18,17 @@ kernelspec:

# Citation

The algorithm for the `inside_outside` and `maximization` methods is described
The default `variational_gamma` method is described in a
[preprint](https://www.biorxiv.org/content/10.64898/2026.01.07.698223v1), and
should be cited by published work using tsdate versions 0.2 or higher:

> Nathaniel S. Pope, Sam Tallman, Ben Jeffery, Duncan Robertson, Yan Wong, Savita Karthikeyan, Peter L. Ralph, and Jerome Kelleher (2026) _Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs_. bioRxiv: 2026.01.07.698223; doi: https://doi.org/10.64898/2026.01.07.698223
The algorithm for the `inside_outside` and `maximization` methods (the defaults
prior to version 0.2) is described
in [our Science paper](https://www.science.org/doi/10.1126/science.abi8264) (citation below,
preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2)).
[Another repository](https://github.com/awohns/unified_genealogy_paper) provides
code to reproduce evaluations of the accuracy and computational requirements of these methods.
The default `variational_gamma` method has not yet been described in print. For the moment,
please cite this github repository if you need a citable reference.

The original _tsdate_ algorithm, which you should cite in published work, is published in:

> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) *A unified genealogy of modern and ancient genomes*. Science **375**: eabi8264; doi: https://doi.org/10.1126/science.abi8264