diff --git a/README.md b/README.md index 0ed72c76..2315add9 100644 --- a/README.md +++ b/README.md @@ -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: diff --git a/docs/citation.md b/docs/citation.md index c1c3c6d4..1dcde0c5 100644 --- a/docs/citation.md +++ b/docs/citation.md @@ -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 - -