From 02f3af12a3adeb0059f9db085178f827cf68623e Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Tue, 11 Jun 2024 12:17:43 +0100 Subject: [PATCH] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a519f9e3..b6e5ba08 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,9 @@ The method is frequently combined with the [tsinfer](https://tsinfer.readthedocs Please refer to the [documentation](https://tskit.dev/tsdate/docs/latest/) for information on installing and using the software. -The discrete-time estimation methods are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2)). We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data. The code to reproduce these results can be found in [another repository](https://github.com/awohns/unified_genealogy_paper). +The algorithms for the original `inside_outside` and `maximization` [methods](https://tskit.dev/tsdate/docs/latest/methods.html) are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (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, which is now the default, has not yet been described in print. For the moment, please cite this github repository if you need a citable reference. + +The citation to use for the original tsdate algorithms is: > 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 -Please cite this paper if you use ``tsdate`` in published work.