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Squashed commit of the following: authored by Alex Zarebski's avatar Alex Zarebski 
commit b3d450a81f6786cf7c6c1a8579945d3f1d063b0e
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Jul 15 14:55:40 2022 +0100

    update documentation

commit c2fd818dc682cd74b43db95ad633f9e7962a2610
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Jul 15 14:55:28 2022 +0100

    improve figure

commit 7cb4b26cce678aabad4592e9874925eaf672a705
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Jul 15 14:50:26 2022 +0100

    update another R script

commit deb3810cf69b7bde617f1ab2ec7df9df01580971
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Jul 15 14:48:41 2022 +0100

    update r script for backwards compatibility

commit c671f9f7487eafd7bbc5ac5ec1f5874f4ed8ff10
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Jul 15 14:35:48 2022 +0100

    incorporate feedback on the first tutorial
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......@@ -6,7 +6,8 @@ There are instructions for the installation of TimTam [[https://github.com/aezar
** Tutorials
- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-0][Tutorial 0]] involves simulating data for subsequent tutorials
- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-0][Tutorial 0]] involves simulating data for subsequent tutorials (feel free to
skip this unless you are interested in simulating your own data.)
- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-1][Tutorial 1]] involves estimating the reproduction number and prevalence assuming
that the death and sampling rate are known using the sequences from
Tutorial 0.
......@@ -36,3 +37,12 @@ Zarebski AE, du Plessis L, Parag KV, Pybus OG (2022) A computationally tractable
birth-death model that combines phylogenetic and epidemiological data. PLOS
Computational Biology 18(2): e1009805.
https://doi.org/10.1371/journal.pcbi.1009805
** Acknowledgements
- This would not have been accomplished without the assistance of my co-authors:
Louis du Plessis, Kris V. Parag, and Oliver G. Pybus.
- Thank you to Yunjun Zhang from Peking University for reading through and
helping to improve documentation on an earlier version of this software.
- Thank you to Tim Vaughan from ETH Zürich for providing helpful advice on
numerous occassions.