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#+title: TimTam
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** Installation
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* Installation
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There are instructions for the installation of TimTam [[https://github.com/aezarebski/timtam2/wiki/Installation][here]].
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** Tutorials
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* Tutorials
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- [[https://github.com/aezarebski/timtam2/wiki/Constant-Parameters-Canonical][Constant Parameters]] considers a constant parameter birth-death-sampling model.
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- [[https://github.com/aezarebski/timtam2/wiki/Constant-Parameters-R0][Constant Parameters and R0]] is similar to the tutorial above, but considers an
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| ... | ... | @@ -16,24 +16,25 @@ There are instructions for the installation of TimTam [[https://github.com/aezar |
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While working through the tutorials, it might be helpful to have the [[https://www.beast2.org/xml/index.html][BEAST2 XML documentation]] handy.
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*** Less polished tutorials
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** Less polished tutorials
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- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-3][Tutorial 3]] simulates an SIR type epidemic and then estimates the effective
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reproduction number through time based off of both genetic and case data.
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- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-4][Tutorial 4]] is the same as Tutorial 3, but assumes that there was no sequenced sampling done during the first half of the epidemic.
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- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-4][Tutorial 4]] is the same as Tutorial 3, but assumes that there was no sequenced
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sampling done during the first half of the epidemic.
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** Glossary
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* Glossary
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Where possible this Wiki should use the terminology outlined in this [[https://github.com/aezarebski/timtam2/wiki/Glossary][glossary]].
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** Related work
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* Related work
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- [[https://doi.org/10.1016/j.jtbi.2020.110400][Manceau /et al/ (2021)]] The probability distribution of the ancestral population
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size conditioned on the reconstructed phylogenetic tree with occurrence data
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- [[https://doi.org/10.1093/sysbio/syac037][Andréoletti /et al/ (2022)]] The Occurrence Birth-Death Process for
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combined-evidence analysis in macroevolution and epidemiology
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** Citing TimTam
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* Citing TimTam
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If you use TIMTAM as part of research that leads to a publication, we ask that
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you cite the following article:
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| ... | ... | @@ -43,11 +44,13 @@ birth-death model that combines phylogenetic and epidemiological data. PLOS |
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Computational Biology 18(2): e1009805.
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[[https://doi.org/10.1371/journal.pcbi.1009805]]
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** Acknowledgements
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* Acknowledgements
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- Thank you to Bernardo Gutierrez for carefully working through the tutorials,
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and providing numerous corrections.
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- This would not have been accomplished without the assistance of my co-authors:
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Louis du Plessis, Kris V. Parag, and Oliver G. Pybus.
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- Thank you to Yunjun Zhang from Peking University for reading through and
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helping to improve documentation on an earlier version of this software.
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- Thank you to Tim Vaughan from ETH Zürich for providing helpful advice on
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numerous occassions. |
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numerous occasions. |
