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Squashed commit of the following: authored by Alex Zarebski's avatar Alex Zarebski 
commit d4d557e527626a6fb33048dfca3fbf0d79713a17
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Sep 2 13:58:25 2022 +0100

    document new materials

commit 7d807888324d9393e1ba8576d280e3c3ca283f19
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Sep 2 13:44:34 2022 +0100

    add new figures

commit 8dbedf79bd8bd06db07fefdd409e588c3c6acc20
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Sep 2 13:44:03 2022 +0100

    add new materials
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...@@ -11,20 +11,17 @@ There are instructions for the installation of TimTam [[https://github.com/aezar ...@@ -11,20 +11,17 @@ There are instructions for the installation of TimTam [[https://github.com/aezar
alternative parameterisation. alternative parameterisation.
- [[https://github.com/aezarebski/timtam2/wiki/Constant-Parameters-History][Constant Parameters and historical prevalence]] extends the R0 example above to - [[https://github.com/aezarebski/timtam2/wiki/Constant-Parameters-History][Constant Parameters and historical prevalence]] extends the R0 example above to
include estimation of historical prevalence. include estimation of historical prevalence.
- [[https://github.com/aezarebski/timtam2/wiki/Variable-Parameters-SIR-Epidemic][Variable Parameters for an SIR Epidemic]] extends the history example above to
include estimation with a changing R0 to model an epidemic.
While working through the tutorials, it might be helpful to have the [[https://www.beast2.org/xml/index.html][BEAST2 XML documentation]] handy.
*** Less polished tutorials *** Less polished 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.)
- *UNDER CONSTRUCTION* [[https://github.com/aezarebski/timtam2/wiki/Tutorial-2][Tutorial 2]] simulates a new data set with a varying birth
rate but otherwise is similar to Tutorial 1. This will show you how to infer
rates that change through time.
- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-3][Tutorial 3]] simulates an SIR type epidemic and then estimates the effective - [[https://github.com/aezarebski/timtam2/wiki/Tutorial-3][Tutorial 3]] simulates an SIR type epidemic and then estimates the effective
reproduction number through time based off of both genetic and case data. reproduction number through time based off of both genetic and case data.
- [[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. - [[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.
While working through the tutorials, it might be helpful to have the [[https://www.beast2.org/xml/index.html][BEAST2 XML documentation]] handy.
** Glossary ** Glossary
Where possible this Wiki should use the terminology outlined in this [[https://github.com/aezarebski/timtam2/wiki/Glossary][glossary]]. Where possible this Wiki should use the terminology outlined in this [[https://github.com/aezarebski/timtam2/wiki/Glossary][glossary]].
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