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Squashed commit of the following: authored by Alex Zarebski's avatar Alex Zarebski 
commit 46bc907f836b213dcaf827f69d8047fb063dcf8d
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed May 25 16:59:00 2022 +0100

    docs for tutorial-3

commit 7c5ebec3cc8547e59565111dde402360923e9f51
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed May 25 15:36:35 2022 +0100

    include result figures from tutorial-3

commit 4a65cd13564fad45da2a547fcaafd2f7c1e92b7e
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed May 25 15:34:23 2022 +0100

    fine tune example

commit 35df34044eff30d8424f5a4f43298637771c0c45
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed May 25 13:06:06 2022 +0100

    get time varying working properly

commit cd00652f81aa0118da1be78d0c5b52062ae57fe5
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed May 25 11:37:44 2022 +0100

    some materials for tutorial-3
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...@@ -13,6 +13,8 @@ There are instructions for the installation of TimTam [[https://github.com/aezar ...@@ -13,6 +13,8 @@ There are instructions for the installation of TimTam [[https://github.com/aezar
- [[https://github.com/aezarebski/timtam2/wiki/Tutorial-2][Tutorial 2]] simulates a new data set with a varying birth rate but otherwise is - [[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 similar to Tutorial 1. This will show you how to infer rates that change
through time. through time.
- [[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.
** Glossary ** Glossary
...@@ -22,8 +24,8 @@ Where possible this Wiki should use the terminology outlined in this [[https://g ...@@ -22,8 +24,8 @@ Where possible this Wiki should use the terminology outlined in this [[https://g
- [[https://doi.org/10.1016/j.jtbi.2020.110400][Manceau /et al/ (2021)]] The probability distribution of the ancestral population - [[https://doi.org/10.1016/j.jtbi.2020.110400][Manceau /et al/ (2021)]] The probability distribution of the ancestral population
size conditioned on the reconstructed phylogenetic tree with occurrence data size conditioned on the reconstructed phylogenetic tree with occurrence data
- *PREPRINT* [[https://doi.org/10.1101/2020.10.27.356758][Andréoletti /et al/ (2020)]] A skyline birth-death process for inferring - [[https://doi.org/10.1093/sysbio/syac037][Andréoletti /et al/ (2022)]] The Occurrence Birth-Death Process for
the population size from a reconstructed tree with occurrences combined-evidence analysis in macroevolution and epidemiology
** Citing TimTam ** Citing TimTam
......