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aezarebski / timtam2

This repository is an implementation of the TimTam likelihood as a BEAST2 package.
https://aezarebski.github.io/timtam/
MIT License
3 stars 0 forks source link

Squashed commit of the following: #56

Closed aezarebski closed 1 year ago

aezarebski commented 1 year ago

commit 4fc537a6189628d55ce529be66359f23067513dd Author: Alexander E. Zarebski 36244258+aezarebski@users.noreply.github.com Date: Wed Dec 21 15:06:55 2022 +0000

Seq only template (#55)

* add template file

* update template file

* fix missing connections

* include working examples

* update xml based on input file

* put the example in the examples directory and add extra details

* include a bdsky example as well

* use the same priors on r0 and sampling

* remove old file

commit b9aca006a833af0d2358dcf931708d96334757c4 Author: Alexander E. Zarebski 36244258+aezarebski@users.noreply.github.com Date: Tue Dec 20 16:21:56 2022 +0000

Seq only boom bust (#54)

* add an example xml that works but is ugly

* fix silly bug in the way parameters where configured

* update the configuration file for intellij

* update the example xml so it has the desired form

* move boom-bust sequence data only example to examples directory

* add default values to these variables

commit 9e7d13abe5414727b9aba0b37fc9584690ce204f Author: Alex Zarebski aezarebski@gmail.com Date: Tue Nov 1 16:57:06 2022 +0000

copy over fix on prior

commit c6721133726197ec755446b1c4f29d9233c8c22d Author: Alex Zarebski aezarebski@gmail.com Date: Tue Nov 1 16:33:19 2022 +0000

use a more sensible version number

commit bfe429f9cbe23ba74c6a8f3574540718f55dabd6 Author: Alex Zarebski aezarebski@gmail.com Date: Tue Nov 1 16:02:57 2022 +0000

adjust version xml to use latest versions

commit bee365b73e1beb9b6b856a70dc542dd5600db447 Author: Alex Zarebski aezarebski@gmail.com Date: Tue Nov 1 16:02:42 2022 +0000

apply migration script to examples

commit b43f0aaf6367c12d22d4f812e97834c443f0779c Author: Alex Zarebski aezarebski@gmail.com Date: Wed Sep 28 17:43:19 2022 +0100

update buildscript to work with 2.7

commit f487d47a38a4eff9995d5409e73465fa403a3e8b Author: Alex Zarebski aezarebski@gmail.com Date: Wed Sep 28 17:42:56 2022 +0100

update version file based on package health checker feedback

commit a9f529f5a4b68b2265a7eada28fd0e69770a370a Author: Alex Zarebski aezarebski@gmail.com Date: Wed Sep 28 17:42:40 2022 +0100

rename the templates directory

commit d5b5e007eca4edf1aa19c717c91c9a54d8a6312e Author: Alex Zarebski aezarebski@gmail.com Date: Wed Sep 28 16:44:05 2022 +0100

remove timtamlogger as was deprecated

commit f1741f23591015c007fbda99a79adfee2d98d2fa Author: Alex Zarebski aezarebski@gmail.com Date: Wed Sep 28 15:44:16 2022 +0100

bring the templates up to date

commit 23c168809e9a317d9fb8f9dc66d447fbf394ad1b Author: Alex Zarebski aezarebski@gmail.com Date: Wed Sep 28 11:53:19 2022 +0100

use the migrate script

commit 7c01b495f07272d21721155e017b3c9d23ab6bae Author: Alex Zarebski aezarebski@gmail.com Date: Fri Sep 2 14:13:27 2022 +0100

fix bug where if only some parameters change initialisation fails

commit 51413a1d351172ad78bb37df13eda3fcd44cffad Merge: 42b9c7c 113971a Author: Alex Zarebski aezarebski@gmail.com Date: Thu Sep 1 15:33:28 2022 +0100

Merge branch 'main' into dev

commit 42b9c7c300d68fbbebe45d41d213bb0b238da10f Author: Alex Zarebski aezarebski@gmail.com Date: Wed Aug 24 16:38:04 2022 +0100

Squashed commit of the following:

commit 41e0dfd0072321b447c25a95999d2429f2c307d8
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 16:13:44 2022 +0100

    further tweaks to the templates

commit 6249209f2f83b0336dcfa36b1bdf7eb6fd71ea61
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 15:53:10 2022 +0100

    tweak template

commit fbc4f8412525a90f44c18967cb4c041c53c2e1b3
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 15:27:16 2022 +0100

    draft template file

commit 29768e3c9cbdbdfbc3dbd6ad0ba0a0d77db43db6
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 15:03:07 2022 +0100

    docs

commit 1b6afc664d852d7206d92dd07dd590f807cd48fb
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 15:02:34 2022 +0100

    fix silly omission

commit 33fab005eb0f8b61a1a64d93b3cfc38af750b28c
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 13:44:00 2022 +0100

    implement the time series r0

commit 58d4c02f35ed9242288fc7f6262399d7c0e96859
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 24 12:36:25 2022 +0100

    document and refactor some existing code

commit a8ce53c888bfe84dcd33560357cc5f2511b22363 Author: Alex Zarebski aezarebski@gmail.com Date: Tue Aug 23 16:48:07 2022 +0100

bug fix for edge case where omega not provided

commit 5a9d7d1acebc248da53cf6abd51f414fa5bb7835 Author: Alex Zarebski aezarebski@gmail.com Date: Mon Aug 22 14:13:34 2022 +0100

Squashed commit of the following:

commit 504daa184ecdfd65f13e0bd36bce1fd5a8bef1ca
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Mon Aug 22 14:10:20 2022 +0100

    finish r0 implementation

commit 12827b8c83c6a4320b44be22ed80bb3f900993f6
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Mon Aug 22 12:07:57 2022 +0100

    fix a broken validation check

commit 07438ceea4307a53139114b0f76f77f51d33cce2
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Mon Aug 22 12:05:11 2022 +0100

    add a convenience function

commit 33cda40479fa97492f1aef0bb33ee489c644a0ed
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Mon Aug 22 12:04:48 2022 +0100

    remove a bunch of dead code

commit e83cb670f2e77d2c79652ac419d8592a4e141526
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Mon Aug 22 11:36:13 2022 +0100

    implement single pass parameter update

commit 50d8344155b29050e0928246389eee2fb992d6ee
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 20 17:29:30 2022 +0100

    use a set to compute the param change times properly

commit 92d0ad659fd2dc804519c2d869839405fd2f16b4
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 20 16:52:07 2022 +0100

    set up for working out the param change times based on unique times

commit a939bd97223f5448adb6e5ab93389fda601bdacc
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 20 15:32:35 2022 +0100

    include inputs for alternative parameterisation

commit dbf13fdcca39a171ab0c33935e5dd81c0aef80b6
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 20 14:45:25 2022 +0100

    organise parameters in a clearer way

commit ed2c265d34679eb53d3df60c0bb7955bcbfd56a2
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Aug 19 16:24:15 2022 +0100

    deprecate the logger as it is no longer needed

commit 4b9f57d224095ec2b50119e2de71c93faee21715 Author: Alex Zarebski aezarebski@gmail.com Date: Thu Aug 11 15:23:17 2022 +0100

include a sanity check that the distribution actually makes sense

commit c2ffd4394c6bbc2f5e452f7782af35da38cdb11b Author: Alex Zarebski aezarebski@gmail.com Date: Wed Aug 10 13:12:28 2022 +0100

Squashed commit of the following:

commit b943a704e944bf950a26f7b8ea2dc65cf83552d9
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 10 13:09:42 2022 +0100

    add an example showing the history check stuff

commit a4732fab3a62aca155e2fc8263b11f2263a0fe85
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Wed Aug 10 12:55:12 2022 +0100

    extend beauti template to support history checks

commit 31ddd3c30552f84beb31792c6a07ce36c5f62572 Author: Alex Zarebski aezarebski@gmail.com Date: Sat Aug 6 17:41:04 2022 +0100

include check that parameter dimensions make sense

commit 88794c6bcd756f70bd4e3642ed6ea478cc4c5f65 Author: Alex Zarebski aezarebski@gmail.com Date: Sat Aug 6 17:06:13 2022 +0100

Squashed commit of the following:

commit 496f723378feac04e2299687d7b39e6173437e0d
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 6 17:03:33 2022 +0100

    bump minor because new feature

commit 2dd6ed3927c1cb6a550f0f19e11debdc7647899d
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 6 16:55:34 2022 +0100

    lint

commit 367540e22fe23a514d1d9ccc76d5af15598f2f34
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Sat Aug 6 16:51:14 2022 +0100

    fix bug where history size wasn't updating properly

commit ceb7b11690b03a21292520760846ba9cb1589935
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Aug 5 14:19:09 2022 +0100

    add run configuration from intellij

commit 2fcadb3999474a68c8042ad158d34285580b349e
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Aug 5 14:15:49 2022 +0100

    add file that helps intellij work out what is happening

commit 52c0f8bbc7ce0dae6a24dfa6616462af699c19f6
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Aug 5 13:47:34 2022 +0100

    implement use of history parameters

commit dec4d39bdf6781e83b4944e0ec5fb5068b470eb7
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Aug 5 13:45:32 2022 +0100

    split the numerical functions out into a separate class

commit 423610f5fb555c20483b66a5b00daaf5eea42cfc
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Fri Aug 5 13:41:55 2022 +0100

    change class name to be more informative

commit 569acb2b4859bd177e7bf88a3eae0bf1befcb130
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Tue Aug 2 18:06:08 2022 +0100

    upgrade the interval terminator class

commit 2b480a81f4c66f902fcdf36c41d6aae555398e5f
Author: Alex Zarebski <aezarebski@gmail.com>
Date:   Tue Aug 2 17:31:54 2022 +0100

    apply code suggestions for clarity