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note about development process
update version number
fix broken link
organise extras
Squashed commit of the following: commit 03bd68723844b1fca0bbe424982e5929818279cb Author: Alex Zarebski <[email protected]> Date: Thu Sep 7 13:17:32 2023 +1000 update documentation commit 4364b7934532868b52400102b910370fa0fea9a3 Author: Alex Zarebski <[email protected]> Date: Thu Sep 7 12:04:59 2023 +1000 update home page commit 694c6d6791a6d30515a3083fc9155700163e0cc6 Author: Alex Zarebski <[email protected]> Date: Thu Sep 7 12:01:06 2023 +1000 fix filenames so everything is tutorial 3 commit db7ebcb0680657a1fbf26b5b1a17e499cb372932 Author: Alex Zarebski <[email protected]> Date: Thu Sep 7 11:57:44 2023 +1000 add new results files commit 0bcbece5a883946a245cd1202cf5663be8e85b82 Author: Alex Zarebski <[email protected]> Date: Thu Sep 7 11:54:11 2023 +1000 include postprocessing figures commit d60cc5ac27130103baa77a354c6e4796d4ebf548 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:47:56 2023 +1000 create another xml that accounts for the varying observation probs commit b8e94197fee66a90f5f9be55add1b66fe4df0017 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:15:34 2023 +1000 set up disasters and r0 commit e1b92c3947c70ae9aecba11ce401f283a7a80879 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:13:26 2023 +1000 record disaster data to file commit 2ebd5c9e1b9e23a4c5b5d4c33822061cb79c9928 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:12:18 2023 +1000 set history checks commit 9889416f28e6d7c5425736f12f15b27649f02412 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:10:54 2023 +1000 remove clock rate ops commit 37036ac427529d200dc7276c36be8fd1212b1180 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:09:09 2023 +1000 first timtam xml commit a55aeadde174672be548978491e3234097bfddb8 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:06:27 2023 +1000 preprocess to get data for beauti commit 3d4620efc77c68b83badf02b64a9e5d827c2f075 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 18:00:59 2023 +1000 get simulation working commit 2dd7dfceea7312ce2eaaf679e0c17a1ad52182b9 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 16:56:17 2023 +1000 include build script for new tutorial commit a8939524adc3126f128581ca84d8dfd9c5ff02c6 Author: Alex Zarebski <[email protected]> Date: Wed Sep 6 16:30:20 2023 +1000 remove old tutorial-3 materials
Squashed commit of the following: commit 3deac49c4b151b9676e62dbde727d1519167cf69 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 15:19:45 2023 +1000 include the diagnostic plot for sequence distribution commit d92e544057cadd7bbc63567fb06a962cc0dd937b Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 15:17:45 2023 +1000 add diagnostic plots commit 202d7eab2efab308a1a7be54cff45f7d17604c0f Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 15:17:13 2023 +1000 update docs commit 6c82b5809c7a31a169b11bae5bbbe2e32f9cd545 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 15:00:46 2023 +1000 use timtamslamR functions to get the prevalence correct commit 3e14c3411be8e868da6870d0aef4a1fc091ac1f6 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 15:00:17 2023 +1000 save the present so we can use it later commit 6ab0b82ebba868cc4b62a2b66154aa95d86f7482 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 15:00:02 2023 +1000 add the tree logger so we can look at prevalence properly commit 42049a6304794dbec1c48e4183ace0dc91dc2b68 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 14:39:11 2023 +1000 update build script commit 746a3b657334f4371033a4e207702c90538ccc60 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 14:39:00 2023 +1000 post processing magically worked out of the box commit 0b9ddd9d74184c4cc08552d96e7e90f3ded99844 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 14:38:41 2023 +1000 new timtam xml commit e40dadd644a743e465689b1e7042abd3e0f6f606 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 14:38:32 2023 +1000 remove env files commit 9754b309d1a43051f655a77688393f8d69fc90ba Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 14:24:59 2023 +1000 include the preprocessing script and its output commit bc78c9428a951592af88e0b865aad10ff72babf0 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 13:27:07 2023 +1000 rename script commit 061aed2c606c05957389f7cc7aec96ea8f313d50 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 13:26:16 2023 +1000 update simulation output files commit e55e47fe8b046101e9872fe5c155b9126a027f82 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 13:11:25 2023 +1000 finish using dates instead of numeric times commit 7e0b5c9113a13e913682d3d237284ef6565e62f4 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 12:03:40 2023 +1000 use datetimes to make dates concrete commit b9690fcce4220ede0852879a76e7a5673fb4a607 Author: Alex Zarebski <[email protected]> Date: Tue Aug 8 11:48:37 2023 +1000 read config from xml rather than hardcoding it
Merge branch 'hist-with-slam'
docs
make use of total_prevalence_log
document the preprocessing step
remove unneeded function defn and add todos
Squashed commit of the following: commit 93c41f7910ce2465ac21f33bab3cc510c584de82 Author: Alex Zarebski <[email protected]> Date: Tue Jun 20 15:36:36 2023 +1000 include link to timtamslamr commit 04aa9983a6c9d095027a4e7a7dfea6f7bab7f080 Author: Alex Zarebski <[email protected]> Date: Tue Jun 20 15:35:29 2023 +1000 include instructions on how to compute backwards times commit dbc2bb659329ae8aceeea1a0b85f8c608dd0b8f5 Author: Alex Zarebski <[email protected]> Date: Mon Jun 19 19:56:19 2023 +1000 update listed versions commit 7f572c3d55048ad0b7f4b520f02443b0ced4fa65 Author: Alex Zarebski <[email protected]> Date: Mon Jun 19 19:51:45 2023 +1000 update history tutorial commit 2f3c286b7c111032038325391913a30dcc8f5180 Author: Alex Zarebski <[email protected]> Date: Mon Jun 19 19:22:21 2023 +1000 include step to compute disaster data
update landing
avoid prevalence figure by default
typo
proof reading tutorial
Merge branch 'drafting-new-t2'
move new tutorial into rough draft section
update build script for tutorial-1 code and fix bug in plotting script
draft new tutorial
include result files
finish setting up xml
remove old materials
new materials
Squashed commit of the following: commit dd9b36d5cde8c2d7c0897bdda5ed8673416bfd7d Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 14:07:18 2022 +0000 update docs commit ca683da2e56ee7a83b4f2a30a6ccd3f8d5a0293f Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 14:02:19 2022 +0000 update images commit 7fe9bd0dc85604ec8b503975aab33d575974eb88 Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 14:01:31 2022 +0000 clean up postprocessing script commit 152387653ad6a1a77018583e08f9bc07d44e6121 Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 13:58:59 2022 +0000 include tree statistics file commit 6024ea233ad62aea515347d2bad30928dc894ce3 Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 13:58:46 2022 +0000 include additional plot of tree statistics commit a193c0717f80d66e0ebdd2af84387f73e6a9ef87 Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 13:32:32 2022 +0000 update xml and post processing commit d5c69dabc9a5e0997ee3edd279d76e8d64271f96 Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 12:50:56 2022 +0000 record some of the tree statistics commit 484a6b531b339ece0b06596c02f9904e30998401 Author: Alex Zarebski <[email protected]> Date: Fri Dec 30 11:46:32 2022 +0000 set up build script and renv
update docs
update image files
update tutorial scripts
update next tutorial
update images