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Toy IBM model #391

Merged
merged 346 commits into from
Mar 8, 2024
Merged

Toy IBM model #391

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9e7e92a
Merge remote-tracking branch 'upstream/master'
twallema Mar 16, 2021
4682539
Merge remote-tracking branch 'upstream/master'
twallema Mar 16, 2021
133d27c
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twallema Mar 16, 2021
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twallema Mar 31, 2021
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twallema Mar 31, 2021
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twallema Apr 1, 2021
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twallema Apr 2, 2021
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twallema Apr 2, 2021
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twallema Apr 6, 2021
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twallema Apr 12, 2021
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twallema Apr 19, 2021
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twallema Apr 20, 2021
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twallema Apr 20, 2021
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twallema May 5, 2021
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twallema May 17, 2021
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twallema May 17, 2021
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twallema May 17, 2021
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twallema May 21, 2021
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twallema May 25, 2021
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twallema May 28, 2021
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twallema May 28, 2021
3617326
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twallema May 31, 2021
8f6e5e9
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twallema May 31, 2021
cd28d52
update 03/06
twallema Jun 3, 2021
38aa590
update sciensano data
twallema Jun 7, 2021
b1fb26e
updated restore prediction
twallema Jun 7, 2021
f7538cb
tryout stratified vaccination model
twallema Jun 7, 2021
b86b98d
finished stratified vaccination model - does not work
twallema Jun 8, 2021
9b0ee8c
Merge remote-tracking branch 'upstream/master'
twallema Jun 8, 2021
1c6a1df
update all data
twallema Jun 18, 2021
a5dd726
update of RESTORE 8
twallema Jun 18, 2021
6ebb6b3
Merge remote-tracking branch 'upstream/master'
twallema Jun 25, 2021
20b5c21
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twallema Jun 28, 2021
478f4e2
Merge branch 'master' into RESTORE-8-updates
twallema Jul 14, 2021
425c345
update data
twallema Jul 14, 2021
5c7411b
bring vaccination function in line with previous bugfix
twallema Jul 14, 2021
fb49e68
expand dims on ICUrec and remove subtraction of dUCUrec with dICU_R
twallema Jul 14, 2021
6cc5861
vectorize vaccination implementation
twallema Jul 14, 2021
7742b74
working first- and second dose vaccination function
twallema Jul 14, 2021
556d273
working multidose model
twallema Jul 14, 2021
62c3be5
implement a draw function for the stratified vaccination model
twallema Jul 15, 2021
35e4295
format vaccination functions of both models and update docstrings
twallema Jul 15, 2021
ad234da
all changes to notebook and models.py
twallema Jul 15, 2021
7c58f23
Merge branch 'RESTORE-8-updates'
twallema Jul 16, 2021
1766490
update policies
twallema Jul 28, 2021
a35fde7
update data
twallema Jul 28, 2021
348dc8b
tryout calibration script
twallema Jul 28, 2021
c8e96c5
plot PSO stratified function
twallema Jul 28, 2021
b013a05
changes to notebook
twallema Jul 28, 2021
afe7692
update data
twallema Aug 24, 2021
443a365
adjusted samples location in function run_MCMC
twallema Aug 24, 2021
bbe5017
Experiment with different ensemble moves
twallema Aug 24, 2021
8612548
reduce number of dimensions down to time (irregardless of dims in out)
twallema Aug 24, 2021
3562de2
bring draw function in line with new calibration
twallema Aug 24, 2021
2f87566
adjust output_to_visuals to sum over all dims except time/draws
twallema Aug 24, 2021
88e5896
tweaks to the model structure
twallema Aug 24, 2021
1640a6f
implementation of split prev_rest parameter for lockdown and relaxation
twallema Aug 24, 2021
f5fb56f
calibration script
twallema Aug 24, 2021
c0a2380
changes to calibration script
twallema Aug 24, 2021
fcf4202
calibration results
twallema Aug 24, 2021
5ecdf41
changes to tryout script
twallema Aug 24, 2021
c01ad1f
fix new age groups in vaccination dataframe
twallema Aug 26, 2021
adfa516
implement new age groups in vaccination campaign in vaccination class
twallema Aug 26, 2021
a470373
remove obsolete code in draw_fcn
twallema Aug 26, 2021
cbf6aaf
introduce effect of leisure mentality changes gradually in the model
twallema Aug 26, 2021
90d1b86
stop vaccination campaign after end of data
twallema Aug 26, 2021
68f3a07
changes to calibration script
twallema Aug 26, 2021
ada66fd
Merge branch 'RESTORE-8-updates' of https://github.com/twallema/COVID…
twallema Aug 26, 2021
d6361e4
Merge branch 'twallema-RESTORE-8-updates'
twallema Aug 26, 2021
643c468
merge master
twallema Aug 26, 2021
ccb4fd1
Merge remote-tracking branch 'upstream/master'
twallema Aug 27, 2021
20eb655
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twallema Aug 27, 2021
712091d
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twallema Sep 1, 2021
b63b953
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twallema Oct 7, 2021
a34c466
Merge remote-tracking branch 'upstream/master'
twallema Oct 11, 2021
7e23704
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twallema Oct 11, 2021
a632b81
implement automatic formatting of initN to desired age groups and test
twallema Oct 12, 2021
ab97f6c
remove old notebook performing the formatting
twallema Oct 12, 2021
45a5aad
cleanup data folder --> remove unused datasets
twallema Oct 12, 2021
eaf40c6
update data readme
twallema Oct 12, 2021
a23c21a
raw willem 2012 data in 10 age bins
twallema Oct 13, 2021
e92db40
raw willem 2012 data in 3 age bins
twallema Oct 13, 2021
e6da655
remove need for more_5_min and more_15_min in interaction matrices
twallema Oct 13, 2021
efb1e6b
delete interim interaction matrices
twallema Oct 13, 2021
3fd5250
update data readme for removal of interim interaction matrices
twallema Oct 13, 2021
eaee03f
implementation of three age options for initN and interaction matrices
twallema Oct 13, 2021
044247d
fixed a bug in extraction of serological data
twallema Oct 14, 2021
358b0c1
add option to contruct_initN to not perform grouping in age bins
twallema Oct 14, 2021
b3d93c8
conversion functions for model pars a and h
twallema Oct 14, 2021
7131302
move hospital data to a folder denoting its age-stratification
twallema Oct 14, 2021
a0a6216
pre-program three age bins in hospital data analysis
twallema Oct 14, 2021
e4905cd
age-stratification and hospitals are now working
twallema Oct 14, 2021
53c6668
implement age_stratification_size in samples_dict preparation function
twallema Oct 14, 2021
4eba5e2
adjust vaccination function to work for 10 age groups only
twallema Oct 14, 2021
40a16a9
changes to calibration script
twallema Oct 14, 2021
912285f
put initN_arr, initN_mun, initN_prov back in place
twallema Oct 14, 2021
5e011ec
initial_state function does not work
twallema Oct 14, 2021
caadce1
make vaccine function working
twallema Oct 14, 2021
5c638ce
fixed reshape size error in vaccination function
twallema Oct 15, 2021
f26fb39
change vaccination dataframe age index to intervalindex
twallema Oct 15, 2021
a95a85d
rename convert_age_stratified_series to convert_age_stratified_property
twallema Oct 15, 2021
4179b8b
manually make age index of spatial vacc data a pd.IntervalIndex
twallema Oct 15, 2021
4e6b53a
vaccination age-interpolation (1)
twallema Oct 15, 2021
5eebc13
vaccination age-interpolation (2)
twallema Oct 15, 2021
a1b6fed
let function construct_initN return a pd.DataFrame
twallema Oct 15, 2021
dc11b2c
vaccination age-interpolation (working)
twallema Oct 15, 2021
bfe4798
vaccination age-interpolation (bugfix)
twallema Oct 15, 2021
e95866b
changes to michiels script
twallema Oct 15, 2021
ac1f2d7
vaccination age-interpolation (bugfix)
twallema Oct 15, 2021
1069035
set progress to true by default
twallema Oct 15, 2021
0e25db4
verified calibration FULL is working for three age groups
twallema Oct 15, 2021
a29ae6e
add effect of variants on transmissiblity to model
twallema Oct 18, 2021
ecadf70
add redundancy to avoid negative susceptible pools due to vaccination
twallema Oct 18, 2021
f8c869b
add path to hospital data to samples_dict init function
twallema Oct 18, 2021
8bfa867
hardcode a good starting estimate for calibration in calibration script
twallema Oct 18, 2021
013c9ae
rename all models in models.py SEIRD --> SEIQRD
twallema Oct 18, 2021
1fb6f0e
update data
twallema Oct 18, 2021
1ed4b3b
update calibrate-COVID-19-SEIQRD-WAVE-1 script
twallema Oct 18, 2021
e01e6ee
modify draw_fcn_WAVE1 to automatically deduce age strat size
twallema Oct 18, 2021
a8a75d0
make model xarray output immutable in function output_to_visuals
twallema Oct 18, 2021
cedb6c1
rename WAVE 1 calibration script
twallema Oct 18, 2021
3cb9315
change SEIRD --> SEIQRD in all calibration script names
twallema Oct 18, 2021
c206025
working visualization script for WAVE 1
twallema Oct 18, 2021
6d6548b
rename folder COVID19_SEIRD --> COVID19_SEIQRD
twallema Oct 18, 2021
bd9ce8f
ajust directory names where relevant
twallema Oct 18, 2021
36f61b1
ajust folder name in sciensano hospital data analysis
twallema Oct 18, 2021
5d4ce7a
intermediate save of adjusting the sciensano data function
twallema Oct 18, 2021
7f60f52
new sciensano public data function
twallema Oct 19, 2021
69fd373
tweaks to calibration/plot_fit WAVE1 due to change in sciensano data
twallema Oct 19, 2021
89cc1ef
fix bug in sciensano public data formatting
twallema Oct 19, 2021
224bb3d
change idx name 'start_week' in spatial public vacc data into 'date'
twallema Oct 19, 2021
eaa83e9
WAVE2 calibration --> R0 method works
twallema Oct 19, 2021
119707f
folder name SEIRD --> SEIQRD
twallema Oct 20, 2021
af5668d
vaccination function works for unidose models
twallema Oct 20, 2021
3f29939
place others.csv directly in get_model_parameters
twallema Oct 20, 2021
dce90c6
fix bug in matrix size of willem2012 matrices
twallema Oct 20, 2021
576e435
calibrate and plot_fit for WAVE2 working
twallema Oct 20, 2021
797b403
update spatial vacc data
twallema Oct 20, 2021
b22c15e
tweaks to stratified vacc calibration
twallema Oct 20, 2021
2fc1bca
automatic dimension reduction in plot_PSO
twallema Oct 21, 2021
a262276
working vaccination module
twallema Oct 21, 2021
5c7a6dd
leave dose E out of vaccination model data analysis for now
twallema Oct 21, 2021
a15e3a2
avoid deprication error in vacc module
twallema Oct 21, 2021
ac09e14
remove print() from plot fit WAVE1
twallema Oct 21, 2021
041bd63
name change for calibration script of wave 1
twallema Oct 21, 2021
53ac9b4
name change for plot fit script of wave 1
twallema Oct 21, 2021
66ad808
calibration script vaccination national model is working
twallema Oct 21, 2021
3681cca
plot fit for vacc national model works
twallema Oct 21, 2021
b573814
adjust method to find start and end of vacc dataframe
twallema Oct 21, 2021
a071810
verified michiels calibration script is working
twallema Oct 21, 2021
d8bdb68
remove sciensano test function
twallema Oct 21, 2021
7c5f8f6
Merge branch 'redo-age-groups'
twallema Oct 21, 2021
a769870
Merge remote-tracking branch 'upstream/master'
twallema Oct 21, 2021
21a0b93
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twallema Oct 28, 2021
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twallema Oct 28, 2021
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twallema Oct 29, 2021
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twallema Nov 10, 2021
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twallema Nov 11, 2021
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twallema Nov 15, 2021
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twallema Nov 16, 2021
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twallema Nov 26, 2021
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twallema Nov 30, 2021
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twallema Dec 1, 2021
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twallema Dec 1, 2021
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twallema Apr 12, 2022
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twallema Apr 20, 2022
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twallema May 3, 2022
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twallema May 9, 2022
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twallema May 16, 2022
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twallema May 24, 2022
66b2dc3
omit zeta from calibration, set to one year on average
twallema May 24, 2022
5105e04
remove zeta from calibration and adjust draw function
twallema May 25, 2022
ddc92fb
new calibration result
twallema May 25, 2022
cc84224
remove old calibration result
twallema May 25, 2022
219c067
tryout new initial states
twallema May 25, 2022
6724304
new initial condition, set l1 to 7 days
twallema May 25, 2022
c0a6658
calibration result 05-25
twallema May 25, 2022
7bf3738
initial condition script
twallema May 25, 2022
59608b0
tweak to plot fit base
twallema May 25, 2022
188f51a
Merge branch 'elaborate-calibration-national-model'
twallema May 25, 2022
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intermittent-save-toy-model
twallema Feb 2, 2024
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toy IBM script
twallema Mar 8, 2024
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