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Split school types #385

Merged
merged 376 commits into from
Oct 20, 2023
Merged

Split school types #385

merged 376 commits into from
Oct 20, 2023
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 18, 2021

  1. update of RESTORE 8

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Commits on Jun 25, 2021

  1. Merge remote-tracking branch 'upstream/master'

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Commits on Jun 28, 2021

  1. Merge remote-tracking branch 'upstream/master'

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Commits on Jul 14, 2021

  1. Merge branch 'master' into RESTORE-8-updates

    @twallema
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  2. update data

    @twallema
    twallema committed Jul 14, 2021
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  3. bring vaccination function in line with previous bugfix

    @twallema
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  4. expand dims on ICUrec and remove subtraction of dUCUrec with dICU_R

    @twallema
    twallema committed Jul 14, 2021
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  5. vectorize vaccination implementation

    @twallema
    twallema committed Jul 14, 2021
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  6. working first- and second dose vaccination function

    @twallema
    twallema committed Jul 14, 2021
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  7. working multidose model

    @twallema
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Commits on Jul 15, 2021

  1. implement a draw function for the stratified vaccination model

    @twallema
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  2. format vaccination functions of both models and update docstrings

    @twallema
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  3. all changes to notebook and models.py

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Commits on Jul 16, 2021

  1. Merge branch 'RESTORE-8-updates'

    @twallema
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Commits on Jul 28, 2021

  1. update policies

    @twallema
    twallema committed Jul 28, 2021
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  2. update data

    @twallema
    twallema committed Jul 28, 2021
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  3. tryout calibration script

    @twallema
    twallema committed Jul 28, 2021
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  4. plot PSO stratified function

    @twallema
    twallema committed Jul 28, 2021
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  5. changes to notebook

    @twallema
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Commits on Aug 24, 2021

  1. update data

    @twallema
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  2. adjusted samples location in function run_MCMC

    @twallema
    twallema committed Aug 24, 2021
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  3. Experiment with different ensemble moves

    @twallema
    twallema committed Aug 24, 2021
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  4. reduce number of dimensions down to time (irregardless of dims in out)

    @twallema
    twallema committed Aug 24, 2021
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  5. bring draw function in line with new calibration

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  6. adjust output_to_visuals to sum over all dims except time/draws

    @twallema
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  7. tweaks to the model structure

    @twallema
    twallema committed Aug 24, 2021
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  8. implementation of split prev_rest parameter for lockdown and relaxation

    @twallema
    twallema committed Aug 24, 2021
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  9. calibration script

    @twallema
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  10. changes to calibration script

    @twallema
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  11. calibration results

    @twallema
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  12. changes to tryout script

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Commits on Aug 26, 2021

  1. fix new age groups in vaccination dataframe

    @twallema
    twallema committed Aug 26, 2021
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  2. implement new age groups in vaccination campaign in vaccination class

    @twallema
    twallema committed Aug 26, 2021
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  3. remove obsolete code in draw_fcn

    @twallema
    twallema committed Aug 26, 2021
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  4. introduce effect of leisure mentality changes gradually in the model

    @twallema
    twallema committed Aug 26, 2021
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  5. stop vaccination campaign after end of data

    @twallema
    twallema committed Aug 26, 2021
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  6. changes to calibration script

    @twallema
    twallema committed Aug 26, 2021
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  7. Merge branch 'RESTORE-8-updates' of https://github.com/twallema/COVID… 

    …19-Model into twallema-RESTORE-8-updates

to fix some merge issues with the data
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  8. Merge branch 'twallema-RESTORE-8-updates' 

    to fix some merge issues
    @twallema
    twallema committed Aug 26, 2021
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  9. merge master

    @twallema
    twallema committed Aug 26, 2021
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Commits on Aug 27, 2021

  1. Merge remote-tracking branch 'upstream/master'

    @twallema
    twallema committed Aug 27, 2021
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  2. Merge remote-tracking branch 'upstream/master'

    @twallema
    twallema committed Aug 27, 2021
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Commits on Sep 1, 2021

  1. Merge remote-tracking branch 'upstream/master'

    @twallema
    twallema committed Sep 1, 2021
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Commits on Oct 7, 2021

  1. Merge remote-tracking branch 'upstream/master'

    @twallema
    twallema committed Oct 7, 2021
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Commits on Oct 11, 2021

  1. Merge remote-tracking branch 'upstream/master'

    @twallema
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  2. Merge remote-tracking branch 'upstream/master'

    @twallema
    twallema committed Oct 11, 2021
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Commits on Oct 12, 2021

  1. implement automatic formatting of initN to desired age groups and test

    @twallema
    twallema committed Oct 12, 2021
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  2. remove old notebook performing the formatting

    @twallema
    twallema committed Oct 12, 2021
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  3. cleanup data folder --> remove unused datasets

    @twallema
    twallema committed Oct 12, 2021
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  4. update data readme

    @twallema
    twallema committed Oct 12, 2021
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Commits on Oct 13, 2021

  1. raw willem 2012 data in 10 age bins

    @twallema
    twallema committed Oct 13, 2021
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  2. raw willem 2012 data in 3 age bins

    @twallema
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  3. remove need for more_5_min and more_15_min in interaction matrices

    @twallema
    twallema committed Oct 13, 2021
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  4. delete interim interaction matrices

    @twallema
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  5. update data readme for removal of interim interaction matrices

    @twallema
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  6. implementation of three age options for initN and interaction matrices

    @twallema
    twallema committed Oct 13, 2021
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Commits on Oct 14, 2021

  1. fixed a bug in extraction of serological data

    @twallema
    twallema committed Oct 14, 2021
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  2. add option to contruct_initN to not perform grouping in age bins

    @twallema
    twallema committed Oct 14, 2021
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  3. conversion functions for model pars a and h

    @twallema
    twallema committed Oct 14, 2021
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  4. move hospital data to a folder denoting its age-stratification

    @twallema
    twallema committed Oct 14, 2021
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  5. pre-program three age bins in hospital data analysis

    @twallema
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  6. age-stratification and hospitals are now working

    @twallema
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  7. implement age_stratification_size in samples_dict preparation function

    @twallema
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  8. adjust vaccination function to work for 10 age groups only

    @twallema
    twallema committed Oct 14, 2021
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  9. changes to calibration script

    @twallema
    twallema committed Oct 14, 2021
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  10. put initN_arr, initN_mun, initN_prov back in place

    @twallema
    twallema committed Oct 14, 2021
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  11. initial_state function does not work

    @twallema
    twallema committed Oct 14, 2021
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  12. make vaccine function working

    @twallema
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Commits on Oct 15, 2021

  1. fixed reshape size error in vaccination function

    @twallema
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  2. change vaccination dataframe age index to intervalindex

    @twallema
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  3. rename convert_age_stratified_series to convert_age_stratified_property

    @twallema
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  4. manually make age index of spatial vacc data a pd.IntervalIndex

    @twallema
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  5. vaccination age-interpolation (1)

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  6. vaccination age-interpolation (2)

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  7. let function construct_initN return a pd.DataFrame

    @twallema
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  8. vaccination age-interpolation (working)

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  9. vaccination age-interpolation (bugfix)

    @twallema
    twallema committed Oct 15, 2021
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  10. changes to michiels script

    @twallema
    twallema committed Oct 15, 2021
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  11. vaccination age-interpolation (bugfix)

    @twallema
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  12. set progress to true by default

    @twallema
    twallema committed Oct 15, 2021
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  13. verified calibration FULL is working for three age groups

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Commits on Oct 18, 2021

  1. add effect of variants on transmissiblity to model

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  2. add redundancy to avoid negative susceptible pools due to vaccination

    @twallema
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  3. add path to hospital data to samples_dict init function

    @twallema
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  4. hardcode a good starting estimate for calibration in calibration script

    @twallema
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  5. rename all models in models.py SEIRD --> SEIQRD

    @twallema
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  6. update data

    @twallema
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  7. update calibrate-COVID-19-SEIQRD-WAVE-1 script

    @twallema
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  8. modify draw_fcn_WAVE1 to automatically deduce age strat size

    @twallema
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  9. make model xarray output immutable in function output_to_visuals

    @twallema
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  10. rename WAVE 1 calibration script

    @twallema
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  11. change SEIRD --> SEIQRD in all calibration script names

    @twallema
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  12. working visualization script for WAVE 1

    @twallema
    twallema committed Oct 18, 2021
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  13. rename folder COVID19_SEIRD --> COVID19_SEIQRD

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  14. ajust directory names where relevant

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  15. ajust folder name in sciensano hospital data analysis

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  16. intermediate save of adjusting the sciensano data function

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Commits on Oct 19, 2021

  1. new sciensano public data function

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  2. tweaks to calibration/plot_fit WAVE1 due to change in sciensano data

    @twallema
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  3. fix bug in sciensano public data formatting

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  4. change idx name 'start_week' in spatial public vacc data into 'date'

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  5. WAVE2 calibration --> R0 method works

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Commits on Oct 20, 2021

  1. folder name SEIRD --> SEIQRD

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  2. vaccination function works for unidose models

    @twallema
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  3. place others.csv directly in get_model_parameters

    @twallema
    twallema committed Oct 20, 2021
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  4. fix bug in matrix size of willem2012 matrices

    @twallema
    twallema committed Oct 20, 2021
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  5. calibrate and plot_fit for WAVE2 working

    @twallema
    twallema committed Oct 20, 2021
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  6. update spatial vacc data

    @twallema
    twallema committed Oct 20, 2021
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  7. tweaks to stratified vacc calibration

    @twallema
    twallema committed Oct 20, 2021
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Commits on Oct 21, 2021

  1. automatic dimension reduction in plot_PSO

    @twallema
    twallema committed Oct 21, 2021
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  2. working vaccination module

    @twallema
    twallema committed Oct 21, 2021
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  3. leave dose E out of vaccination model data analysis for now

    @twallema
    twallema committed Oct 21, 2021
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  4. avoid deprication error in vacc module

    @twallema
    twallema committed Oct 21, 2021
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  5. remove print() from plot fit WAVE1

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  6. name change for calibration script of wave 1

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  7. name change for plot fit script of wave 1

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  8. calibration script vaccination national model is working

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  9. plot fit for vacc national model works

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  10. adjust method to find start and end of vacc dataframe

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  11. verified michiels calibration script is working

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  12. remove sciensano test function

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  13. Merge branch 'redo-age-groups'

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  2. omit zeta from calibration, set to one year on average

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  1. remove zeta from calibration and adjust draw function

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  2. new calibration result

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  3. remove old calibration result

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  4. tryout new initial states

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  5. new initial condition, set l1 to 7 days

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  6. calibration result 05-25

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  7. initial condition script

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  8. tweak to plot fit base

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  9. Merge branch 'elaborate-calibration-national-model'

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  2. construct matrices

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  3. split primary/secundary vs tertiary education

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  1. native datetime implementation ramp function

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  2. simplified VOC function

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  3. omit datetime conversion from vacc efficacy

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  4. get conversion to datetime dates out of contact function

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  5. closure of uni's not implemented well --> fix

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  6. un-panda-ify the belgian school holidays function

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    twallema committed Jun 26, 2023
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  7. fix bugs

    @twallema
    twallema committed Jun 26, 2023
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  8. vaccination function

    @twallema
    twallema committed Jun 26, 2023
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  9. f_h func, seasonality func

    @twallema
    twallema committed Jun 26, 2023
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  10. works

    @twallema
    twallema committed Jun 26, 2023
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  11. pandas datetime from policy function national model

    @twallema
    twallema committed Jun 26, 2023
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  12. ODE model

    @twallema
    twallema committed Jun 26, 2023
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Commits on Jun 27, 2023

  1. clean up ODE models

    @twallema
    twallema committed Jun 27, 2023
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  2. clean up SDE models

    @twallema
    twallema committed Jun 27, 2023
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  3. remove three beta's from spatial model

    @twallema
    twallema committed Jun 27, 2023
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  4. belongs to previous

    @twallema
    twallema committed Jun 27, 2023
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  5. removes pandas from TDPF spatial

    @twallema
    twallema committed Jun 27, 2023
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  6. calibration scripts

    @twallema
    twallema committed Jun 27, 2023
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  7. scenario notebooks

    @twallema
    twallema committed Jun 27, 2023
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  8. calibration results

    @twallema
    twallema committed Jun 27, 2023
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  9. update python version to 3.11

    @twallema
    twallema committed Jun 27, 2023
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  10. update reference dictionary

    @twallema
    twallema committed Jun 27, 2023
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  11. add nationally aggregated data in the estimation of spatial model

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    twallema committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. fix wrong abbreviation september in sciensano blood data

    @twallema
    twallema committed Jun 28, 2023
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  2. rearrange environment

    @twallema
    twallema committed Jun 28, 2023
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  3. fix wrong data in sciensano blood sero data

    @twallema
    twallema committed Jun 28, 2023
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  4. set limburg to 0.9

    @twallema
    twallema committed Jun 28, 2023
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  5. incorporate pySODM changes

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    twallema committed Jun 28, 2023
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Commits on Jul 3, 2023

  1. more inclusive TDPF

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    twallema committed Jul 3, 2023
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  2. update calibration provincial model

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    twallema committed Jul 3, 2023
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  3. plotfit/calibrate toestanden

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    twallema committed Jul 3, 2023
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  4. the vaccine incidences for some weird ass reason

    @twallema
    twallema committed Jul 3, 2023
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Commits on Jul 5, 2023

  1. calibration results

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    twallema committed Jul 5, 2023
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Commits on Aug 20, 2023

  1. mky

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    twallema committed Aug 20, 2023
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  2. mkay?

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    twallema committed Aug 20, 2023
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