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WIP: DA updates of the whole state vector #195

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WIP: DA updates of the whole state vector #195

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Commits on Sep 8, 2020

  1. Adds function + keyword argument to limit the length of the static ne… 

    …twork series
    @glwagner
    glwagner committed Sep 8, 2020
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  2. imports numpy into epidemic data storage

    @glwagner
    glwagner committed Sep 8, 2020
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  3. Style updates

    @glwagner
    glwagner committed Sep 8, 2020
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  4. Moves epidemic data storage initialization to joint epidemic assimila… 

    …tion script, sets upper limit on stored contact networks
    @glwagner
    glwagner committed Sep 8, 2020
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  5. Moves epidemic data storage initialization to joint epidemic assimila… 

    …tion script, sets upper limit on stored contact networks
    @glwagner
    glwagner committed Sep 8, 2020
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  6. Prints a bit more info in joint_epidemic_assimilation

    @glwagner
    glwagner committed Sep 8, 2020
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  7. Updates run script for intervention scenario

    @glwagner
    glwagner committed Sep 8, 2020
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Commits on Sep 9, 2020

  1. Merge branch 'master' into glw/limit-static-network-length

    @odunbar
    odunbar committed Sep 9, 2020
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  2. well... it now runs, but requires massive memory and is very slow

    @odunbar
    odunbar committed Sep 9, 2020
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Commits on Sep 10, 2020

  1. reduce memory/increase speed of closure, introduce optional closure u… 

    …pdate
    @odunbar
    odunbar committed Sep 10, 2020
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  2. sparse matrix form (NOT CHECKING POSDEF YET) of closure

    @odunbar
    odunbar committed Sep 10, 2020
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  3. naming

    @odunbar
    odunbar committed Sep 10, 2020
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Commits on Sep 11, 2020

  1. 2x speed up of closure with basic numba loop

    @odunbar
    odunbar committed Sep 11, 2020
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Commits on Sep 17, 2020

  1. plotting and savestates

    @odunbar
    odunbar committed Sep 17, 2020
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Commits on Sep 18, 2020

  1. minor edits

    @odunbar
    odunbar committed Sep 18, 2020
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  2. run scripts for 1e5 experiments

    @odunbar
    odunbar committed Sep 18, 2020
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  3. plot at same frequency as savedata, numbering of datafiles

    @odunbar
    odunbar committed Sep 18, 2020
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  4. n_sweeps =1

    @odunbar
    odunbar committed Sep 18, 2020
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  5. removed print

    @odunbar
    odunbar committed Sep 18, 2020
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Commits on Sep 19, 2020

  1. updated joint_epidemic_assimilation.py to enable parameters learning.

    Jinlong authored and Jinlong committed Sep 19, 2020
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  2. parallel cpu flag reinstated

    @odunbar
    odunbar committed Sep 19, 2020
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  3. Merge branch 'glw/limit-static-network-length' of https://github.com/… 

    …dburov190/risk-networks into glw/limit-static-network-length
    @odunbar
    odunbar committed Sep 19, 2020
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Commits on Sep 21, 2020

  1. Merge branch 'master' into glw/limit-static-network-length

    @odunbar
    odunbar committed Sep 21, 2020
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Commits on Sep 22, 2020

  1. moved plotting script in file

    @odunbar
    odunbar committed Sep 22, 2020
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  2. Temp commented master_eqn plots, added max steps to ensemble time series

    @odunbar
    odunbar committed Sep 22, 2020
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  3. less frequent batch updates for master_time_series

    @odunbar
    odunbar committed Sep 22, 2020
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Commits on Sep 23, 2020

  1. addressed review

    @odunbar
    odunbar committed Sep 23, 2020
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  2. removed building entire cov

    @odunbar
    odunbar committed Sep 23, 2020
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  3. reintroduce plotting, only save trace of sum over entire timeseries

    @odunbar
    odunbar committed Sep 23, 2020
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  4. temp change u100+s runscript

    @odunbar
    odunbar committed Sep 23, 2020
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Commits on Sep 25, 2020

  1. resolved sum-to-one bug using observations.XYZ, and np.unique bug

    @odunbar
    odunbar committed Sep 25, 2020
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  2. temporary test scripts for jinlong

    @odunbar
    odunbar committed Sep 25, 2020
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Commits on Sep 29, 2020

  1. implemented the error catching for svd convergence issue.

    @jinlong83
    jinlong83 committed Sep 29, 2020
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  2. roc/tpr plot tools for the new style of save-data

    @odunbar
    odunbar committed Sep 29, 2020
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  3. also catch the svd hidden in null_space

    @odunbar
    odunbar committed Sep 29, 2020
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Commits on Sep 30, 2020

  1. included os

    @odunbar
    odunbar committed Sep 30, 2020
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Commits on Oct 2, 2020

  1. implemented a while loop to avoid svd convergence issue.

    @jinlong83
    jinlong83 committed Oct 2, 2020
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  2. unified runscripts

    @odunbar
    odunbar committed Oct 2, 2020
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  3. removed extra script

    @odunbar
    odunbar committed Oct 2, 2020
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Commits on Oct 5, 2020

  1. implemented while loops for all svds to avoid the convergence issue.

    @jinlong83
    jinlong83 committed Oct 5, 2020
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  2. minor changes to the svd while loop implementation.

    @jinlong83
    jinlong83 committed Oct 5, 2020
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Commits on Oct 8, 2020

  1. population -> user population in plots

    @odunbar
    odunbar committed Oct 8, 2020
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  2. contact network array->dictionary bugfix for interventions

    @odunbar
    odunbar committed Oct 8, 2020
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  3. updated sum_to_one

    @odunbar
    odunbar committed Oct 8, 2020
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Commits on Oct 9, 2020

  1. bug in plot for E when user population < population

    @odunbar
    odunbar committed Oct 9, 2020
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Commits on Oct 12, 2020

  1. bugfix to sum_to_one

    @odunbar
    odunbar committed Oct 12, 2020
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  2. deactivated the parameters learning for sensor data.

    @jinlong83
    jinlong83 committed Oct 12, 2020
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  3. easier ROC curves at multiple times

    @odunbar
    odunbar committed Oct 12, 2020
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Commits on Oct 14, 2020

  1. Remove comments, fix style, rename some variables

    @dburov190
    dburov190 committed Oct 14, 2020
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  2. Implement 'full_global' update for no-batching case

    @dburov190
    dburov190 committed Oct 14, 2020
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  3. prevalence for each ensemble member is different

    @odunbar
    odunbar committed Oct 14, 2020
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  4. some more verbose flags, excludes sum to one

    @odunbar
    odunbar committed Oct 14, 2020
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  5. set full_svd true for all

    @odunbar
    odunbar committed Oct 14, 2020
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Commits on Oct 15, 2020

  1. add global flag default

    @odunbar
    odunbar committed Oct 15, 2020
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  2. added some verbose prints, added clip_susceptible function

    @odunbar
    odunbar committed Oct 15, 2020
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Commits on Nov 10, 2020

  1. Clean up

    @dburov190
    dburov190 committed Nov 10, 2020
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  2. Fix 'plot_ensemble_states' function

    @dburov190
    dburov190 committed Nov 10, 2020
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  3. Bring 'backward_forward' up to the runnable state

    @dburov190
    dburov190 committed Nov 10, 2020
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Commits on Nov 11, 2020

  1. Fix bug in 'backward_forward'; increase ic-alpha

    @dburov190
    dburov190 committed Nov 11, 2020
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Commits on Nov 12, 2020

  1. Reduce 'closure_update_interval' in 'backward_forward'

    @dburov190
    dburov190 committed Nov 12, 2020
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Commits on Nov 13, 2020

  1. Clean up

    @dburov190
    dburov190 committed Nov 13, 2020
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