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Tutorial: Porting An Existing Model (Influenza-Epidemia) To MSR #162

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Tutorial: Porting An Existing Model (Influenza-Epidemia) To MSR #162

wants to merge 58 commits into from

Commits on Jun 6, 2024

  1. skeleton of tutorial file wo/ code yet ported into it

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. Merge branch 'main' of github.com:CDCgov/multisignal-epi-inference in… 

    …to 135-UPX3-instantiate-cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 7, 2024
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  2. very minor edit

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 7, 2024
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Commits on Jun 11, 2024

  1. move some content from sandbox to here

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 11, 2024
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Commits on Jun 20, 2024

  1. Merge branch 'main' into 135-UPX3-instantiate-cfas-epidemia-for-flu-m… 

    …odel-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 20, 2024
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  2. remove poetry lock

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. further additions; not yet taking into account DHM's math suggestions

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 21, 2024
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  2. Merge branch 'main' into 135-UPX3-instantiate-cfas-epidemia-for-flu-m… 

    …odel-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 21, 2024
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Commits on Jun 25, 2024

  1. Merge branch 'main' into 135-UPX3-instantiate-cfas-epidemia-for-flu-m… 

    …odel-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jun 25, 2024
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Commits on Jul 3, 2024

  1. Merge branch 'main' into 135-UPX3-instantiate-cfas-epidemia-for-flu-m… 

    …odel-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 3, 2024
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  2. updating writing here to match my sandbox

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    AFg6K7h4fhy2 committed Jul 3, 2024
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Commits on Jul 17, 2024

  1. merge w/ main to update

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 17, 2024
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Commits on Jul 22, 2024

  1. merge origin/main

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    AFg6K7h4fhy2 committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 23, 2024
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Commits on Jul 25, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 25, 2024
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  2. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 25, 2024
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  3. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 25, 2024
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Commits on Jul 29, 2024

  1. Merge branch 'main' into 135-UPX3-instantiate-cfas-epidemia-for-flu-m… 

    …odel-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 30, 2024
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  2. cfaepim updates

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 30, 2024
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  3. update writing section

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    AFg6K7h4fhy2 committed Jul 30, 2024
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  4. try to change observation class and Rt class

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    AFg6K7h4fhy2 committed Jul 30, 2024
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  5. updated remarks post DHM meeting

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 30, 2024
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  6. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 31, 2024
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  2. add toml to fix deptry

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Jul 31, 2024
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  3. again try adding toml

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    AFg6K7h4fhy2 committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 1, 2024
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  2. some minor updates to obs and rt

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 1, 2024
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  3. correct key context

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 1, 2024
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  4. DHM updates

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    AFg6K7h4fhy2 committed Aug 1, 2024
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  5. Update model/src/pyrenew/transformation/builtin.py 

    Co-authored-by: Dylan H. Morris <[email protected]>
    @AFg6K7h4fhy2 @dylanhmorris
    AFg6K7h4fhy2 and dylanhmorris committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
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    AFg6K7h4fhy2 committed Aug 2, 2024
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  2. pre- and post- DHM updates

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    AFg6K7h4fhy2 committed Aug 2, 2024
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Commits on Aug 5, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 5, 2024
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  2. add logging, need to change init days back to 8

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. logging and reorganizing

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 6, 2024
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  2. modify obs

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 6, 2024
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  3. dhm comments; samples working; still some bugs w/ step size

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 6, 2024
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  4. fix deptry

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. add docs, try getting validate, NamedTuple

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 7, 2024
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  2. vectorization, plotting (unfinished), some diagnostics

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 7, 2024
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  3. fix deptry

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. post dhm edits and comments

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    AFg6K7h4fhy2 committed Aug 8, 2024
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  2. proper pre-obs

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    AFg6K7h4fhy2 committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 9, 2024
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Commits on Aug 12, 2024

  1. synth data + forecast + comments

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. attempt additional plotting and saving

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 13, 2024
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  2. fix deptry

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 13, 2024
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  3. slight changes DHM meeting

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    AFg6K7h4fhy2 committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 14, 2024
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Commits on Aug 16, 2024

  1. further plotting changes; need to add quantile eval. changes back

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    AFg6K7h4fhy2 committed Aug 16, 2024
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  2. fix arviz from GLM PR

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 16, 2024
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  3. template forecasttools usage

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    AFg6K7h4fhy2 committed Aug 16, 2024
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Commits on Aug 19, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 19, 2024
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Commits on Aug 23, 2024

  1. Merge remote-tracking branch 'origin/main' into 135-UPX3-instantiate-… 

    …cfas-epidemia-for-flu-model-via-msr
    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 23, 2024
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  2. attempt fix rpy2 issues

    @AFg6K7h4fhy2
    AFg6K7h4fhy2 committed Aug 23, 2024
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  3. change sus prior to positive normal

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    AFg6K7h4fhy2 committed Aug 23, 2024
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