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231 establish table of active NPIs according to Corona Datenplattform and reported infection data #443

Merged
merged 110 commits into from
Sep 5, 2023
Merged

231 establish table of active NPIs according to Corona Datenplattform and reported infection data #443

merged 110 commits into from
Sep 5, 2023

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mknaranja
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@mknaranja mknaranja commented Nov 10, 2022 •
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Merge Request - GuideLine Checklist

Guideline to check code before resolve WIP and approval, respectively.
As many checkboxes as possible should be ticked.

Checks by code author:

  • There is at least one issue associated with the pull request.
  • The branch follows the naming conventions as defined in the git workflow.
  • New code adheres with the coding guidelines
  • Tests for new functionality has been added
  • A local test was succesful
  • There is appropriate documentation of your work. (use doxygen style comments)
  • If new third party software is used, did you pay attention to its license? Please remember to add it to the wiki after successful merging.
  • If new mathematical methods or epidemiological terms are used, has the glossary been updated ? Did you provide further documentation ?
    is present or referenced. Please provide your references.
  • The following questions are addressed in the documentation*: Developers (what did you do?, how can it be maintained?), For users (how to use your work?), For admins (how to install and configure your work?)
  • For documentation: Please write or update the Readme in the current working directory!

Checks by code reviewer(s):

  • Is the code clean of development artifacts e.g., unnecessary comments, prints, ...
  • The ticket goals for each associated issue are reached or problems are clearly addressed (i.e., a new issue was introduced).
  • There are appropriate unit tests and they pass.
  • The git history is clean and linearized for the merge request.
  • Coverage report for new code is acceptable.

Closes #231
Closes #412
Closes #413
Closes #414

mknaranja and others added 29 commits March 28, 2022 17:53
@mknaranja
transformation of NPI data
545ae4b
@mknaranja
directory for raw data changed; new data separated by comma
3115bf3
@mknaranja
auxiliary files were read twice
a485663
@mknaranja
small redesign and WIP of evaluation against confirmed infections
ed9e10e
@mknaranja
small redesign and further WIP on NPI activation
888d524
@mknaranja
Compute incidence per county
dc2e9b2
@mknaranja
Activation of NPIs implmented; without deactivation by stronger NPIs;…
31e8aca 
… without aggregation
@mknaranja
Compute incidence value, aggregate NPIs, use delay possible
f31ba8a
@mknaranja
further validation and minor items
c25384f
@mknaranja
outsourcing of validation to function
a636221
@mknaranja
Extension and correction for incidence-independent cats; WIP
09dc291
@mknaranja
Validation for fine=1 completed
a2122a1
@mknaranja
remove placeholder categories
8a8322a
@mknaranja
outsourcing of analysis and plot to WIP function; correction if inden…
9ca0041 
…tation for fine_res=0
@mknaranja
Start of NPI combination matrix use; WIP
57d4c69
@mknaranja
Read combination matrix and export to clean format
b6b3379
@mknaranja
Make combination matrix dataframe
4d1e4f7
@mknaranja
todo combination matrix
4c0c8ab
@mknaranja
todo combination matrix
5664fc7
@mknaranja
incidence_thresholds_to_npis now also contains subcode end, not only …
4a12894 
…threshold
@mknaranja
exclusion loops now started
85a29db
@mknaranja
if clause for check
868d68d
@mknaranja
Deactivation of exclusive NPIs
b255c30
@mknaranja
Correction and extension for delayed NPI implementation or lifting
df1480f
@mknaranja
Further correction of NPI start and end date for delays with extensiv…
977df04 
…e example
@mknaranja
correct formatting; no other change
da29e98
@mknaranja
remove printouts and replace deprecated pandas append
7f11dbf
@patricklnz
fix errors
671e9a9
@patricklnz
rework activation/lifting of incidence dependent NPIs
65596e7
@mknaranja mknaranja linked an issue Nov 10, 2022 that may be closed by this pull request
Transformation of NPI data and preliminary analysis #231
Closed
@mknaranja mknaranja force-pushed the 231-npi-data branch 2 times, most recently from 5b0d0ca to 5d00464 Compare August 16, 2023 11:53
@SciCompMod SciCompMod deleted a comment from patricklnz Aug 28, 2023
mknaranja
mknaranja commented Sep 1, 2023
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Hi @patricklnz & @annawendler,

I went through the all your changes since April and reduced some of the redundant functionality. I hope that I did not introduce new errors. Please check this.

Furthermore, the tests would need to be adapted as I renamed and reduced the number of introduced functions. Could you take over here?

pycode/memilio-epidata/memilio/epidata/defaultDict.py Outdated Show resolved Hide resolved
pycode/memilio-epidata/memilio/epidata/getDataIntoPandasDataFrame.py Show resolved Hide resolved
pycode/memilio-epidata/memilio/epidata/getNPIData.py Outdated Show resolved Hide resolved
pycode/memilio-epidata/memilio/epidata/getNPIData.py Outdated Show resolved Hide resolved
pycode/memilio-epidata/memilio/epidata/getNPIData.py Outdated Show resolved Hide resolved
mknaranja
mknaranja commented Sep 4, 2023
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Looks good so far. Have you finished here @patricklnz and @annawendler ? I just saw there is one final comment on the multiple zeros. Can you answer that?

I just merged the main into the branch.

patricklnz
patricklnz approved these changes Sep 5, 2023
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Approved!

@patricklnz patricklnz merged commit 429ffb3 into main Sep 5, 2023
@patricklnz patricklnz deleted the 231-npi-data branch September 5, 2023 08:48
mknaranja added a commit that referenced this pull request Sep 5, 2023
@mknaranja @patricklnz @annawendler
231 establish table of active NPIs according to Corona Datenplattform…
0904a39 
… and reported infection data (#443)

Establish table of active NPIs according to Corona Datenplattform and reported infection data.

---------

Co-authored-by: patricklnz <[email protected]>
Co-authored-by: Anna Wendler <[email protected]>
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Reviewers

@annawendler annawendler annawendler left review comments

@patricklnz patricklnz patricklnz approved these changes

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@mknaranja mknaranja

@patricklnz patricklnz

@annawendler annawendler

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@mknaranja @patricklnz @annawendler