Propagate geomapper changes into JHU #297
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Propagate NYC and pylint hotfix for JHU
…ty issue template. Edited existing templates to make more relevant.
EMR: diff uploads
* README * data processing script * demo/tutorial notebooks Changes include: * updated data sources * Added state->HHS region mappings * new HRR weights * new JHU UID mappings by hand * 2019 population from US Census Bureau * Puerto Rico population from 2010 * Shortcut crosswalks Removed unused code
* Removed old sources, since we now pull from the internet * Renamed cross files, since they are tables * Added new mapping tables * Updated population figures * Added HHS mapping
* added the functions zip_to_state_code, zip_to_state_id (and the convert_* versions), zip_to_msa and convert_zip_to_msa * added two functions add_geocode and replace_geocode meant to consolidate the logic in the utility and reduce the code size by a factor of 5. These functions work along side with the rest of the deprecated functions and are meant to replace e.g. zip_to_msa(df, ...) with replace_geocode(df, "zip", "msa", ...). * renamed functions that referred to fips or county interchangeably to consistently use fips, e.g. zip_to_county to zip_to_fips * enforced the string type on all geocodes, with zero padding as necessary * renamed instances of stcode to state_code for clarity * removed non-JHU UID functions for JHU conversion * updated tests to match Bugfixes: * Removed .0000, 9xxx in output mappings - fixes most of #254 * Puerto Rico deaths should now be reported - fixes #179 * Generally fixes #215
Merged quidel_covidtest and quidel_flutest
Add issue templates
* fix linter issues in both geo_data_proc and geomap * make private _load_crosswalk * add deprecation warnings * add and update docstrings * update and fix tests Other updates: * made global variable for HHS source file * add Puerto Rico megaFIPS 72000 and its population * update static files
Comment typo Co-authored-by: chinandrew <[email protected]>
Small code consistency change Co-authored-by: chinandrew <[email protected]>
Co-authored-by: Alex Reinhart <[email protected]>
Prepare for public release
* Correct README information about JHU fixes * Remove JHU NYC county splitting * Add Dmitry to authorship comments in geo_data_proc and geomap
…icators into rf_geo_refactor
implement claims-only hospitalization indicator
* Change 'national' -> 'nation' for consistency with #207 * Enforce FIPS and ZIP from_code when going to 'nation' level
* if 'bucket_name' param is empty, do not archive * typo fix to comment in geo_data_proc
…icators into rf_geo_refactor
* keep the JHU entries for the counties that Kansas City contributes to (were deleted previously, leading to missing counts) * fix bug that deleted the Puerto Rico Unassigned and Out of State JHU UIDs * delete the New York County splitting that was previously necessary * add New York County UIDs back to the crosswalk
Further refactoring for the geo coding utility
korlaxxalrok
approved these changes
Oct 7, 2020
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#217 merged into main because delphi_utils doesn't have an associated deployment branch. This PR applies those changes to JHU automation.