344 create dynamic low case count thresholds#353
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kgostic
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Co-authored-by: Katie Gostic <uep6@cdc.gov>
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LGTM, but please address the failing build due to outdated roxygen documentation by running roxygenize() locally and pushing
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This update is meant to coincide with the PR in epinow2 CDCgov/cfa-epinow2-pipeline#353 to add in pathogen-specific low case count thresholds. This PR just adds disease-specific low case count thresholds that can be read into the epinow2 pipeline.
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reviewed again. Looking good
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Overview:
Create pathogen-specific low case count thresholds to use for labeling each state-pathogen pair as "n_low_case_counts" in the diagnostic file. "n_low_case_count" is assigned if the past week OR the week before that have less then X ED visits where X is the specified threshold. The state-pathogen pairs with a n_low_case_count flag will have their Rt values nulled and growth categories edited to "Not Estimated" in the post-processing repo.
Changes:
Coinciding PR:
Coincides with PR in config generator CDCgov/cfa-config-generator#73 where the threshold are provided in the src/cfa_config_generator/utils/epinow2/constants.py file.