Deploy renamed nancodes to production #1045
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Generalize code that selects columns to use in finding unique rows. Now uses all columns up to but not including the first column that starts with "val_", "se_", etc (any column name that we do or can report in the contingency tables). Discuss column ordering/naming behavior in contingency pipeline comments.
readr's column guessing procedure only uses the first 1000 lines, by default, of a file to guess variable type for each column. If a column is completely missing for the first 1000 lines, it is read in as a logical which causes parsing failures if the column contains non-boolean values later, outside the type guessing range. This happens when reading in output files if an indicator was newly added. To correctly specify these, use the column specification from the input file/s. All columns included in input files are at least partially non-missing and sorted alphabetically (indepdendent of missingness), so we should always see non-missing values in the first 1000 lines.
[fb-package] Create script to combine contingency tables by group over all dates
Rename nancodes
Change max age of google-symptoms to 6 days
Fix bad field spelling on sircal log
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Description
We renamed some NAN codes in response to feedback in prep for the nans rollout. All other changes along for the ride.
Changelog
Itemize code/test/documentation changes and files added/removed.
#1043, Fix bad field spelling on sircal log#1040, Change max age of google-symptoms to 6 days#1044, Rename nancodes#1039, [fb-package] Create script to combine contingency tables by group over all dates