Add requested variables and contingency tables

[davidkretch]

Description

Add the requested v0.2 variables and contingency tables from the new contingency tables requirements document.

I have compared the results of this version with the version on main and the vaccinated and concerned_sideeffects (now worried_vaccine_sideeffects) match exactly. I compared results for survey responses submitted 3/21-3/27 at the state/age (now agefull) level.

One issue I noticed: the pct_cli and pct_ili metrics, which use compute_numeric, do not receive standard errors.

Changelog

• In contingency_variables.R, add v0.2 grouping and indicator variables and new names/categories. Reorganize all variables to match the order in the requirements spreadsheet for easy checking.

• In contingency_indicators.R, add all requested contingency tables by region and group (e.g. nation, state, age, gender, etc.) and all requested indicators, e.g. vaccinated, hesitant, etc.

[davidkretch]

Hello, we realized that some of the codings in this need to be updated, e.g. hcw should be "Healthcare worker" rather than 1, etc. We will update asap.

[nmdefries]

This is just from an initial look-through; I haven't checked all the variable definitions in detail.

I was hoping that you'd base this off the contingency-tables-fb-sandbox branch, which already has a lot of these variables defined. Please take a look there to verify your definitions, especially the "hesitant and" ones. The race-based variables are there as well.

I believe Alex sent an email about this, but race is stripped from the microdata because of privacy concerns. To get race, you'll need to use the raw data.

Did you get a chance to run this and compare the output to existing tables?

we realized that some of the codings in this need to be updated, e.g. hcw should be "Healthcare worker" rather than 1

I think hcw is supposed to be boolean, so it seems fine.

[nmdefries]

@davidkretch Hold off on rebasing/merging this into the contingency-table-fb-sandbox branch, I'm sending an email with more info.

[davidkretch]

This has now been updated with the changes discussed over the last week.

[nmdefries]

Some definitional issues and some items defined here already exist in variables.R. We should just rename those items to save computational effort. There are a couple things I want to check in with Sarah about and I'll follow up when possible.

[nmdefries]

Some variable + comment clean-up.

[davidkretch]

I've made the requested updates and verified that the updated version's output matches the previous version with the exception of the contingency table for grouping variable eligiblepregsmokeobese.

[nmdefries]

This is looking great!! I'm just going to run this on my own machine and compare to previous table output.

[nmdefries]

A couple details and then this is good to go! All calculations except pct_vaccinated matched tables produced by my current code 👍

[nmdefries]

@capnrefsmmat Could you merge this as well?