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Examples of exploring synthetic healthcare data from the Agency for Healthcare Research and Quality in the United States Department of Health and Human Services.

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Synthetic Healthcare Data

README from Observable Framework default documentation

This is an Observable Framework project. To start the local preview server, run:

yarn dev

Then visit https://localhost:3000 to preview your project.

For more, see https://observablehq.com/framework/getting-started.

Project structure

A typical Framework project looks like this:

.
├─ docs
│  ├─ components
│  │  └─ timeline.js           # an importable module
│  ├─ data
│  │  ├─ launches.csv.js       # a data loader
│  │  └─ events.json           # a static data file
│  ├─ example-dashboard.md     # a page
│  ├─ example-report.md        # another page
│  └─ index.md                 # the home page
├─ .gitignore
├─ observablehq.config.js      # the project config file
├─ package.json
└─ README.md

docs - This is the “source root” — where your source files live. Pages go here. Each page is a Markdown file. Observable Framework uses file-based routing, which means that the name of the file controls where the page is served. You can create as many pages as you like. Use folders to organize your pages.

docs/index.md - This is the home page for your site. You can have as many additional pages as you’d like, but you should always have a home page, too.

docs/data - You can put data loaders or static data files anywhere in your source root, but we recommend putting them here.

docs/components - You can put shared JavaScript modules anywhere in your source root, but we recommend putting them here. This helps you pull code out of Markdown files and into JavaScript modules, making it easier to reuse code across pages, write tests and run linters, and even share code with vanilla web applications.

observablehq.config.js - This is the project configuration file, such as the pages and sections in the sidebar navigation, and the project’s title.

Command reference

Command Description
yarn install Install or reinstall dependencies
yarn dev Start local preview server
yarn build Build your static site, generating ./dist
yarn deploy Deploy your project to Observable
yarn clean Clear the local data loader cache
yarn observable Run commands like observable help

README for Data Build Tool (dbt)

[On a new computer] Clone the repo, then run: Set up environment:

python3 -m venv .venv 

Activate the environment:

source .venv/bin/activate

Install dependencies:

pip install -r requirements.txt

Updating the environment

Install pip-tools:

pip install pip-tools

Compile dependencies:

pip-compile 

Initializing a dbt project:

dbt init healthcare_data

Building the datasets

  1. Generate the synthetic healthcare data schemas using the data dictionary:
cd healthcare_data
python scripts/generate_syh_dr_data_models.py ~/data/syh_dr https://www.ahrq.gov/sites/default/files/wysiwyg/data/SyH-DR-Codebook.pdf
  1. Generate the synthetic healthcare data (takes ~5 minutes):
dbt run
  1. Verify that you can query the data on the command line:
## To build a specific data model:

Use `--select` in dbt:

```bash
syhdr_medicare_outpatient_2016

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Examples of exploring synthetic healthcare data from the Agency for Healthcare Research and Quality in the United States Department of Health and Human Services.

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