Exploratory walkthrough of data ingestion / viz from cancerprof and a basic Shiny app

[vsriram24]

Includes R code in QMD files to explore data ingestion, munging, and visualization (using {leaflet} and {tmap}) for cancer incidence data. Also includes directories of publicly-sourced shape files for geospatial data visualization.

Next steps are to comment / clean code as well as remove any hard-coded elements, and then port this over into a Shiny app so that data visualization can be explored further.

[vsriram24]

This branch also includes the creation of a basic Shiny app.

[seankross]

We should talk about this database schema, I'm not convinced this is the best way forward.

[seankross]

Generally speaking this is a great start. Both of my main comments are pretty high level, let's chat about it when you get the chance.

[vsriram24]

@seankross data ingestion now exists separately from the Shiny app. The latest updates on this branch include a separate pipeline that ingests SCP Washington state county-level data and puts it into the Fred Hutch postgreSQL database. Let me know your feedback on this PR when you have the chance.

[seankross]

Hey @vsriram24, unfortunately I am just now getting to this. Which files do I need to run in what order to get the Shiny app to work?

[vsriram24]

Hi @seankross, for this branch, there's no need to worry about the Shiny app. You can just run R/ingest-scp.R to evaluate the data ingestion pipeline. Note that you will have to create a .Renviron file within the oncarto/ directory that contains the postgreSQL database information for the data saving step at the end of the script to work. I'll include a comment in the baseline-app PR to explain how to run the Shiny app.

[seankross]

@vsriram24 in that case I am only going to give feedback on R/ingest-scp.R in this PR unless you want feedback on other changes here.