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GeoDaCenter / covid

COVID Atlas alpha code
https://geodacenter.github.io/covid/
GNU General Public License v3.0
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Add hospital data as point layer #32

Closed Makosak closed 4 years ago

Makosak commented 4 years ago

Add COVIDCareMap hospitals as a point layer to click/off to help planning for hospital + planner crowd: https://www.covidcaremap.org/maps/us-healthcare-system-capacity/#3.85/38.63/-93.09

We're already using this as data for county levels, but our healthcare "customers" noted that being able to explore hospitals as points with data attached would be super.

bertday commented 4 years ago

Hello everyone!

I've been enjoying checking out this repo and seeing what's under the hood of the COVID Atlas. I'm especially curious about how the WebAssembly wrapper for GeoDa, as well as how some of the data flows work. Kudos on a nicely executed and much-needed reporting tool!

I'd love to help in some capacity if I can; @Makosak had suggested this issue could use a volunteer. If it's alright with the team, I'd love to look into how the COVIDCareMap is pulling hospitals and see what it would take to get that data into COVID Atlas. I can do some quick research tonight and follow up on this thread!

-Robert

RandomFractals commented 4 years ago

@rbrtmrtn you can also look at this repo to see where they get those numbers from too:

https://github.com/JieYingWu/COVID-19_US_County-level_Summaries

more info on that data set here: https://www.kaggle.com/jieyingwu/covid19-us-countylevel-summaries

See data sources list for hospital visits: https://www.kaggle.com/jieyingwu/covid19-us-countylevel-summaries#hospital_visits.csv

Makosak commented 4 years ago

Hey guys! Thanks for all this. For the point layer, we were planning on going with the dataset from COVIDCare map (linked above in initial comment) as it's from 2018 and is open to live edits -- also the Northwestern group was using that dataset, so it seems to be vetted. We're already using this as county-level estimates in the application, but wanted to add it as a clickable point layer to the map that planners/health groups could explore.

For new datasets, let's add a separate issue so the team can chime in for each one, etc. We already have several datasets planned to roll out in coming weeks, and lots of issues still left, gah!

RandomFractals commented 4 years ago

yeah, makes sense. that covidcare map has a decent repo to pull that data for the hospitals map view layer: https://github.com/covidcaremap/covid19-healthsystemcapacity

bertday commented 4 years ago

Thank you @Makosak and @RandomFractals for these notes!

I did some digging and it looks like COVIDCareMap publishes a file called us_healthcare_capacity-facility-CovidCareMap.geojson. Just to confirm, is that dataset you were planning on using?

The raw file is a bit large to bring into the browser directly (6.5 MB). The COVIDCareMap folks seem to be processing all of their visualization data into Mapbox-style vector tiles which they host themselves; this is what I'm seeing in the network calls:

https://www.covidcaremap.org/maps/us-healthcare-system-capacity/data/tiles/3/1/2.pbf

I was wondering if there were any thoughts around how to handle a larger dataset like this from a technical standpoint. I could try pulling the GeoJSON in directly, but at that size it will most likely add some lag time when you launch the app, and possibly degrade performance as you're using the map.

A few suggestions I had:

Would love to hear any other thoughts or perspectives on this—thanks everyone! Tagging @lixun910 and @linqinyu as well. (By the way, hello! 😄)

Makosak commented 4 years ago

+1 Sounds good @rbrtmrtn! Maybe see if we can bring their tiles over first? If that doesn't work or they're not interested we'd flip to serving our own but to not duplicate efforts, etc.

lixun910 commented 4 years ago

@rbtmrtn <10M is ok, not worth to tiling. what you need to is to reduce the geojson file size by:

  1. only keep id and lat/lon in geojson
  2. save any other information (needed on the map) to another csv file, which will be loaded separately

see the content of the geojson file, a lot of redundant information which can be dropped off to reduce the file size significantly:

"features": [ { "type": "Feature", "properties": { "Staffed All Beds": NaN, "Staffed All Beds - SOURCE": "None", "Staffed ICU Beds": NaN, "Staffed ICU Beds - SOURCE": "None", "Licensed All Beds": NaN, "Licensed All Beds - SOURCE": null, "All Bed Occupancy Rate": NaN, "All Bed Occupancy Rate - SOURCE": "None", "ICU Bed Occupancy Rate": NaN, "ICU Bed Occupancy Rate - SOURCE": "None", "Name": "IU HEALTH UNIVERSITY HOSPITAL", "Hospital Type": "GENERAL ACUTE CARE", "Address": "550 UNIVERSITY BLVD", "Address_2": null, "City": "INDIANAPOLIS", "State": "IN", "Zipcode": 46202, "County": "MARION", "County_FIPS": "18097", "DH-OBJECTID": null, "HCRIS-Provider Number": null, "HIFLD-ID": "100", "DH-ID": null, "HCRIS-ID": null, "CCM_ID": "100" }, "geometry": { "type": "Point", "coordinates": [ -86.17656161499997, 39.77528332600008 ] } },

On Thu, Apr 9, 2020 at 10:57 AM Marynia notifications@github.com wrote:

+1 Sounds good @rbrtmrtn https://github.com/rbrtmrtn! Maybe see if we can bring their tiles over first? If that doesn't work or they're not interested we'd flip to serving our own but to not duplicate efforts, etc.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GeoDaCenter/covid/issues/32#issuecomment-611667031, or unsubscribe https://github.com/notifications/unsubscribe-auth/AASPYT56OY3VZUY4NFV4K6DRLYEBZANCNFSM4L3F4IJA .

qinyun-lin commented 4 years ago

The Berkeley group also has hospital data that we need to incorporate. They have a severity index for each hospital. Maybe combine these? They also have lat & long ready.

bertday commented 4 years ago

Hi team! I just had a few followup questions about adding hospitals to the map.

Looking forward to getting everyone's thoughts on this!

lixun910 commented 4 years ago

Maybe Marynia can point out more what our stakeholders want? I think the point layer could just be “an overlay you toggle on/off”, so people will see these hospitals (with simple symbol e.g. point, to not draw users attention to the county/state level map). Then, it won’t impact existing spatial analysis methods.

It will not work with cartogram, which is has no geography/projection.

Xun

On Apr 11, 2020, at 10:17 PM, Robert Martin notifications@github.com wrote:

an overlay you toggle on/off

Makosak commented 4 years ago

Yes for this one just a click on/off, no graduated symbol for this (at least for now), with click enabled pop up window with more details. Users would zoom to an area of interest and click on this layer for more exploration.

We may have to fix the user session first -- right now if you zoom in and click different feature it resets the map, and for this feature to work as expected will need to keep in the zoomed area. I added this to different issue and some sample code from an old project project.

To test adding a layer, the reservation boundary is a simple issue and also high-need, would be similar click on/off feature?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/GeoDaCenter/covid/issues/32#issuecomment-612660789, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAULPEBFHJLZG5PYXU3SH3RMIFMJANCNFSM4L3F4IJA .

-- Marynia A. Kolak, PhD, MFA, MS Assistant Director of Health Informatics Assistant Instructional Professor in Geographic Information Science Center for Spatial Data Science at the University of Chicago

RandomFractals commented 4 years ago

here is a decent hospitals and beds map for inspiration:

https://maps.ruralopportunitymap.us/harvard-covid-scorecard

plus: https://maps.ruralopportunitymap.us/urban-exodus

ariisrael commented 4 years ago

#32: Add hospital data as point layer