4 ms·

Johns Hopkins Covid-19 Github Data Repo

85 points by mchirico 7y ago

tlrobinson 7y ago
Another interesting repo I came across: https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus https://github.com/midas-network/COVID-19/tree/master/parame...
b1gtuna 7y ago
Is it possible to view the number of tests ran? I keep seeing in the news that the current numbers for US are probably very off as very little tests are performed.
- Frost1x 7y ago
  I've heard this argument but it skews in both directions, I imagine. You'll have mild cases that recover where no test is ran that skews the data to the "more harmful than being presented" but I suspect there are also cases, especially for those with other preexisting conditions, where deaths also didn't run a test. Those cases would skew the data in the opposite, "less harmful than being presented" side. You essentially have a huge mess of amalgamated/non-systematically collected data. Even in controlled settings you get a lot of censored data to deal with. RT-PCR tests are reasonable these days in cost, but it isn't cheap by any means and I suspect many early cases weren't checking or didn't have the capability to check. The question is: which way is the data skewed more towards? I know absolutely nothing about the chinese healthcare system. Even if you do, there's a significant amount of guesswork. Only now as it spreads are we starting to get more controlled tests that give us more accurate data. For now, I have a tendency to trust the raw data until I see definitive evidence of skewness otherwise.
- TallGuyShort 7y ago
  Interestingly, the CDC website no longer has these numbers. A week ago, their main COVID-19 landing page had a table of positive tests, negative tests, and pending tests (total tests was in the neighborhood of 450). That seems to have disappeared, with a subset of those statistics here: https://www.cdc.gov/coronavirus/2019-ncov/cases-in-us.html https://www.cdc.gov/coronavirus/2019-ncov/cases-in-us.html.
braindongle 7y ago
If you want to do your own analytics on these data, here's one approach, which I'm using. Start your project as a vanilla Git repo, then add the JH repo as a submodule. git submodule add https://github.com/CSSEGISandData/COVID-19 Then you can do pulls to have the latest data. git submodule update --remote COVID-19 Have cron run that daily and your data are always fresh.
- saber6 7y ago
  Is there any real downsides to pulling in external repos as submodules?
  - zro 7y ago
    It can be a bit of a gotcha when trying to share your work with others. They'll have to clone with --recursive or the submodules will come up as empty folders for them.
fierarul 7y ago
I just used this repo yesterday to create a chart of the ongoing cases on http://covid.410go.net http://covid.410go.net It shows that China numbers have been going down for the past 2 weeks. This is not highlighting in the news...
- Karunamon 7y ago
  Those numbers for China are likely not trustworthy, keeping in mind they come from the government there. They're still keeping WHO inspectors out.
  - shi314 7y ago
    Then why is WHO chairman praising China?
    - remarkEon 7y ago
      Same reason Steve Kerr did.
  - Out_of_Characte 7y ago
    Not WHO inspectors, WHO has lots of chinese allegiance, The CDC is the organisation who is blocked from entering. https://www.foxnews.com/health/us-health-officials-on-coronavirus-outbreak https://www.foxnews.com/health/us-health-officials-on-corona... https://www.washingtontimes.com/news/2020/jan/30/china-asks-cdc-help-investigate-wuhan-virus/ https://www.washingtontimes.com/news/2020/jan/30/china-asks-... https://www.nationalreview.com/2017/06/world-health-organization-corrupt-wasteful/ https://www.nationalreview.com/2017/06/world-health-organiza... Google also seems to heavely favour WHO's website compared to alternative sources of information. Probaly all in order to combat "fake news" some dystopian world we live in.
- crtlaltdel 7y ago
  i've seen more than one article that at the least references this, such as https://www.latimes.com/world-nation/story/2020-03-03/virus-alarms-sound-worldwide-but-china-sees-crisis-ebbing https://www.latimes.com/world-nation/story/2020-03-03/virus-...
mkchoi212 7y ago
This is pretty great! Being able to see the progress of the virus over time could be interesting. Could maybe reveal some patterns about human movement + interaction??
- athrowaway3z 7y ago
  The different protocols for testing patients around the world are producing to much noise to make general claims.
jdoliner 7y ago
Not sure if this has been on HN already but Johns Hopkins also has a covid dashboard up, presumably using the data present in the repo: https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594...

85 points by mchirico 7y ago

Another interesting repo I came across: https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus https://github.com/midas-network/COVID-19/tree/master/parame...

b1gtuna 7y ago

Is it possible to view the number of tests ran? I keep seeing in the news that the current numbers for US are probably very off as very little tests are performed.

Frost1x 7y ago
I've heard this argument but it skews in both directions, I imagine. You'll have mild cases that recover where no test is ran that skews the data to the "more harmful than being presented" but I suspect there are also cases, especially for those with other preexisting conditions, where deaths also didn't run a test. Those cases would skew the data in the opposite, "less harmful than being presented" side. You essentially have a huge mess of amalgamated/non-systematically collected data. Even in controlled settings you get a lot of censored data to deal with. RT-PCR tests are reasonable these days in cost, but it isn't cheap by any means and I suspect many early cases weren't checking or didn't have the capability to check. The question is: which way is the data skewed more towards? I know absolutely nothing about the chinese healthcare system. Even if you do, there's a significant amount of guesswork. Only now as it spreads are we starting to get more controlled tests that give us more accurate data. For now, I have a tendency to trust the raw data until I see definitive evidence of skewness otherwise.
TallGuyShort 7y ago
Interestingly, the CDC website no longer has these numbers. A week ago, their main COVID-19 landing page had a table of positive tests, negative tests, and pending tests (total tests was in the neighborhood of 450). That seems to have disappeared, with a subset of those statistics here: https://www.cdc.gov/coronavirus/2019-ncov/cases-in-us.html https://www.cdc.gov/coronavirus/2019-ncov/cases-in-us.html.

braindongle 7y ago

If you want to do your own analytics on these data, here's one approach, which I'm using. Start your project as a vanilla Git repo, then add the JH repo as a submodule. git submodule add https://github.com/CSSEGISandData/COVID-19 Then you can do pulls to have the latest data. git submodule update --remote COVID-19 Have cron run that daily and your data are always fresh.

saber6 7y ago
Is there any real downsides to pulling in external repos as submodules?
- zro 7y ago
  It can be a bit of a gotcha when trying to share your work with others. They'll have to clone with --recursive or the submodules will come up as empty folders for them.

fierarul 7y ago

I just used this repo yesterday to create a chart of the ongoing cases on http://covid.410go.net http://covid.410go.net It shows that China numbers have been going down for the past 2 weeks. This is not highlighting in the news...

Karunamon 7y ago
Those numbers for China are likely not trustworthy, keeping in mind they come from the government there. They're still keeping WHO inspectors out.
- shi314 7y ago
  Then why is WHO chairman praising China?
  - remarkEon 7y ago
    Same reason Steve Kerr did.
- Out_of_Characte 7y ago
  Not WHO inspectors, WHO has lots of chinese allegiance, The CDC is the organisation who is blocked from entering. https://www.foxnews.com/health/us-health-officials-on-coronavirus-outbreak https://www.foxnews.com/health/us-health-officials-on-corona... https://www.washingtontimes.com/news/2020/jan/30/china-asks-cdc-help-investigate-wuhan-virus/ https://www.washingtontimes.com/news/2020/jan/30/china-asks-... https://www.nationalreview.com/2017/06/world-health-organization-corrupt-wasteful/ https://www.nationalreview.com/2017/06/world-health-organiza... Google also seems to heavely favour WHO's website compared to alternative sources of information. Probaly all in order to combat "fake news" some dystopian world we live in.
crtlaltdel 7y ago
i've seen more than one article that at the least references this, such as https://www.latimes.com/world-nation/story/2020-03-03/virus-alarms-sound-worldwide-but-china-sees-crisis-ebbing https://www.latimes.com/world-nation/story/2020-03-03/virus-...

mkchoi212 7y ago

This is pretty great! Being able to see the progress of the virus over time could be interesting. Could maybe reveal some patterns about human movement + interaction??

athrowaway3z 7y ago
The different protocols for testing patients around the world are producing to much noise to make general claims.

jdoliner 7y ago

Not sure if this has been on HN already but Johns Hopkins also has a covid dashboard up, presumably using the data present in the repo: https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594...