For R users, the R package tabulizer and function extract_tables() will extract a list() of the tables in a pdf like the WHO one.
This extracts data.frames (in the latest one - number 45) out of the report.
The multi-line headings in the first (China) table mean that the automated reading doesn't work well, and for table 2 it brings in as character due to the headings. But this is sortable.
Paul
Paul Bivand | Associate Director, Statistics & Analysis | Learning and Work Institute Paul Bivand | Cyfarwyddwr Cynorthwyol Ystadegau a Dadansoddiad |Sefydliad Dysgu a Gwaith
e. [log in to unmask] <mailto:[log in to unmask]> |<mailto:[log in to unmask] <mailto:[log in to unmask]> > | tw. @LWPaulBivand | dt. 020 7840 8335
w. www.learningandwork.org.uk <http://www.learningandwork.org.uk/> <http://www.learningandwork.org.uk/ <http://www.learningandwork.org.uk/> > | @LearnWorkUK | t. 020 7582 7221
3rd Floor | 89 Albert Embankment | London | SE1 7TP
https://www.learningandwork.org.uk/ourevents/ <https://www.learningandwork.org.uk/ourevents/>
-----Original Message-----
From: email list for Radical Statistics <[log in to unmask]> On Behalf Of Thomas Cox
Sent: 06 March 2020 17:12
To: [log in to unmask]
Subject: covid-19 briefing in Washington DC by the JHU team
There is a web-available briefing that is planned for 1:30 Eastern Time (6:30 PM UK time) at the following link
https://coronavirus.jhu.edu/
From that page:
Live Webcast
3/6/2020 • 1:30pm ET
Join us here for a live webcast, as Johns Hopkins experts provide a coronavirus briefing for Capitol Hill officials in Washington, D.C.
Thomas Cox PhD RN
[log in to unmask]
On Friday, March 6, 2020, 11:27:44 AM EST, Thomas Cox <[log in to unmask]> wrote:
John,
The 'normal' privacy standards do not apply with regard to communicable diseases, and have officially been relaxed for Covid-19.
The state health departments, CDC personnel, physicians, all have obligations to share data - with as minimal protected information as possible to prevent errors in identification.
As to reporting. Here in the US state and local health departments perform tests. If tests are positive they are then tested again by the CDC. But the initial reporting would be by localities and it is likely that JHU workers are contacting localities and and may not be waiting for the second level of confirmation. I have no idea what the false positive rate might be for the tests, nor the false negatives.
Now there is something of an anomaly with the JHU data. Usually, by this time, there has been a large jump in global, and US data. but I am not seeing it yet. That said, there are certainly thousands more cases outside Mainland China since I prepared my graph yesterday.
The virus at this point, is well-seeded in virtually all sections of the US except for the upper midwest. Why there aren't cases there is baffling, but I suspect it is in part a lack of testing, as opposed to a lack of spread.
Thomas Cox PhD RN
[log in to unmask]
On Friday, March 6, 2020, 10:28:11 AM EST, John Whittington <[log in to unmask]> wrote:
At 04:09 06/03/2020, Thomas Cox wrote:
>OK, I decided to go take a look at how the JHU data is collected and
>here is their quickie summary. As suspected, they incorporate WHO data,
>but go further in case identification, albeit still with efforts to
>confirm cases. Here is the description: ....
Thanks (I've been rather tied up with work, so have been quiet for a bit).
I imagine that they probably have more detailed information about the methodology, so I'll see if I can find and study that.
>" Our primary data source is DXY, an online platform run by members of
>the Chinese medical community .... we found DXY cumulative case counts
>to frequently lag other sources; we therefore manually update these
>case numbers throughout the day when new cases are identified.
>To identify new cases, we monitor various twitter feeds, online news
>services, and direct communication sent through the dashboard. .... "
There are clearly things that I need to learn since, as I have implied, I would have thought that, for most countries, there would be only one primary source of data (some sort of 'official figures'), so I'm not clear as to what the 'other sources' are.
We also need to understand how they can "manually update these case numbers throughout the day when new cases are identified". Given that I presume that none of the sources contain any patient identifiers, on the face of it I cannot see how they can ascertain whether or not "new cases" that they think they have identified were, or were not, already included in the figures they are 'updating' - which would seem to carry a significant risk of 'double counting' some cases.
I'll see what I can discover!
Kind Regards,
John
----------------------------------------------------------------
Dr John Whittington, Voice: +44 (0) 1296 730225
Mediscience Services Fax: +44 (0) 1296 738893
Twyford Manor, Twyford, E-mail: [log in to unmask] <mailto:[log in to unmask]>
Buckingham MK18 4EL, UK
----------------------------------------------------------------
******************************************************
Please note that if you press the 'Reply' button your message will go only to the sender of this message.
If you want to reply to the whole list, use your mailer's 'Reply-to-All' button to send your message automatically to [log in to unmask] <mailto:[log in to unmask]>
Disclaimer: The messages sent to this list are the views of the sender and cannot be assumed to be representative of the range of views held by subscribers to the Radical Statistics Group. To find out more about Radical Statistics and its aims and activities and read current and past issues of our newsletter you are invited to visit our web site www.radstats.org.uk.
*******************************************************
******************************************************Please note that if you press the 'Reply' button yourmessage will go only to the sender of this message.If you want to reply to the whole list, use your mailer's'Reply-to-All' button to send your message automaticallyto [log in to unmask]: The messages sent to this list are the views of the sender and cannot be assumed to be representative of the range of views held by subscribers to the Radical Statistics Group. To find out more about Radical Statistics and its aims and activities and read current and past issues of our newsletter you are invited to visit our web site www.radstats.org.uk.*******************************************************
****************************************************** Please note that if you press the 'Reply' button your message will go only to the sender of this message. If you want to reply to the whole list, use your mailer's 'Reply-to-All' button to send your message automatically to [log in to unmask] Disclaimer: The messages sent to this list are the views of the sender and cannot be assumed to be representative of the range of views held by subscribers to the Radical Statistics Group. To find out more about Radical Statistics and its aims and activities and read current and past issues of our newsletter you are invited to visit our web site www.radstats.org.uk. *******************************************************
This message contains confidential information and is intended only for the individual(s) addressed in the message. If you are not the named addressee, you should not disseminate, distribute, or copy this e-mail. If you are not the intended recipient, you are notified that disclosing, distributing, or copying this e-mail is strictly prohibited.
******************************************************
Please note that if you press the 'Reply' button your
message will go only to the sender of this message.
If you want to reply to the whole list, use your mailer's
'Reply-to-All' button to send your message automatically
to [log in to unmask]
Disclaimer: The messages sent to this list are the views of the sender and cannot be assumed to be representative of the range of views held by subscribers to the Radical Statistics Group. To find out more about Radical Statistics and its aims and activities and read current and past issues of our newsletter you are invited to visit our web site www.radstats.org.uk.
*******************************************************
|