Full version controlled source code for Covid19 Model

The request was partially successful.

Dear Imperial College London,

Question with respect to the COVID-19 model developed by the MRC Centre for Global Infectious Disease Analysis.

I am aware that a 'partial' git repository has been made available at
https://github.com/mrc-ide/covid-sim

Unfortunately for accountability, this git repository is insufficient. Git version control gives a history of code changes, unfortunately, Imperial has intentionally released their code with no prior history.

For this, I refer to
https://github.com/mrc-ide/covid-sim/com...

The commit marked 'Squash history for public release'

The act of squashing takes all prior changes and merges them into one commit, hence removing all history.

I request that in the public interest and to ensure public trust, you release all prior history (unredacted/unsquashed) of the Covid19 model in a git repository.

Yours faithfully,

Sarjan Narwan

IMPFOI, Imperial College London

Dear Mr Narwan,

This is to acknowledge receipt of your request below, made under the Freedom of Information Act. The College will respond to your request by 22 June.

Yours,

Freedom of Information Team
Imperial College London 

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IMPFOI, Imperial College London

Dear Mr Narwan,

 

Thank you for your Freedom of Information Act request, below.

 

On 1 June, Imperial’s COVID-19 Response Team published the script to
reproduce its 16 March coronavirus report (commonly referred to as
[1]Report 9). The code, script and documentation is [2]available on
Github. All assumptions are documented in the report and are available on
Github. Further information about the release and the code-check
certification can be found on the [3]College’s news pages

 

If you are unhappy with the way that we have handled your request, you can
ask us to conduct a review. Please make your representation in writing
within 40 days of the date you received this response. If you remain
dissatisfied with how Imperial College has handled your request, you may
then approach the [4]Information Commissioner’s Office.

 

Yours,

 

Freedom of Information Team

[5]Imperial College London 

 

 

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Dear Imperial College London,

Please pass this on to the person who conducts Freedom of Information reviews.

I am writing to request an internal review of Imperial College London's handling of my FOI request 'Full version controlled source code for Covid19 Model'.

The response given ignores the specificity I required, I acknowledged that an incomplete record was published on GitHub which you have just repeated. What I asked for was the full unsquashed history, including the state of the code when Neil Ferguson made his prediction which would include the approximately 15k lines of code file in one file.

`The code, script and documentation is [2]available on Github`
As I acknowledged in my request, I am aware of the existence of this repository, however as I had also mentioned, this is incomplete.

`On 1 June, Imperial’s COVID-19 Response Team published the script to
reproduce its 16 March coronavirus report`
This is not the script used to produce the report, I requested access to that.

I do not believe you have provided any additional information or provided any useful information with respect to my request. If this is not handled correctly I will be escalating this to the ICO.

A full history of my FOI request and all correspondence is available on the Internet at this address: https://www.whatdotheyknow.com/request/f...

Yours faithfully,

Sarjan Narwan

IMPFOI, Imperial College London

Dear Mr Narwan,

 

This is to acknowledge receipt of your request for an Internal Review
below.

 

In case it was not clear, there is additional information on Github that
was published after receipt of your FOI request. That is the information
that was referred to in our response to you dated 15 June.

 

You have asked for "the full unsquashed history, including the state of
the code when Neil Ferguson made his prediction which would include the
approximately 15k lines of code file in one file". We are dealing with two
similar requests as follows:

 

o "the C code referred to by Professor Neil Ferguson of the Faculty of
Medicine on Twitter on 22/03/2020 before it was refactored or
extended"; and

 

o "an original source code file used to generate the predictions
undergirding the now famous paper predicting catastrophic death from
the coronavirus.  I am writing to make an FOI request for this
original C code file.  It is rumored to be some 15,000 lines of source
code."

 

It would seem that you are asking for the same thing, but I would be
grateful if you could confirm that.

 

Yours,

 

Anita Hunt

Access to Information Manager

Central Secretariat

[1]Imperial College London  I South Kensington Campus I Faculty Building
Level 4 I London SW7 2AZ

Tel: +44 (0)20 7594 5107

 

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Dear IMPFOI,

"It would seem that you are asking for the same thing, but I would be
grateful if you could confirm that."
This is mostly true, the main thing I'd like to see is that large C file similar to the other requests, however in addition I'd like to see the version control history. This essentially acts as a historical record of changes. The full version controlled history would include the ~15k C file, but in addition, it would also give the history so these other requests would probably be asking for a subset of what I'm asking for.

"In case it was not clear, there is additional information on Github that
was published after receipt of your FOI request. That is the information
that was referred to in our response to you dated 15 June."

Sorry, I may be confused, could you provide a link to the additional information that fulfills this request? Also on my side, I don't see any responses made on the 15 June.

https://www.whatdotheyknow.com/request/f...

Yours sincerely,

Sarjan Narwan

IMPFOI, Imperial College London

Dear Mr Narwan,

Thank you for the clarification. We shall respond to your Internal Review by 20 July.

Please accept our apologies for the typo, our response to your initial request was dated 22 June.

Yours,

Freedom of Information Team
Imperial College London 

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IMPFOI, Imperial College London

Dear Mr Narwan,

Thank you for your Internal Review request. Your Freedom of Information
Act request was for: the large C file similar to the other requests,
however in addition I'd like to see the version control history. This
essentially acts as a historical record of changes. The full version
controlled history would include the ~15k C file, but in addition, it
would also give the history.

In response to your FOI request, Imperial College provided links to the
then newly published information which would enable people to reproduce
the 16 March COVID-19 report (commonly referred to as Report 9). You asked
for a review because the published information was not the C code you had
requested and did not include the full version-controlled history.

Professor Ferguson has now provided a file containing the original code.
Due to the file size, we are unable to send it by email. We can share the
file with you via Imperial College’s file exchange system. I would be
grateful if you could provide a direct email address so that we can send
you details of how to access the files.

We do not have the version history between this version and the released
version, but you should be able to compare the files to see the changes.

Please note that this code is undocumented and input parameter file
formats have changed slightly between this version and the current version
at [1]https://github.com/mrc-ide/covid-sim. The only documentation we have
is on this site.

We are unable to provide one of the population files used to generate the
Report 9 figures as it is the intellectual property of another party
([2]Landscan) available to the public under commercial licence. It is
therefore exempt from disclosure by virtue of Section 43 of the Freedom of
Information Act which protects from disclosure information that if
released would prejudice any party’s commercial interests. As this
information is available to members of the public for a fee, the exemption
at Section 21 of the Freedom of Information Act which exempts information
that is reasonably available to the applicant by other means also applies.

You may find the references below to all of the published code and
code-checks helpful:

o Report 9 [3]https://zenodo.org/record/3865491#.XvG6d... (source
code [4]https://github.com/mrc-ide/covid-sim/tre...)
refactor and extended code in collaboration with Microsoft and Github
was shared on 27-04, source code published 01-6. Certified on 01-06.
o Nature article [5]https://zenodo.org/record/3893138#.XvG66...
(source code [6]https://github.com/codecheckers/covid19m...)
Certified on 13-06.
o Report 23 [7]https://zenodo.org/record/3893617#.XvG6x... (source
code [8]https://github.com/sje30/covid19model-re...)  Certified on
14-06.

 

Having reviewed the College’s original response and your request for a
review, I am satisfied that the College has now met its obligations under
the Freedom of Information Act. If you are unhappy with the outcome of my
review of your request, you have the right to complain to the
[9]Information Commissioner’s Office.  

Yours,

 

Anita Hunt

Access to Information Manager

Central Secretariat

[10]Imperial College London  I South Kensington Campus I Faculty Building
Level 4 I London SW7 2AZ

Tel: +44 (0)20 7594 5107

 

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Dear IMPFOI,

Can you send it to this email?

[email address]

Also is there a reason the link to the files can't be posted here?

Otherwise, assuming that it is true that no version control history exists prior to it being posted to GitHub I am satisfied with the response.

Yours sincerely,

Sarjan Narwan

Sarjan Narwan left an annotation ()

For anyone who's interested. This is what was sent to me (uploaded to my google drive).

https://drive.google.com/file/d/1cwTDgvU...