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A few days, CiSE gave us a proof of the edited text and formatted
PDF. After comparing the edited text with our text, I noticed some minor
editorial issues that have been corrected in this commit. The parts that
were wrong (or could be improved in the proof) have been listed and will be
submitted to the journal.
In particular, following the recommendation from the editor, the
biographies were extended with a full listing of each author's affiliation,
I also added our ORCID IDs in the biographies.
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Given the new appendix/supplement structure, it was necessary to go through
the answers and correct them. I also generally edited them and added a
top-level letter to the editors (to directly copy-paste into the webpage).
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Some minor edits were made to the paper to shorten it. In particular the
example of IPOL was removed from the main body of the paper, and we'll just
rely on the more extensive review of IPOL in the appendix. I also updated
the referee report to account for the new Appendix A that is just an
extended introduction.
Also, I noticed that the Menke+20 paper that we replicate here has recently
been published in the iScience journal. So its bibliography was updated
from the bioarXiv information to the journal information.
Also, the number of words (after removing abstract and captions and
accounting for figures) is now only printed when the project is built with
'--no-appendix'. This was done because this information is
extra/annoying/unnecessary for the case where there is an appendix.
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Thanks a lot Boud for adding that script in your own project and linking it
here. Since the raw file (without context of the whole project) is very
hard to understand for the users, I switched the URL to the navigable URL
the link is actually on the filename. It will always show the most recent
version of this script, not the particular snapshot of now. But infact that
is better, since we can make it better and improve it over time. Maybe even
by the end of this paper's referee review will be able to include it in
Maneage's core branch.
I also removed the link to this discussion at the first paragraph of
Section IV (proof of concept). Since that is just the introduction, and
going into this level of detail there could be confusing for the
readers. Having the name of the script in the proper place is more direct
and understandable for the readers.
Thanks again Boud for the nice work on this ;-).
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This commit adds the SWH URL of the statistical verification
script to the paper and tidies up the corresponding answer in
'1-answer.txt'. The script file includes more extensive
documentation than the earlier 'make' version of the method.
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The only issue that still remains is how to address statistical
reproducibility, and I am in touch with Boud to do this in the best way
possible (it has been highlighted with '#####'s in the answers.
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There is an answer for all the referee points now. I also did some minor
edits in the paper. But we are still over the limit by around 250 words.
The only remaining point that is not yet addressed (and has '####' around
it) is the discussion on parallelization and its effect on reproducibility.
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This commit is intended to be submittable quality.
Point 56 was removed, and the later points renumbered,
because it was a point of Reviewer 5 described what we
have done - it was not a criticism to respond do. :)
The current word count (without abstract and references)
is 6091.
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This commit only modifies "peer-review/1-answer.txt", giving
answers to Reviewer 4; these mostly take into account David's
email list of proposed answers. No changes are done to
"paper.tex".
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Copyediting of points 16 to 32 (paper.tex +
peer-review/1-answer.txt) is done in this commit.
TODO list:
2. paper lacking focus
9. tidy up README-hacking.md for appearance on website
App B.G. similar to Figure ?? - ref missing
29. website: README-hacking.md and tutorial "on same page"
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This commit updates "paper.tex" and "peer-review/1-answer.txt"
for the first 15 (out of 59!) reviewer points, excluding
points 2 (not yet done) and 9 (README-hacking.md needs
tidying).
A fix to "reproduce/analysis/make/paper.mk" for the
links in the appendices is also done in this commit (the same
algorithm as for paper.tex is added). The links in the appendices
are not (yet) clickable.
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This commit does a minor copyedit of "peer-review/1-answer.txt",
mostly just at the top, plus some hashes to highlight an
unanswered concern; and removes the @ symbols (and full stops)
from email addresses in the peer review email in order to reduce
our feeding of email harvesters (spiders that collect email addresses
for spammers).
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Raul's added point on the answer to the referee was very good, so I edited
it a little to be more clear (and removed his name).
Also, after looking in a few parts of the text, I fixed a few typos.
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With this commit, I am just adding several minor corrections to the
answer to the referees. They are very minor typos. I would only
emphasize the fact that in Maneage there is the "Minimal complexity"
criteria, and because of that, even if the project is not able to be
executed in the future, the interested reader could have a look at the
analysis steps (because it is in plain text). Note that I put "Raul" at
the beginning of the line, so my name should have to be removed in the
final document to be sent to the referees.
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A new directory has been added at the top of the project's source called
'peer-review'. The raw reviews of the paper by the editors and referees has
been added there as '1-review.txt'. All the main points raised by the
referees have been listed in a numbered list and addressed (mostly) in
'1-answers.txt'. The text of the paper now also includes all the
implemented answers to the various points.
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