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2020-11-27Merged with Boud's corrected answers (generally very similar)Mohammad Akhlaghi-107/+155
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.
2020-11-26All the referee points have been answeredMohammad Akhlaghi-34/+68
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.
2020-11-26All questions have now been responded toBoud Roukema-104/+170
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.
2020-11-25Points 33-35 handled in answer to reviewersBoud Roukema-14/+27
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".
2020-11-25Reviewer points 16 to 32Boud Roukema-31/+42
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"
2020-11-25Reviewer points 1-15; appendix clickable linksBoud Roukema-63/+78
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.
2020-11-24List of answers - minor copyeditBoud Roukema-11/+14
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).
2020-11-23Minor edits and correctionsMohammad Akhlaghi-5/+8
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.
2020-11-23Minor corrections to referees answerRaul Infante-Sainz-6/+13
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.
2020-11-23First draft of all the points addressed by the refereesMohammad Akhlaghi-0/+1040
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.