Revision edits

[jaybee84]

Purpose

Resolves #231 , #232 , #232

Directions for reviewers

HI All, I have ported all recent edits to GH from the word doc. Please review all changes and check if they address reviewer comments. No need to edit the word doc anymore. I was able to build the docx version locally and will be happy to do the track changes once we have finalized all edits.

Which areas should receive a particularly close look?

• All new edits
• Please make sure to check the Author contribution section to make sure everything looks good.

Is there anything that you want to discuss further?

Is the pull request ready for review?

YES

Manuscript checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

• [ ] All changes to text follow "one sentence per line" [Manubot instructions]
• [ ] All citations follow the Manubot citation instructions
• [ ] All changes or additions to tables follow the Manubot table instructions
• [ ] All figures follow the Manubot figure instructions
• [ ] All terms that need to be added to glossary have been added to #50
• [ ] There are no new spelling errors identified by the Manubot spellchecker

[AppVeyorBot]

AppVeyor build 1.0.667 for commit 97602837a902a6b703348939086e98cbda973afa is now complete....

Found 9 potential spelling error(s). Preview:

content/02.intro.md:17:TODO content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/10. figure_legends.md:3:Barplot content/12. box_2_definitions.md:7:undirected content/12. box_2_definitions.md:24:ImageNet content/13. box_3_MLtasks.md:12:subtyping content/13. box_3_MLtasks.md:13:heterogenous content/13. box_3_MLtasks.md:16:subpopulations The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.667-9760283.html
  • manuscript-1.0.667-9760283.pdf
  • spelling-errors-1.0.667-9760283.txt
  • spelling-error-locations-1.0.667-9760283.txt

[AppVeyorBot]

AppVeyor build 1.0.669 for commit e3ca52385f6a56c600b2bc579cd3ac6426a7b0b2 is now complete.

Found 12 potential spelling error(s). Preview:

content/02.intro.md:17:TODO content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/15. box_2_definitions.md:7:undirected content/15. box_2_definitions.md:24:ImageNet content/16. box_3_MLtasks.md:12:subtyping cont...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.669-e3ca523.html
  • manuscript-1.0.669-e3ca523.pdf
  • spelling-errors-1.0.669-e3ca523.txt
  • spelling-error-locations-1.0.669-e3ca523.txt

[AppVeyorBot]

AppVeyor build 1.0.671 for commit bd5ccef0c2b76549e39dfa0c2364090d7ea5252c is now complete.

Found 11 potential spelling error(s). Preview:

content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/15. box_2_definitions.md:7:undirected content/15. box_2_definitions.md:24:ImageNet content/16. box_3_MLtasks.md:12:subtyping content/16. box_3_MLtasks.md:13:...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.671-bd5ccef.html
  • manuscript-1.0.671-bd5ccef.pdf
  • spelling-errors-1.0.671-bd5ccef.txt
  • spelling-error-locations-1.0.671-bd5ccef.txt

[jaybee84]

@jaclyn-taroni please do your review/edits on this PR

[AppVeyorBot]

AppVeyor build 1.0.672 for commit 6a260ad2757961384ccbde88d7d57f13c220827d is now complete.

Found 14 potential spelling error(s). Preview:

content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/05.model-complexity.md:33:ALS content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/15. box_2_definitions.md:7:undirect...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.672-6a260ad.html
  • manuscript-1.0.672-6a260ad.pdf
  • spelling-errors-1.0.672-6a260ad.txt
  • spelling-error-locations-1.0.672-6a260ad.txt

[jaybee84]

I.e., if you're referencing diagnostic decision support in the main text – "(Box 3a"), is that because one of the studies cited in that passage fit that bill?

@jaclyn-taroni This is exactly the case.

[jaybee84]

@jaclyn-taroni I realize now that I responded to only half your comment above:

The main way I arrived at the content of the box was by reviewing the main citations to see what were the major tasks those papers were referring to. Box 3a-d are cited in the sections that had references to papers which intended to do those tasks. Box 3e is the only one which is not referenced in our sections, but I added this due to my prior knowledge about a recent paper in neurofibromatosis which is partially focused on this problem.

[jaclyn-taroni]

👍🏻 keeping this in mind as I review where the references to Box 3 are inserted and how the tasks are defined (in progress)

[jaybee84]

@jaclyn-taroni Thanks! If you get the chance to cut some words, that would be great too. We are currently over the word limit. I am also planning to do word count edit once your PR is in.

[jaybee84]

@jaclyn-taroni @allaway our one week extension request was accepted.

@jaclyn-taroni I am hoping to send the updated manuscript to Casey and Justin by Feb 22 (wed) so that they have one week to review before our submission deadline is up. Please let me know if this timeline sounds ok, or if I can help in any way to keep us on track with the timeline :)

[jaclyn-taroni]

@jaybee84 Do you want to update the LASSO reference I added as a TODO in my branch here? That also extends to anything else that was edited in the Word doc but didn't get added here that I missed.

I am aiming to wrap up my edits today and potentially address #234 (but I think we can all work on #234 in parallel).

[jaybee84]

@jaclyn-taroni

Do you want to update the LASSO reference I added as a TODO in my branch here?

-added

That also extends to anything else that was edited in the Word doc but didn't get added here that I missed.

WIP

[AppVeyorBot]

AppVeyor build 1.0.675 for commit e39e8f726d0b7953db2d47f1ba376a0bbe8496c5 is now complete.

Found 14 potential spelling error(s). Preview:

content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/05.model-complexity.md:33:ALS content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/15. box_2_definitions.md:7:undirect...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.675-e39e8f7.html
  • manuscript-1.0.675-e39e8f7.pdf
  • spelling-errors-1.0.675-e39e8f7.txt
  • spelling-error-locations-1.0.675-e39e8f7.txt

[AppVeyorBot]

AppVeyor build 1.0.676 for commit b34f13974d2520a3b74ba3905f9c62a21ef73a38 is now complete.

Found 14 potential spelling error(s). Preview:

content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/05.model-complexity.md:33:ALS content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/15. box_2_definitions.md:7:undirect...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.676-b34f139.html
  • manuscript-1.0.676-b34f139.pdf
  • spelling-errors-1.0.676-b34f139.txt
  • spelling-error-locations-1.0.676-b34f139.txt

[AppVeyorBot]

AppVeyor build 1.0.677 for commit 2cb9bc411031a8d6829bd3e89e64758712464b2a is now complete.

Found 14 potential spelling error(s). Preview:

content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/05.model-complexity.md:33:ALS content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/15. box_2_definitions.md:7:undirect...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.677-2cb9bc4.html
  • manuscript-1.0.677-2cb9bc4.pdf
  • spelling-errors-1.0.677-2cb9bc4.txt
  • spelling-error-locations-1.0.677-2cb9bc4.txt

[jaybee84]

That also extends to anything else that was edited in the Word doc but didn't get added here that I missed.

@jaclyn-taroni between your edits on #242 and my latest updates I think we have everything covered.

[AppVeyorBot]

AppVeyor build 1.0.679 for commit c26f74155145e2b4cd9897afdc44fc6cf7d18f6d is now complete.

Found 14 potential spelling error(s). Preview:

content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/05.model-complexity.md:33:ALS content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:curation content/13. figure_legends.md:3:Barplot content/14. box_1_MLtasks.md:21:subtyping c...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.679-c26f741.html
  • manuscript-1.0.679-c26f741.pdf
  • spelling-errors-1.0.679-c26f741.txt
  • spelling-error-locations-1.0.679-c26f741.txt