How to ...?

 

For authors

For recommenders

For reviewers


 

For authors

 

To prepare a preprint

-No specific format is required. Just be sure that lines are numbered and that tables and figures are located in the main text, not at the end of the manuscript.
-When your preprint is ready, post it on a preprint server, such as bioRxiv or arXiv.
-When the article has appeared on this server, you can submit it to PCI Ecol (see next paragraph).

To submit a preprint

To submit a preprint, when the article has appeared on the preprint server,
1) Go to https://ecology.peercommunityin.org/ and log in
2) Click on the green 'SUBMIT A PREPRINT' button
3) Complete the form (title, authors, DOI, abstract, keywords, thematic fields)
4) Suggest recommenders by clicking on the blue 'SUGGEST RECOMMENDERS' button. Each time you suggest a new recommender, you can add others, or remove a suggested recommender by clicking on the orange ‘REMOVE’ button
5) Complete your submission by clicking on the green 'COMPLETE YOUR SUBMISSION' button. This will result in your submission being sent to the managing board for validation.

To submit a preregistration of a study

To submit a preregistration of a study, you should first post it on a dedicated server (e.g. OSF) or on a publicly accessible personal website (e.g. GitHub) - make sure you obtain a DOI (e.g., by linking the GitHub repository with Zenodo; see instructions here ). Post your preregistration as a pdf, doc, or Rmd document. Follow the OSF template (note: we consider points 3 and 4 interchangeable). Once the preregistration is complete and appears on a public server/repository,

1) Go to https://ecology.peercommunityin.org/ and log in
2) Click on the green 'SUBMIT A PREPRINT' button
3) Complete the form (title, authors, DOI, abstract, keywords, thematic fields - choose "preregistration" as one of the thematic fields)
4) Suggest recommenders by clicking on the blue 'SUGGEST RECOMMENDERS' button. Each time you suggest a new recommender, you can add others, or remove a suggested recommender by clicking on the orange ‘REMOVE’ button
5) Complete your submission by clicking on the green 'COMPLETE YOUR SUBMISSION' button. This will result in your submission being sent to the managing board for validation.

A summary of the preregistration recommendation workflow can be found here.

What to keep in mind...

One preregistration might cover a larger body of work and result in multiple different preprints. Please note when you expect this might occur. We recognize that your study might undergo unplanned changes, which is normal when conducting research. We ask that you document how you decide to adjust your study along the way and we recommend doing this in a version-controlled environment such as GitHub so recommenders and reviewers can see what happened (and why) at every step of the process. If these changes are major, please contact us in advance because it might lead to another review of your preregistration (an updated version). If the changes are minor, please explicitly discuss them in your preprint.

What happens after submission?

After you submit your preregistration, the Recommender assigned to your preregistration will go through the following process:

  1. Does the preregistration follow the OSF template? (note: we consider points 3 and 4 interchangeable) For more info about preregistrations see: https://cos.io/prereg/, https://cos.io/our-services/prereg-more-information/.
    • No? Send to authors, ask them to resubmit after following the template. If they do and it is acceptable, move to next point
    • Yes? Move to next point.
  2. Is it clear that the preregistration will result in an empirical study (and is not an idea(s) that might never be tested)?
    • No? Send to authors, ask them to resubmit after making the work empirical (give some feedback)
    • Yes? Send out for peer review
  3. Is the preregistration scientifically valid? After 1-2 revisions during the peer review process, the Recommender will decide whether peer reviews indicate the work is scientifically valid
    • No? Reject preregistration
    • Yes? Recommend preregistration

Post-study peer review

If a preregistration is recommended, conduct your study, post a preprint at a repository, and SUBMIT the preprint to PCI Ecology for the final stage of peer review. Note: if you realize that major changes are needed to your recommended preregistration, please contact us in advance because it might lead to another review of your preregistration (an updated version).

In your preprint, please cite your recommended preregistration and explain any differences between the two documents that might have arisen while conducting your study.

The Recommender will go through the following process:

  1. Is the preprint consistent with the recommended preregistration? If not, are the differences reasonable (still scientifically valid and changes implemented based on predictions rather than posthoc analyses of data part way through study) and well documented (e.g., in the preprint and at a version-controlled document e.g., at GitHub)?
    • No? Reject the preprint. Suggest authors re-conduct the study in a way that is more consistent with the recommended preregistration. This option might result in a new preprint that would need to be submitted to PCI Ecology for post-study peer review.
    • Yes? Recommend preprint
  2. One preprint may represent only part of a preregistration, which might cover a larger body of research. If this is the case, require the authors to state why the other parts are not included and when the other parts will be submitted for post-study peer review. The preregistration will not be considered complete until all preprints resulting from the preregistration pass the post-study peer review. The Recommender will note in their recommendation whether the preregistration is complete or not.

For an example of version-tracked preregistrations that follow the OSF template, please see: https://github.com/corinalogan/grackles

Policy on withdrawing preregistrations

In the event that authors wish to withdraw their preregistration submission, they may do so at any time by contacting PCI Ecology.

Policy on preregistrations with incomplete preprints

Recommended preregistrations will not be considered completed until all preprints resulting from the preregistration pass post-study peer review at PCI Ecology. In the event that authors do not submit all of the resulting preprints from a given preregistration for post-study peer review at PCI Ecology, their preregistration recommendation will be labeled "Incomplete". This practice is to ensure that, for example, negative results are not hidden in the "file drawer" and that the entire preregistration is addressed through the resulting preprints.

To modify a submission before it has been validated by the managing board

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS' —> 'YOUR SUBMITTED PREPRINTS' in the top menu.
3) To add or remove suggested recommenders: click on the black 'ADD/MANAGE' button in the middle of the line referring to the preprint in question, and add or remove suggested recommenders. Click on the green 'COMPLETE YOUR SUBMISSION' button when you have finished.
4) To modify the title, authors, DOI, abstract, keywords, or disciplines: click on the black 'VIEW / EDIT' button at the right end of the line referring to the preprint in question, and then click on the black 'EDIT ARTICLE' button.
5) Click on the blue 'SUBMIT' button when you have completed your modifications. This will result in the submission being sent to the managing board for validation.

To cancel a submission

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS' —> 'YOUR SUBMITTED PREPRINTS' in the top menu.
3) Click on the black 'VIEW / EDIT' button at the right end of the line referring to the preprint in question.
4) Click on the orange 'CANCEL A SUBMISSION’ button.

To suggest (additional) recommenders

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS' —> 'YOUR SUBMITTED PREPRINTS' in the top menu.
3) Click on the black 'ADD/MANAGE' button in the middle of the line referring to the preprint in question and add or remove suggested recommenders.
4) Click on the green 'COMPLETE YOUR SUBMISSION' button when you have finished.

To reply to the reviewers’ and recommenders’ comments and submit a new version of the preprint or preregistration

1) Deposit the new version of your preprint/preregistration on the preprint/preregistration server (e.g. bioRxiv / OSF) of your choice.
2) Go to https://ecology.peercommunityin.org/ and log in
3) Go to 'YOUR CONTRIBUTIONS' —> 'YOUR SUBMITTED PREPRINTS' in the top menu.
4) Click on the black ‘VIEW / EDIT' button at the right end of the line referring to the preprint in question.
5) If you wish to modify the title, authors, DOI, abstract, keywords, or disciplines: click on the black 'EDIT ARTICLE' button. Click on the blue 'SAVE' button when you have finished your modifications.
6) Click on the blue 'WRITE, EDIT OR UPLOAD YOUR REPLY TO RECOMMENDER' button. On this page, you can write or paste your text, upload your reply as a PDF file, and upload a document with the modifications marked in TrackChange mode.
-You can save a draft version of your reply by clicking on the blue 'SAVE' button (you can then continue to modify your reply until it is ready for sending, at which point you move on to step 7).
7) To send your reply to the managing board, click on the green 'SAVE AND SUBMIT YOUR REPLY' button.


For recommenders

 

To recommend a postprint

1) Go to https://ecology.peercommunityin.org/ and log in
2) Click on the blue 'RECOMMEND A POSTPRINT' button. You will be asked to declare that you have no conflict of interest with the authors or the content of the article.
3) Complete the form (title, authors, source, DOI, abstract, keywords, disciplines) and click on the blue 'CONTINUE' button
4) To choose your co-recommenders (co-authors of your recommendation), select one or more co-recommenders from the list of PCI Ecology recommenders and click on the blue 'ADD' button.
5) To write your recommendation, click on the black 'WRITE/EDIT YOUR RECOMMENDATION' button and complete the form (recommendation title, recommendation).
-You can save a draft version of your recommendation by clicking on the blue 'SAVE' button (you can then continue to write or modify your recommendation, moving on to step 5 when it is ready to send)
6) When you have completed your recommendation, click on the green 'SAVE AND SUBMIT YOUR RECOMMENDATION' button. This will result in the recommendation being sent to the managing board for validation. Your co-recommenders will receive your recommendation.

To handle the evaluation of a preprint

1) Go to https://ecology.peercommunityin.org/ and log in
2) If you wish to act as the recommender handling the evaluation of a preprint but have not been invited to do so, go to 'REQUEST FOR INPUT'—> 'CONSIDER PREPRINT SUBMISSION' in the top menu to see the list of preprints still requiring a recommender, and then go to step 3.
3) If you have been invited to act as the recommender handling the evaluation of a preprint, go to 'REQUEST FOR INPUT'—> 'DO YOU AGREE TO INITIATE A RECOMMENDATION?' in the top menu.
4) Click on the black 'VIEW' button at the right end of the line referring to the preprint in question to obtain information about the preprint.
5) Indicate whether you agree or decline the invitation to act as the recommender handling the evaluation of the preprint by clicking on the green or orange buttons. If you click on the green button, you will be asked to declare that you have no conflict of interest with authors or the content of the article.
6) You will then be invited to seek reviewers (you can postpone the invitation of reviewers by clicking on the blue 'DONE' button, but you will then need to follow the instructions 'to invite reviewers' at a later stage).
-To request a review from someone not included in the PCI Ecology database: click on the black ‘CHOOSE A REVIEWER FROM OUTSIDE PCI ECOLOGY DATABASE’ button and complete the form (first name, last name and e-mail address of the reviewer). You can change the subject and/or the message if you wish. You should then click on the blue 'SEND E-MAIL' button at the end of the form.
-To request a review from someone listed in the database of PCI Ecology: click on the green ‘CHOOSE A REVIEWER FROM PCI ECOLOGY’ button. A search engine and a filter based on thematic fields may be used. Select a reviewer by clicking on the black ‘ADD’ button at the right end of the corresponding line. You can modify the subject and/or the message of the e-mail before sending it to the reviewer concerned. Then, click on the blue 'SEND E-MAIL' button at the end of the form.
7) When you have sent invitations to all your chosen reviewers, click on the blue 'DONE 'button.

To request reviews

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the black 'CHOOSE A REVIEWER' button in the line corresponding to the preprint considered.
-To invite a review from someone not included in the database of PCI Ecology: click on the black ‘CHOOSE A REVIEWER FROM OUTSIDE PCI ECOLOGY DATABASE’ button and complete the form (first name, last name and e-mail address of the reviewer). You can change the subject and/or the message if you wish. Then, click on the blue 'SEND E-MAIL' button at the end of the form.
-To choose a reviewer from the PCI Ecology database: click on the green ‘CHOOSE A REVIEWER FROM PCI ECOLOGY’ button. A search engine and a filter based on thematic fields may be used. Select a reviewer by clicking on the black ‘ADD’ button at the right end of the corresponding line. You can modify the subject and/or the message of the e-mail before sending it. Then, click on the blue 'SEND E-MAIL' button at the end of the form.
4) When you have sent invitations to all your chosen reviewers, click on the blue 'DONE 'button.

To send a reminder to reviewers

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the blue 'SEND A REMINDER' button located just to the right of the name of the reviewer concerned.
4) You can modify the subject and/or the message of the e-mail before sending it. Then, click on the blue 'SEND E-MAIL' button.

To cancel a request for a review

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the orange 'SEND A CANCELLATION NOTIFICATION' button located just to the right of the reviewer concerned.
4) You can modify the subject and/or the message of the e-mail before sending it. Then, click on the blue 'SEND E-MAIL' button.

To send a review due message to reviewers

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the blue 'SEND AN OVERDUE MESSAGE' button located just to the right of the name of the reviewer concerned.
4) You can modify the subject and/or the message of the e-mail before sending it. Then, click on the blue 'SEND E-MAIL' button.

To check the e-mails you have already sent to an invited reviewer

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the black 'E-MAILS' button located just to the right of the name of the reviewer concerned. E-mails are listed in chronological order, from oldest to most recent.

To view the reviews

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the black ‘VIEW’ button located just to the right of the name of the reviewer who has completed his/her review. You can also click on the black 'CHECK & EDIT' button at the right end of the corresponding line.

To view author's reply

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the black 'CHECK & EDIT' button at the right end of the corresponding line.
4) Click on the blue link 'Download author’s reply’

To communicate your decision or write a recommendation

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'—> 'YOUR RECOMMENDATIONS OF PREPRINTS' in the top menu.
3) Click on the black 'CHECK & EDIT' button at the right end of the corresponding line.
4) Click on the black 'WRITE OR EDIT YOU DECISION / RECOMMENDATION’ button.
5) Indicate your decision by selecting 'I RECOMMEND THIS PREPRINT', 'THIS PREPRINT MERITS REVISION' or 'I REJECT THIS PREPRINT'.
6) Choose a decision or recommendation title (this is of particular importance only for decisions to recommend the preprint concerned) and write or copy/paste your decision or recommendation text.
-You can save a draft version of your decision or recommendation text by clicking on the blue 'SAVE' button (you will then have to go through steps 0 to 5 to complete your recommendation).
7) To send your decision or recommendation to the managing board for validation, click on the green 'SAVE AND COMPLETE' button. This will result in your decision or recommendation being sent to the managing board for validation.

To request an additional round of reviews from the reviewers

Follow the steps described in the rubric 'to request reviews’.


For reviewers

 

To read a preprint/preregistration before deciding whether or not to agree to review it

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'REQUESTS FOR INPUT' —> 'DO YOU AGREE TO REVIEW A PREPRINT?' in the top menu.
3) You can read the preprint by clicking on the blue hyperlink to the digital object identifier (DOI) in the line corresponding to the preprint considered.

To accept or decline an invitation to review a paper/preregistration

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'REQUESTS FOR INPUT' —> 'DO YOU AGREE TO REVIEW A PREPRINT' in the top menu.
3) Click on the black 'ACCEPT OR DECLINE' button at the right end of the line corresponding to the preprint/preregistration in question.
4) At the bottom of the page, click on either the green ‘YES, I AGREE TO REVIEW THIS PREPRINT’ button, or the orange ‘NO THANKS, I’D RATHER NOT’ button.

To read a preprint/preregistration after agreeing to review it

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS' —> 'YOUR REVIEWS' in the top menu.
3) You can read the preprint/preregistration by clicking on the blue hyperlink to the digital object identifier (DOI) in the line corresponding to the preprint considered.

To write, edit or upload your review

1) Go to https://ecology.peercommunityin.org/ and log in
2) Go to 'YOUR CONTRIBUTIONS'->'YOUR REVIEWS' in the top menu
3) Click on the black 'VIEW/EDIT' button at the right end corresponding to the preprint concerned.
4) Click on the black 'WRITE, EDIT OR UPLOAD YOUR REVIEW' button at the bottom right.
5) You can now write, modify or upload your review.
-You can save a draft version of your review by clicking on the blue 'SAVE' button (you will then have to go through steps 0 to 4 to complete your review).
-When you have written or uploaded your review, click on the green 'SAVE & SUBMIT YOUR REVIEW' button. Your review is not considered to be complete until you have clicked on this button.