Registered Reports

Author Guidelines for Registered Reports

A Registered Report is a form of empirical article offered at Nature Ecology & Evolution in which the methods and proposed analyses are pre-registered and peer reviewed prior to research being conducted. High quality protocols are provisionally accepted for publication before data collection commences. This format is designed to minimize publication bias and research bias in hypothesis-driven research, while also allowing the flexibility to conduct exploratory (unregistered) analyses and report serendipitous findings.

Overview of the process

Initial submissions will include a description of the key research question(s) and background literature, hypotheses, experimental procedures, analysis pipeline, a sampling plan (statistical power analysis or Bayesian equivalent), and pilot data (where applicable). Please use this template to prepare your Stage 1 submission.

Initial submissions will be assessed by the editorial team for strength of scientific advance and suitability for a broad, multidisciplinary audience. Those that meet our criteria will then be sent for in-depth peer review (Stage 1). Following review, the article will be either rejected, revised, or accepted in principle for publication. After acceptance in principle (AIP), the authors will proceed to conduct the study, adhering exactly to the peer-reviewed procedures. When the study is complete the authors will submit their finalised manuscript for re-review (Stage 2) and will upload their raw data, study materials, and computer code (if relevant) to a publicly accessible file-sharing service. Pending further peer review to ensure a sensible interpretation of the findings, the manuscript will be published regardless of the significance or direction of the results.

Stage 1: Initial manuscript submission

Nature Ecology & Evolution aims to publish research of outstanding significance. For this reason, the editors select only the most scientifically promising manuscripts for in-depth peer review. Stage 1 submissions should include the manuscript (details below) and a brief cover letter. Authors are welcome to submit presubmission enquires for advice on the likely suitability of a study as a Registered Report. However, please note that we cannot commit to sending a manuscript for in-depth review until a complete Stage 1 submission has been evaluated by the editors.

The Stage 1 cover letter should include:

A brief scientific case for consideration. The journal aims to publish research that represents a significant scientific advance and is of relevance to a broad, multidisciplinary audience. High-value replication studies are welcome in addition to novel studies.
A statement confirming that all necessary support (e.g. funding, facilities) and approvals (e.g. ethics) are in place for the proposed research. Note that manuscripts will be generally considered only for studies that are able to commence immediately; however authors with alternative plans are encouraged to contact the journal office for advice.
An anticipated timeline for completing the study if the initial submission is accepted.
A statement confirming that the authors agree to share their raw data, any digital study materials, and computer code (if relevant) for all published results.
A statement confirming that, following Stage 1 acceptance in principle, the authors agree to register their approved protocol on a recognized repository, either publicly or under private embargo until submission of the Stage 2 manuscript.
A statement confirming that if the authors later withdraw their paper, they agree to the Journal publishing a short summary of the pre-registered study under a section Withdrawn Registrations.

Manuscript preparation guidelines - Stage 1

Initial Stage 1 submissions should include the sections listed below. More detail for the contents of each section can be found in the template document .

Introduction

Methods

Ethics information (if relevant for studies with humans or animals)
Pilot data (optional)
Study design (with information on controls, randomization, and blinding, if relevant)
Sampling plan (containing a power analysis where possible)
Analysis plan (full details of data preprocessing and analytical steps)

Data Availability

Code Availability

References

Figures (optional but encouraged)

Table of hypotheses (mandatory)

Peer Review of Stage 1 submissions

In considering papers at the registration stage, reviewers will be asked to assess:

The importance of the research question(s) and relevance for a broad, multidisciplinary audience.
The extent to which the proposed study can satisfactorily answer the research question(s).
The logic, rationale, and plausibility of the proposed hypotheses.
The soundness and feasibility of the methodology and analysis pipeline (including statistical power analysis where appropriate).
Whether the clarity and degree of methodological detail is sufficient to exactly replicate the proposed experimental procedures and analysis pipeline.
Whether the authors have pre-specified sufficient outcome-neutral tests for ensuring that the results obtained are able to test the stated hypotheses, including positive controls and quality checks.

Following Stage 1 peer review, manuscripts will be rejected outright, offered the opportunity to revise, or accepted in principle.

Any deviation from the stated experimental procedures, regardless of how minor it may seem to the authors, could lead to rejection of the manuscript at Stage 2. In cases where the pre-registered protocol is altered after AIP due to unforeseen circumstances (e.g. change of equipment or unanticipated technical error), the authors must consult the editors immediately for advice, and prior to the completion of data collection. Minor changes to the protocol may be permitted according to editorial discretion. In such cases, AIP would be preserved and the deviation reported in the Stage 2 submission. If the authors wish to alter the experimental procedures more substantially following AIP but still wish to publish their article as a Registered Report then the manuscript must be withdrawn and resubmitted as a new Stage 1 submission. Note that registered analyses must be undertaken, but additional unregistered analyses can also be included in a final manuscript (see below).

Stage 2: Full manuscript submission

Once the study is complete, authors prepare and resubmit their manuscript for full review, with the following additions:

The Stage 2 cover letter must confirm:

That the manuscript includes a link to the public archive containing anonymized study data, digital materials/code and the laboratory log. Within the manuscript, this information should appear in two separate sections, entitled ‘Data availability’ and ‘Code availability’.
That the manuscript contains a link to the approved Stage 1 protocol in a standalone section entitled ‘Protocol Registration’.
That, for primary Registered Reports, no data for any pre-registered study (other than pilot data included at Stage 1) was collected prior to the date of AIP. For secondary Registered Reports, authors should confirm that no data (other than pilot data included at Stage 1) was subjected to the pre-registered analyses prior to AIP.

Submission of raw data:

Anonymized raw data, processed data, and computer code (if relevant) must be made freely available in a public repository. Authors are free to use any repository that renders data and materials freely and publicly accessible and provides a digital object identifier (DOI) to ensure that the data remain persistent, unique and citable.
Data files ideally will be time stamped to show that data was collected after AIP and not before. Other than pre-registered and approved pilot data, no data acquired prior to the date of AIP is admissible in the Stage 2 submission. Raw data must be accompanied by guidance notes or meta-data to assist other scientists in replicating the analysis pipeline. Authors are also expected to upload any relevant analysis scripts and other experimental materials that would assist in replication.
Supplementary figures, tables, or other text (such as supplementary methods) should be included as standard supplementary information that accompanies the paper. The raw data itself should be archived (see above) rather than submitted to the journal as supplementary material.
The Stage 2 manuscript must also contain a link to the registered protocol (deposited following AIP) in a standalone section entitled ‘Protocol Registration’.

Disallowed revisions:

Apart from minor stylistic revisions, the Introduction cannot be altered from the approved Stage 1 submission, and the stated hypotheses cannot be amended or appended. At Stage 2, any description of the rationale or proposed methodology that was written in future tense within the Stage 1 manuscript should be changed to past tense. Any textual changes to the Introduction or Methods (e.g. correction of typographic errors) must be clearly marked in the Stage 2 submission. Any relevant literature that appeared following the date of AIP should be covered in the Discussion.

Results & Discussion:

The outcome of all registered analyses must be reported in the manuscript, except in rare instances where a registered and approved analysis is subsequently shown to be logically flawed or unfounded. In such cases, the authors, reviewers, and editor must agree that a collective error of judgment was made and that the analysis is inappropriate. In such cases the analysis would still be mentioned in the Methods but omitted with justification from the Results.
It is reasonable that authors may wish to include additional analyses that were not included in the registered submission. For instance, a new analytic approach might become available between AIP and Stage 2 review, or a particularly interesting and unexpected finding may emerge. Such analyses are admissible but must be clearly justified in the text, appropriately caveated, and reported in a separate section of the Results titled “Exploratory analyses”. Authors should be careful not to base their conclusions entirely on the outcome of statistically significant post hoc analyses.
Authors reporting null hypothesis significance tests are required to report exact p values, effect sizes and confidence intervals for all inferential analyses.

Peer Review of Stage 2 submissions

The resubmission will most likely be considered by the same reviewers as in Stage 1, but could also be assessed by new reviewers. In considering papers at Stage 2, reviewers will be asked to decide:

Whether the data are able to test the authors’ proposed hypotheses by satisfying the approved outcome-neutral conditions (such as quality checks, positive controls)
Whether the Introduction, rationale and stated hypotheses are the same as the approved Stage 1 submission (required)
Whether the authors adhered precisely to the registered experimental procedures
Whether any unregistered post hoc analyses added by the authors are justified, methodologically sound, and informative
Whether the authors’ conclusions are justified given the data

Reviewers are informed that editorial decisions will not be based on the perceived importance, novelty or conclusiveness of the results. Thus while reviewers are free to enter such comments on the record, they will not influence editorial decisions. Reviewers at Stage 2 may suggest that authors report additional post hoc tests on their data; however authors are not obliged to do so unless such tests are necessary to satisfy one or more of the Stage 2 review criteria.

Manuscript withdrawal

It is possible that authors with AIP may wish to withdraw their manuscript following or during data collection. Possible reasons could include major technical error, an inability to complete the study due to other unforeseen circumstances, or the desire to submit the results to a different journal. In all such cases, manuscripts can of course be withdrawn at the authors’ discretion. However, the journal will publicly record each case in a section called Withdrawn Registrations. This section will include the authors, proposed title, the abstract from the approved Stage 1 submission, and brief reason(s) for the failure to complete the study. Partial withdrawals are not possible; i.e. authors cannot publish part of a registered study by selectively withdrawing one of the planned experiments. Such cases must lead to withdrawal of the entire paper. Studies that are not completed by the agreed Stage 2 submission deadline (which can be extended in negotiation with the editorial office) will be considered withdrawn and will be subject to a Withdrawn Registration.

Reviewer Guidelines for Registered Reports

The review process for Registered Reports is divided into two stages. At Stage 1, reviewers assess study proposals before data are collected. At Stage 2, reviewers consider the full study, including results and interpretation.

Stage 1 manuscripts will include only an Introduction, Methods (including proposed analyses), and Pilot Data (where applicable). In considering papers at Stage 1, reviewers will be asked to assess:

The importance of the research question(s) and relevance for a broad, multidisciplinary audience
The extent to which the proposed study can satisfactorily answer the research question(s)
The logic, rationale, and plausibility of the proposed hypotheses
The soundness and feasibility of the methodology and analysis pipeline (including statistical power analysis)
Whether the clarity and degree of methodological detail would be sufficient to replicate exactly the proposed experimental procedures and analysis pipeline
Whether the authors provide a sufficiently clear and detailed description of the methods to prevent undisclosed flexibility in the experimental procedures or analysis pipeline
Whether the authors have considered sufficient outcome-neutral conditions (e.g. absence of floor or ceiling effects; positive controls) for ensuring that the results obtained are able to test the stated hypotheses.

Following Stage 1 peer review, manuscripts will be accepted, offered the opportunity to revise, or rejected outright. Manuscripts that pass peer review will be issued an acceptance in principle (AIP), indicating that the article will be published pending successful completion of the study according to the pre-registered methods and analytic procedures, as well as a defensible and evidence-based interpretation of the results.

Following completion of the study, authors will complete the manuscript, including Results and Discussion sections. These Stage 2 manuscripts will more closely resemble a regular article format. The manuscript will then be returned to the reviewers, who will be asked to appraise:

Whether the data can test the authors’ proposed hypotheses by satisfying the approved outcome-neutral conditions (such as quality checks, positive controls)
Whether the Introduction, rationale and stated hypotheses are the same as the approved Stage 1 submission (required)
Whether the authors adhered precisely to the registered experimental procedures
Whether any unregistered post hoc analyses added by the authors are justified, methodologically sound, and informative
Whether the authors’ conclusions are justified given the data

Reviewers at Stage 2 may suggest that authors report additional post hoc tests on their data; however authors are not obliged to do so unless such tests are necessary to satisfy one or more of the Stage 2 review criteria. Please note that editorial decisions will not be based on the perceived importance, novelty, or conclusiveness of the results.