03 · What You Need to Know
What In-Principle Acceptance Protects and What It Does Not
What Exactly Does In-Principle Acceptance Mean?
In-principle acceptance is an editorial decision made after a Registered Report successfully completes Stage 1 peer review.
At that stage, the journal has evaluated the research question, theoretical or empirical rationale, proposed methodology, and intended analyses before the principal results are known.
The journal's commitment is based on the scientific value of the proposed investigation and the adequacy of its methods rather than the eventual direction or statistical significance of the findings.
Researchers then conduct the approved study and prepare a Stage 2 manuscript reporting what was done and what was found.
The distinctive feature of IPA is that the editorial decision concerning the study's scientific value is made prospectively. The final manuscript nevertheless remains subject to conditions established by the journal.
In-principle acceptance
A conditional commitment to publish a study that satisfies the approved protocol and the journal's Stage 2 requirements.
Final publication acceptance
The journal's decision to accept the completed manuscript after the relevant final review and editorial requirements have been satisfied.
What Does IPA Actually Protect Researchers Against?
The principal protection concerns publication decisions based on the direction or perceived attractiveness of the results.
Under conventional publication practices, studies reporting statistically significant, novel, or hypothesis-supporting findings may be more likely to attract editorial interest than studies producing null or unexpected results.
Registered Reports seek to reduce this form of publication bias by evaluating the research question and methods before the main findings are known.
Once IPA has been granted, a study should not lose its publication commitment merely because the results are statistically nonsignificant, contradict the original prediction, or appear less exciting than anticipated.
This protection is particularly valuable when the research question is important regardless of which plausible outcome occurs.
However, IPA does not guarantee that every possible result will be informative. The study must still be conducted and reported in a manner that supports defensible conclusions.
What Happens Between Stage 1 Acceptance and Final Publication?
The conventional Registered Report process involves two main stages of editorial evaluation, separated by study implementation.
Stage 1 review
The journal evaluates the research rationale, design, methods, and planned analyses before the principal results are known.
In-principle acceptance
The journal approves the proposed study subject to specified conditions. The accepted protocol becomes the reference against which subsequent implementation and reporting are evaluated.
Study implementation
Researchers conduct the investigation, document relevant decisions, and preserve records of consequential departures from the approved plan.
Stage 2 submission
The completed manuscript reports the methods actually used, results obtained, deviations from the approved protocol, and interpretation of the findings.
Stage 2 review and editorial decision
The journal evaluates compliance with the IPA conditions, the integrity of implementation and reporting, and whether the conclusions are justified.
Journals may differ in how they organize these stages, publish approved protocols, manage amendments, or conduct final review. Researchers should consult the specific journal's current policy rather than assume that every Registered Report follows identical procedures.
What Do Reviewers Evaluate at Stage 2?
Stage 2 review generally focuses on whether the completed study corresponds sufficiently to the approved Stage 1 protocol and whether the resulting manuscript provides an accurate account of the evidence.
Reviewers may examine whether the research procedures were implemented as approved, whether the planned analyses were reported, and whether consequential deviations have been disclosed and justified.
They also evaluate whether the results are presented accurately and whether the discussion avoids conclusions that exceed what the design and findings can support.
The distinction from Stage 1 peer review is important. Stage 1 establishes the prospective adequacy of the proposed investigation. Stage 2 examines the integrity and interpretation of its implementation.
Reviewers should not simply reconsider whether the study is interesting because the findings are unexpected or statistically nonsignificant.
Can a Registered Report Be Rejected Because Its Results Are Null?
Under the conventional Registered Report model, null results alone should not be grounds for rejection after IPA.
Suppose a carefully designed experiment finds no statistically significant difference between two interventions. If the approved methods were followed and the findings are reported appropriately, the absence of statistical significance should not invalidate the publication commitment.
Nevertheless, researchers must interpret the result in relation to its uncertainty and the study's ability to detect or estimate effects of substantive importance.
A nonsignificant result does not automatically demonstrate equivalence or the absence of an effect. Similarly, a statistically significant result does not guarantee that an effect is practically meaningful.
The principles for publishing null and unexpected findings are therefore closely connected to the purpose of IPA.
Can Unexpected or Opposite-Direction Findings Jeopardize Publication?
Unexpected findings should not, by themselves, jeopardize publication under the Registered Report model.
A hypothesis may predict a positive effect, while the observed estimate suggests a negative effect. Such findings may challenge the original theoretical explanation and provide important information.
The authors should report the approved analysis accurately and interpret the result according to the design, uncertainty, and relevant assumptions.
They should not rewrite the original hypothesis to make the finding appear predicted, nor should they selectively emphasize exploratory analyses that produce a more favorable interpretation.
Unexpected findings can motivate additional investigations. These should be distinguished from the analyses approved at Stage 1.
Which Problems Could Threaten Publication After IPA?
Although the precise grounds vary by journal, several categories of problems may affect the conditional publication commitment.
| Potential problem |
Why it matters |
Appropriate response |
| Major unexplained protocol deviation |
The completed study may no longer correspond to the approved design. |
Disclose the deviation, justify it, and consult the editor where required. |
| Failure to conduct approved primary analyses |
The principal confirmatory evaluation may be missing. |
Report the planned analyses when meaningful and explain any necessary departures. |
| Serious implementation failure |
The resulting evidence may not adequately address the approved question. |
Document the problem and assess whether the study remains interpretable. |
| Incomplete or selective reporting |
Readers cannot accurately evaluate the findings or protocol compliance. |
Provide complete reporting consistent with the journal's requirements. |
| Unsupported interpretation |
Conclusions may exceed what the evidence establishes. |
Revise claims to reflect the design, estimates, uncertainty, and limitations. |
| Research-integrity or ethical violations |
The integrity or legitimacy of the research may be compromised. |
Follow applicable institutional, journal, and regulatory procedures. |
These situations do not necessarily lead to automatic rejection. Their consequences depend on severity, timing, transparency, corrective action, and the journal's policies.
A minor, justified deviation should not be treated as equivalent to a fundamental failure to implement the approved study.
What If the Study Design Must Change After IPA?
Research implementation may reveal circumstances that were not anticipated during Stage 1 review.
Recruitment may proceed more slowly than expected, a measurement instrument may become unavailable, or a technical problem may require an alternative procedure.
Such changes do not automatically invalidate IPA. However, consequential revisions may require editorial consultation or approval before implementation.
The original protocol should remain identifiable, and the researchers should document the revised decision, its rationale, timing, and implications for the intended inference.
Changes made before relevant outcome information is examined generally raise different concerns from revisions selected after observing the results.
The appropriate response is examined in greater detail through changes to an approved Registered Report design.
Does IPA Protect Against Recruitment Failure?
Not automatically. A Registered Report may receive IPA on the basis of a particular sampling plan and its expected capacity to produce informative evidence.
If recruitment falls substantially below the approved target, the resulting study may have less statistical precision or power than anticipated.
The implications depend on the reason for the shortfall, the approved stopping rules, the achieved sample, and the journal's conditions.
For example, stopping at a prespecified recruitment deadline is different from stopping early because the interim results appear favorable.
Researchers should communicate serious recruitment problems promptly when required and explain their effects on the planned analyses.
The original sample-size justification and stopping rules provide an important reference for evaluating such departures.
Can Reviewers Demand New Analyses at Stage 2?
Reviewers may request additional analyses when they are needed to clarify reporting, evaluate assumptions, investigate methodological problems, or support an appropriate interpretation.
However, the Registered Report model is intended to protect the approved confirmatory analyses from being replaced merely because reviewers find the results uninteresting or inconsistent with expectations.
Additional analyses should be distinguished from those prospectively approved at Stage 1.
For example, a reviewer might reasonably request a sensitivity analysis examining the consequences of missing data. That analysis need not become a retrospectively declared primary test.
The treatment of exploratory analyses in Registered Reports is relevant when new questions arise during Stage 2 review.
Can a Journal Withdraw IPA?
In-principle acceptance is conditional, and journals may retain authority to withdraw the commitment under circumstances specified in their policies.
Potential grounds may include serious breaches of the approved protocol, research-integrity concerns, failure to meet essential conditions, or other substantial problems affecting the legitimacy or interpretability of the study.
Withdrawal should not be equated with ordinary disagreement about whether a null result is interesting. The purpose of the Registered Report model is to prevent the eventual findings from becoming the basis for reversing an otherwise valid prospective publication commitment.
Researchers should examine the journal's written conditions for IPA and retain the relevant editorial correspondence.
Watch Out
Do not interpret IPA as permission to depart freely from the approved protocol. A justified change may be acceptable, but consequential amendments should be communicated and documented according to the journal's requirements. Transparency alone does not guarantee that a substantially altered study will continue to satisfy the original acceptance conditions.
What Happens if the Journal Cannot Complete Publication?
Registered Reports involve commitments made by a particular journal, but circumstances such as journal closure, editorial restructuring, or changes in publication arrangements may complicate their fulfillment.
Policies concerning transfers, journal continuity, and the treatment of previously granted IPA vary. Researchers should not assume that an acceptance commitment automatically transfers to another publisher or journal.
If publication arrangements become uncertain, contact the journal or publisher and retain the original acceptance documentation.
A publicly accessible Stage 1 protocol or registration may help establish the history of the research, but it does not itself create an enforceable publication commitment from a different journal.
How Can Researchers Protect Their IPA Status?
The most practical approach is to treat the approved Stage 1 protocol as the reference document governing the study.
Maintain an accessible copy of the approved manuscript, analysis plan, editorial conditions, and relevant correspondence.
During implementation, document consequential decisions, monitor adherence to the approved procedures, and identify problems early enough to seek editorial guidance when necessary.
Before Stage 2 submission, compare the completed methods and analyses against the approved protocol. This should include outcomes, sampling, exclusions, statistical models, and any approved contingencies.
The purpose is not to conceal deviations or force inappropriate analyses. It is to ensure that the journal can evaluate what changed, why it changed, and whether the study still provides credible evidence.
