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Structuring a paper

Describing your method so another researcher could repeat it

Enough detail to reproduce the study, plus a reason for every design decision you made.

A methodology section explains what you did and why it was the right way to answer your question. Give enough detail that another researcher could repeat the study — design, participants, materials, procedure, and analysis — and justify each decision rather than only reporting it. Write in past tense, and describe what you actually did.

THE PROCESS

Step by step

State the design and the logic behind it

Open by naming the design — experimental, longitudinal, ethnographic, comparative case study — and connecting it to your research question in a sentence. This paragraph orients everything that follows. A reader who knows the design can predict most of the section and will notice immediately if something does not fit.

Describe who or what you studied

Report the population, how you recruited or sampled from it, the final number, and the inclusion and exclusion criteria you applied. Give the demographic or contextual characteristics that plausibly affect the outcome, and account for attrition. Say how the sample size was decided, whether by power analysis, saturation, or practical constraint.

Specify materials, instruments, and measures

Name every instrument with its version, and cite validated scales rather than describing them from scratch. For equipment, give manufacturer and model where it affects the measurement. If you built or adapted an instrument, say what you changed and put the full version in an appendix.

Walk through the procedure in order

Narrate what happened from a participant’s point of view, in chronological order, including timing, setting, and sequence. This is the part a replicator reads most closely, so ambiguity here is expensive. Anything a competent researcher would have to guess belongs in this paragraph.

Explain how the data were analyzed

Name the analysis, the software with its version, and the assumptions you checked. State how you handled missing data, outliers, and multiple comparisons before you saw the results, if that is how it happened. For qualitative work, describe the coding approach, who coded, and how disagreements were resolved.

Record ethics, approvals, and consent

Give the approving body and the protocol number, and describe how consent was obtained and how identifying data were protected. Where the study was preregistered, cite the registration. One accurate paragraph here prevents a round of reviewer queries.

Report deviations honestly

Studies rarely run exactly as planned. Say where the executed protocol departed from the proposal or preregistration, and why. A stated deviation is a methodological detail; an unstated one that a reader detects from the results is a credibility problem.

Written for replication, read for credibility

The stated purpose of a methods section is reproducibility: a competent researcher in your field should be able to run your study from your description alone. That is the standard to write against, and it is a useful one because it is testable. Hand the draft to a colleague and ask which step they would have to guess at.

In practice, most readers are not replicating anything. They are deciding whether to believe your results, and the methods section is where they form that judgment. Vague sampling, an unnamed instrument, or an analysis chosen after the fact all register as reasons for caution, whatever the results say.

These two audiences pull in the same direction, which is convenient. Detail sufficient for replication is also detail sufficient for trust. Where they conflict — long procedural material that helps a replicator but slows a reader — the appendix or a supplementary file resolves it.

Justification is the part most drafts skip

The difference between an adequate methods section and a strong one is whether choices are explained. “Semi-structured interviews were conducted” tells a reader what happened. “Semi-structured interviews were chosen because the study needed comparability across participants while leaving room for practices the literature had not anticipated” tells them why, and pre-empts the obvious reviewer question.

Justify the decisions where a reasonable researcher could have chosen otherwise: the design, the sampling strategy, the instrument, the analysis, and the sample size. You do not need to defend routine steps such as randomizing trial order. A useful filter is to ask whether a reviewer might write “why this and not the alternative?” in the margin.

Justification does not mean claiming your method was optimal. Constraints are legitimate reasons, stated plainly: “a cross-sectional design was used because the cohort was only accessible during a single term” is honest and complete. The corresponding limitation then goes in the discussion, where a reader is already expecting it.

The standard order, and why it runs that way

Most methods sections move from design, to participants or materials, to procedure, to analysis, to ethics. The order is not arbitrary: it goes from the general frame to specific operations, so each subsection makes sense in light of the one before it. Readers scan for the subheadings, so use them even when the journal does not require them.

Field conventions vary in the details. Laboratory papers often separate Materials from Apparatus; qualitative work adds sections on researcher positionality and on trustworthiness; mixed-methods papers need an explicit statement of how the strands connect and in what sequence. Look at two recent papers in your target journal and follow their subheadings rather than inventing your own.

Keep results out of this section entirely. A sentence such as “participants performed better after training” belongs in the results, even when it appears while describing the procedure. The boundary is strict for a reason: it lets a reader evaluate the method before knowing what it produced.

  • Design — the approach and its fit with the question.
  • Participants or materials — who or what, how selected, how many.
  • Procedure — chronological, from the participant’s perspective.
  • Analysis — the tests or coding, plus software and assumptions.
  • Ethics — approval, consent, data protection, registration.

How much detail is enough

The threshold is functional, not a word count: include anything that would change the result if it were done differently. Room lighting rarely matters; the interval between training and testing usually does. When you are unsure, ask what you would want to know if you were reading someone else’s version of your study.

Standardized procedures can be cited rather than described. If you used a published protocol or a validated scale, one citation plus the details you changed is enough, and it is more useful than a paraphrase of the original paper. Reserve full description for anything you designed yourself.

Length problems in this section are usually structural. Move interview schedules, full item lists, and detailed coding frames to appendices or supplementary material, and keep the running text at the level a reader can follow in a single pass. Word limits are a reason to relocate detail, not to omit it.

Qualitative methods carry the same obligations

Qualitative sections sometimes get written as if the method were self-evident, with a sentence naming thematic analysis and nothing else. The same requirements apply: how participants were selected and why those people, how much data was collected, how coding proceeded, who did it, and how the analysis moved from codes to themes. Naming the specific tradition you are following, and citing it, does a lot of this work.

Trustworthiness needs its own treatment, since the checks differ from quantitative ones. Describe what you actually did — member checking, an audit trail, independent coding of a subset, negative case analysis — rather than asserting rigor in general terms. Where you claim saturation, say what told you it had been reached.

Positionality belongs here in many traditions, briefly and concretely. State the relationship between you and the setting and how it shaped access and interpretation. Two or three sentences that name a specific effect are worth more than a paragraph of general reflexive language.

Tense, voice, and person

Write the methods in past tense throughout, because the study is finished. The most common tense error is text carried over from a proposal, where the same material was necessarily in the future: “participants will complete two sessions” has to become “participants completed two sessions”. Search for “will” before submitting.

The active-versus-passive question is genuinely field-dependent. Many journals now prefer “we randomized participants to two conditions” for its clarity about who did what; others still expect the impersonal “participants were randomized”. Either is acceptable prose. Pick the one your target journal uses and apply it consistently rather than alternating.

Avoid the hybrid that appears in a lot of drafts: passive constructions with a hidden agent, such as “it was decided that the second measure would be dropped”. Decided by whom, and when? Naming the actor and the timing turns an evasive sentence into a methodological fact.

FAILURE MODES

What goes wrong, and what to do instead

Describing a choice without saying why you made it.

Add a clause of justification to each non-obvious decision — the design, the sample, the instrument, the analysis. One clause each is usually enough.

Leaving future tense in place from the proposal or preregistration.

Convert the whole section to past tense and search the text for “will” and “is going to” before submission.

Reporting the protocol you planned rather than the one you ran.

Describe what actually happened, including deviations, and explain them briefly. Reviewers treat a documented deviation as normal and an undocumented one as a red flag.

Naming software without a version, or a statistical test without its assumptions.

Give version numbers, and state which assumptions you checked and what you did when they were violated. This is what makes the analysis auditable.

Letting findings creep into the procedure paragraph.

Move any sentence containing an outcome into the results. The methods section should read the same whether the study worked or not.

For qualitative work, describing coding as though it happened by itself.

Say who coded, on what basis, how many coders were involved, and how disagreements were resolved. Cite the specific analytic tradition you followed.

Questions writers ask about this

What is the difference between methods and methodology?

Methods are the specific procedures — the sampling, instruments, and analysis. Methodology is the reasoning that makes those procedures appropriate for the question, including the epistemological position behind them. Journal articles usually label the section “Methods” and expect mostly procedure with brief justification; theses often require a longer “Methodology” chapter that argues for the approach itself.

What tense should the methodology section be in?

Past tense, because the work is complete: “participants were recruited”, “we analyzed the transcripts”. Present tense appears only for things that remain true regardless of your study, such as what an instrument measures. A proposal, by contrast, is written in future tense throughout — which is why converted proposals need a careful pass.

How long should a methods section be?

In a journal article, commonly 10 to 20 percent of the word count; in a thesis, a full chapter. Length is driven by how much a reader must know to reproduce the work, so a study using a standard published protocol will have a short section and a novel procedure a long one. Move bulky material to appendices rather than cutting it.

Should I use passive voice in the methods?

Only if your field does. Passive constructions such as “samples were incubated” remain standard in much of the natural sciences, while many social science and medical journals now prefer the active “we incubated the samples”. Both are correct English; the mistake is switching between them within a section.

Do I include ethics approval in the methods section?

Yes, unless the journal has a separate declarations section — check the author guidelines, because many now collect it at submission instead. Name the approving committee and the protocol number, and describe how informed consent was obtained and how identifying data were handled. Studies exempt from review should say so and state the basis for the exemption.

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