Researching includes a number of activities:
- Identifying the broader problem (significance)
- Identifying the knowledge gap
- Deciding on research questions
- Deciding how to carry out the study (methods rationale)
- Collecting data (methods procedure)
- Analysing and presenting data (methods/results)
Research decisions = Introduction & Methods
Note that these activities directly map onto the Introduction and Methods in a typical IMRaD paper.
Note taking
The best way to capture your research decisions is while you’re doing the research. That means keeping a journal where you keep track of decisions (e.g. daily), using a file versioning system, and documenting relentlessly.
Journal entries example (AI-generated)
- “2026-04-10, 14:30: Abandoned stratified sampling after discovering registry lacks demographic flags; switched to convenience sampling with quota caps (max 20 per clinic) to maintain variation control.”
- “Read Chen et al. (2025) 16:00: Realized current RQ ignores moderation effect they identified; added interaction term or gap remains unaddressed.”
- “Preliminary correlation r=0.04 suggests null; decided to split analysis by chronic vs. acute cases before abandoning hypothesis—checking for Simpson’s paradox.”
- “Equipment calibration failed 2026-04-08 09:00; switched to Protocol B (manual measurement), accepting ±2 mm precision loss for remaining n=15.”
- Considered propensity scoring but sample too small; retained covariate adjustment
But this is in an ideal world. However, as a relative beginner it’s difficult to know which decisions will matter, so more often than not, you need re-construct your reasoning. And in the case of the broader problem or even the knowledge gap, you may not even known yourself what the reasoning was — there a chance you simply ‘inherited’ the project and reasoning from your supervisor, without ever making these decisions yourself.
Prompted reconstructing
A helpful approach I find is to use freewriting with writing prompts to recover most of the reasoning. You set a timer for 10 minutes per prompt, and just write about that prompt.
Here are six prompts you can use to capture all the ideas that come up when you think through the key elements of your Introduction and Methods.
- Why does this study exist? (Introduction: Significance) Why was this research done at all? Why this topic, and what larger gap, problem, uncertainty, or poorly understood area in the field was it meant to contribute to?
- What was missing before this study? (Introduction: Knowledge gap) Before this work was done, what specific thing was still unknown, unclear, or untested within that larger problem?
- What did this study aim to learn or establish? (Introduction: Study aims/research questions) What exactly was this study trying to determine, test, or clarify? Finish the sentence: “This study asks what / whether / how / to what extent …”
- What did this study not attempt to cover? (Introduction: Study scope) What related questions or directions were intentionally left out of this paper, even if they are part of the broader project or field?
- Why was this approach appropriate? (Methods: Rationale) Why was this particular approach chosen for this study? What made it a reasonable or practical way to address the question, given the constraints?
- How did you collect and analyse the data? (Methods: Procedure) Which variables did you measure, how did you measure them, what tools/methodologies/protocols/steps did you use? Where there any practical constraints?
Write more than you think you need.
Repetition and contradiction are actually helpful at this stage.
You may find that you still have gaps in your reasoning after doing this exercise. In that case, you can:
- Ask your supervisor or read the grant proposal (for the broader problem/broader knowledge gap)
- Carry out additional literature review (for the specific knowledge gap)
Research is not linear
You will likely find that you want to refine your research questions or conduct extra data analyses while you’re interpreting your findings. That’s normal and actually part of the research process.
See also: Two types of writing