Method Writing

Source: https://github.com/aipoch/medical-research-skills

When to Use

Use this skill when you need to:

1. Draft or substantially revise the Methods section of a scientific manuscript to make the study reproducible.
2. Align a manuscript with IMRAD conventions and ensure the Methods content matches what is reported in Results.
3. Ensure compliance with study-type reporting guidelines (e.g., CONSORT for RCTs, STROBE for observational studies, PRISMA for systematic reviews/meta-analyses).
4. Prepare a submission for a specific journal with strict formatting, word limits, and required declarations (ethics, funding, data availability).
5. Address reviewer comments about missing methodological detail, unclear procedures, or insufficient statistical reporting.

Key Features

• Reproducible Methods prose: Produces fluent paragraph-based Methods text suitable for final manuscripts (not bullet lists).
• IMRAD-compatible structure: Organizes Methods content into standard subsections (design, setting, participants/samples, procedures, outcomes, statistics, ethics).
• Guideline-driven completeness: Maps content to reporting checklists (CONSORT/STROBE/PRISMA and others) to reduce omissions.
• Experimental and procedural specificity: Captures materials, equipment, calibration, conditions, controls, replicates, and step-by-step procedures.
• Statistical transparency: Specifies assumptions, tests, effect sizes, confidence intervals, multiple-comparison control, missing-data and outlier handling.
• Data management and integrity: Documents collection formats, preprocessing, storage, access control, anonymization, and compliance constraints.
• Field-specific terminology: Applies discipline conventions (biomedical, molecular biology, chemistry/pharma, neuroscience) and consistent nomenclature.
• Journal tailoring: Adapts wording and required declarations to match author guidelines and editorial expectations.

Reference materials (optional, if present in the repository):

• references/imrad_structure.md
• references/reporting_guidelines.md
• references/writing_principles.md

Dependencies

• None (documentation/writing skill; no runtime dependencies).

Example Usage

Input (what you provide)

Study context

• Design: randomized, double-blind, placebo-controlled trial
• Setting: single academic hospital, 2023-2024
• Participants: adults 18-65 with condition X; key inclusion/exclusion criteria
• Intervention: Drug A 50 mg daily vs placebo for 8 weeks
• Outcomes: primary outcome Y at week 8; secondary outcomes Z1-Z3
• Randomization/blinding: block randomization (block size 4), allocation concealment via central web system
• Sample size: power 0.8, alpha 0.05, expected effect size d=0.5
• Statistics: intention-to-treat; mixed-effects model; Holm correction; report Cohen's d and 95% CI
• Ethics: IRB approval ID; written informed consent
• Data handling: de-identified dataset; stored on encrypted server; access limited to study team

Target constraints

• Journal: requires CONSORT adherence and structured Methods subsections
• Style: full paragraphs only; define abbreviations at first use

Output (a runnable Methods section draft)

Methods

Study design and oversight. We conducted a randomized, double-blind, placebo-controlled, parallel-group trial to evaluate the efficacy of Drug A compared with placebo over 8 weeks. The protocol was approved by the Institutional Review Board of [Institution] (approval ID: [ID]). All participants provided written informed consent before any study procedures were performed.

Participants. Adults aged 18-65 years with a diagnosis of condition X were recruited from [clinic/service] between [month year] and [month year]. Key inclusion criteria were [criterion 1], [criterion 2], and [criterion 3]. Key exclusion criteria were [criterion 1], [criterion 2], and current use of [medication/class] within [time window]. Eligibility was confirmed by [assessment method], and baseline characteristics were collected at enrollment.

Randomization and blinding. Participants were assigned in a 1:1 ratio to Drug A or placebo using computer-generated block randomization with a fixed block size of 4. Allocation concealment was implemented through a centralized web-based randomization system accessible only to the study pharmacist. Participants, investigators, outcome assessors, and statisticians remained blinded to group assignment until database lock.

Intervention and procedures. Participants in the intervention group received Drug A 50 mg orally once daily for 8 weeks; the control group received a matching placebo on the same schedule. Study medication was dispensed at baseline and week 4, and adherence was assessed by pill count and participant diary. Concomitant treatments were permitted only if stable for at least [duration] before enrollment and unchanged during follow-up. Safety was monitored at each visit by adverse-event assessment and [laboratory/clinical measures], with severity graded using [standard].

Outcomes. The primary outcome was outcome Y measured at week 8 using [instrument/scale], where higher scores indicate [direction]. Secondary outcomes included Z1-Z3 assessed at baseline, week 4, and week 8 using [methods]. All outcomes were collected by trained assessors following a standardized operating procedure.

Sample size. The planned sample size was calculated to provide 80% power to detect a standardized mean difference of 0.5 in the primary outcome between groups at a two-sided alpha level of 0.05. Allowing for an anticipated attrition rate of [x%], we aimed to enroll [N] participants.

Statistical analysis. Analyses followed the intention-to-treat principle and included all randomized participants with available outcome data. The primary analysis used a linear mixed-effects model with fixed effects for treatment group, time, and their interaction, and a random intercept for participant to account for repeated measures. Model assumptions were assessed by inspection of residual plots and formal normality testing (Shapiro-Wilk). For secondary outcomes, p values were adjusted for multiple comparisons using the Holm method. Effect sizes are reported as Cohen's d with 95% confidence intervals (CIs) for continuous outcomes and as odds ratios (ORs) with 95% CIs for binary outcomes, as applicable. Missing data were handled using [complete-case analysis / multiple imputation], with sensitivity analyses performed under [assumption]. All tests were two-sided with a significance threshold of 0.05 after adjustment where applicable. Analyses were performed using [software, version].

Data management and availability. Data were recorded in [system], exported to [format], and stored on an encrypted institutional server with access restricted to authorized study personnel. Identifiers were removed and replaced with study codes prior to analysis. A data dictionary and analysis code are available at [repository/link] subject to [conditions], in accordance with [GDPR/HIPAA/other] requirements.

Implementation Details