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Agent E2 - Qualitative Coding Specialist - Systematic coding and theme development. Covers codebook development, coding strategies, saturation assessment, and CAQDAS guidance.

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auto-empirical-research-skills
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$ npx -y skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill e2 --agent claude-code

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Agent E2 - Qualitative Coding Specialist - Systematic coding and theme development. Covers codebook development, coding strategies, saturation assessment, and CAQDAS guidance.

SKILL.md

e2.SKILL.md
name: e2
description: |
  Agent E2 - Qualitative Coding Specialist - Systematic coding and theme development.
  Covers codebook development, coding strategies, saturation assessment, and CAQDAS guidance.
version: "12.0.1"

⛔ Prerequisites (v8.2 — MCP Enforcement)

`diverga_check_prerequisites("e2")` → must return `approved: true` If not approved → AskUserQuestion for each missing checkpoint (see `.claude/references/checkpoint-templates.md`)

Checkpoints During Execution

  • 🟠 CP_CODING_APPROACH → `diverga_mark_checkpoint("CP_CODING_APPROACH", decision, rationale)`
  • 🟠 CP_THEME_VALIDATION → `diverga_mark_checkpoint("CP_THEME_VALIDATION", decision, rationale)`

Fallback (MCP unavailable)

Read `.research/decision-log.yaml` directly to verify prerequisites. Conversation history is last resort.

---

E2: Qualitative Coding Specialist

Role

Expert in systematic qualitative data coding, codebook development, theme identification, and saturation assessment. Guides researchers through rigorous coding processes for thematic analysis, grounded theory, and content analysis.

Core Capabilities

1. Codebook Development Approaches

Deductive (A Priori) Coding

**When to Use:**

  • Literature-driven research
  • Theory-testing studies
  • Structured content analysis
  • Pre-defined frameworks (e.g., SDT, TPB)

**Process:**

deductive_coding:
  step_1_literature_review:
    action: "Extract key constructs from theoretical framework"
    output: "Initial code list with definitions"

  step_2_operationalization:
    action: "Define codes with inclusion/exclusion criteria"
    output: "Structured codebook"

  step_3_pilot_coding:
    action: "Test codebook on 10-20% of data"
    output: "Refined codebook"

  step_4_reliability_check:
    action: "Calculate inter-rater reliability (Kappa)"
    output: "Reliability metrics, codebook adjustments"

**Example Deductive Codebook (Self-Determination Theory):**

code: "autonomy_support"
definition: "Teacher actions that support student self-direction and choice"
when_to_use:
  - "Teacher offers choices"
  - "Teacher solicits student input"
  - "Teacher acknowledges feelings"
when_not_to_use:
  - "Teacher gives commands without rationale"
  - "Generic praise without choice element"
example_quotes:
  - "The teacher said 'you can choose to work alone or in pairs'"
  - "She asked us what topics we wanted to explore"
related_codes: ["autonomy_thwarting", "intrinsic_motivation"]
parent_theme: "motivational_climate"

Inductive (Emergent) Coding

**When to Use:**

  • Exploratory research
  • Phenomenological studies
  • Grounded theory
  • Under-researched phenomena

**Process:**

inductive_coding:
  phase_1_open_coding:
    approach: "Line-by-line, no preconceptions"
    output: "100-200 initial codes"

  phase_2_axial_coding:
    approach: "Group codes by similarity, identify patterns"
    output: "30-50 focused codes"

  phase_3_selective_coding:
    approach: "Identify core categories and relationships"
    output: "8-15 themes with subthemes"

**Example Inductive Code Evolution:**

evolution:
  open_codes:
    - "student_mentions_chatbot_patience"
    - "student_appreciates_no_judgment"
    - "student_feels_safe_making_errors"

  focused_code: "psychological_safety"

  theme: "non-judgmental_learning_environment"

  definition: "Learners perceive AI chatbot as safe space for practice without fear of negative evaluation"

Hybrid (Deductive + Inductive)

**Best Practice for Social Science:**

hybrid_approach:
  step_1: "Start with literature-derived codes (deductive)"
  step_2: "Remain open to emergent codes (inductive)"
  step_3: "Track code sources (deductive vs. emergent)"
  step_4: "Report both a priori and emergent themes"

  example:
    deductive_codes: ["engagement", "motivation", "self-efficacy"]
    emergent_codes: ["technical_frustration", "privacy_concern", "gamification_appeal"]

2. Coding Strategies by Methodology

Thematic Analysis (Braun & Clarke, 2006)

**Six-Phase Process:**

phase_1_familiarization:
  activities:
    - "Read and re-read entire dataset"
    - "Note initial ideas and patterns"
    - "Highlight interesting passages"
  tools: ["Annotation software", "Memo writing"]
  output: "Annotated transcripts, research journal notes"
  time_estimate: "20-30% of total coding time"

phase_2_initial_coding:
  activities:
    - "Systematic line-by-line coding"
    - "Create code labels"
    - "Organize data extracts by code"
  tools: ["CAQDAS", "Excel", "Index cards"]
  output: "Initial codebook (50-150 codes typical)"
  quality_check:
    - "Every data item coded"
    - "Data extracts retain context"
    - "Codes are specific enough to be meaningful"

phase_3_theme_searching:
  activities:
    - "Collate codes into potential themes"
    - "Mind mapping of relationships"
    - "Create theme tables"
  techniques:
    - "Post-it note sorting"
    - "Mind maps"
    - "Thematic tables"
  output: "Candidate themes (8-15 typical)"

phase_4_theme_review:
  level_1_review:
    action: "Check themes against coded data extracts"
    criteria: "Internal homogeneity (coherence within theme)"
  level_2_review:
    action: "Check themes against entire dataset"
    criteria: "External heterogeneity (distinction between themes)"
  output: "Refined themes, thematic map"

phase_5_theme_defining:
  activities:
    - "Name each theme"
    - "Write theme descriptions (2-3 paragraphs)"
    - "Identify essence of each theme"
    - "Define subthemes if needed"
  output:
    - "Final theme definitions"
    - "Thematic structure"
  quality_criteria:
    - "Theme names are concise and informative"
    - "Definitions capture unique contribution"
    - "No significant overlap between themes"

phase_6_report_writing:
  activities:
    - "Select vivid quotations"
    - "Write analytic narrative"
    - "Link themes to research question"
    - "Situate findings in literature"
  output: "Fi
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