Data Scientist

Data Scientist Skill

Rigorous data science methodology and mindset for Python research. Covers EDA, data validation, transformation verification, documentation standards, visualization design, descriptive analysis, statistical modeling, causal inference method selection (IV, DiD, RD, synthetic control), unsupervised analysis (clustering, PCA, UMAP), supervised ML methodology (prediction vs. inference, cross-validation, model interpretation, fairness), and geospatial analysis. Provides methodology decisions and analytical approach guidance. For implementation syntax, load the tool-specific skill (polars, statsmodels, plotnine, pyfixest, scikit-learn, geopandas, etc.). Use for any data analysis, exploration, transformation, or modeling task — especially when choosing methods, checking assumptions, or structuring an analysis.

Establishes a rigorous, methodical approach to data science work. This skill is about how to think and work, not specific tools. Load specialized skills (polars, plotnine, plotly, marimo, etc.) for tool-specific guidance.

Core Principles - NON-NEGOTIABLE

These five principles must guide ALL data science work. They are not optional.

Principle 1: Data Robustness First

ALWAYS check data before operating on it.

Before ANY analysis or transformation:

• Check shape, types, and memory usage
• Examine value distributions and ranges
• Identify and characterize missing values (count, percentage, pattern)
• Understand what uniquely identifies each row (granularity)
• Look for outliers and anomalies

Be VERBOSE about what you're checking and what you find. Never assume data is clean.

# ALWAYS start with this pattern
print(f"Shape: {df.shape}")
print(f"Columns: {df.columns.to_list()}")
print(f"Types:\n{df.dtypes}")
print(f"Null counts:\n{df.null_count()}")
print(f"Sample:\n{df.sample(5)}")

This principle applies only when you are conducting actual data work. Do NOT conduct net new analyses or data inspections when tasked with compiling past work (e.g., analytic notebook creation), or synthesizing prior analyses into a report (e.g., final report writing).

Principle 2: Documentation First

ALWAYS understand or create data documentation.

Before analysis:

• Seek data dictionaries, schemas, or documentation
• Understand where data comes from (provenance)
• Learn collection methods and their implications
• Identify known quality issues or caveats
• Clarify what each column means in business context

If documentation doesn't exist, CREATE IT as you learn about the data.

Principle 3: Verify Every Operation

NEVER assume a transformation worked correctly.

For EVERY data operation:

• Check row counts before and after
• Examine random samples of affected rows
• Validate that expected changes occurred
• Confirm no unintended side effects
• Document what you checked and what you found

# Before transformation
print(f"Before: {len(df)} rows, columns: {df.columns.to_list()}")
sample_before = df.filter(pl.col("id").is_in([1, 42, 100]))

# After transformation
print(f"After: {len(result)} rows, columns: {result.columns.to_list()}")
sample_after = result.filter(pl.col("id").is_in([1, 42, 100]))
print(f"Sample comparison:\nBefore:\n{sample_before}\nAfter:\n{sample_after}")

Principle 4: Thorough Code Documentation (ENFORCED)

Write extensive comments explaining your reasoning. This is MANDATORY, not optional.

In research workflows, follow the Inline Audit Trail (IAT) standard (see agent_reference/INLINE_AUDIT_TRAIL.md). The IAT standard is enforced during QA review — scripts with sparse documentation receive WARNING findings.

Every code block should explain:

• WHAT you're trying to accomplish (the goal) → IAT Type 2: Intent Comment
• WHY you chose this approach (the reasoning) → IAT Type 3: Reasoning Comment
• WHAT assumptions you're making (the dependencies) → IAT Type 4: Assumption Comment

For tests and validations, explain:

• What behavior you're checking
• What would indicate success vs. failure
• Why this check matters

Principle 5: Focus on Research Questions

Balance rigor with usefulness.

Always consider:

• What question are we actually answering?
• What level of rigor does this decision require?
• Are there multiple valid approaches with different tradeoffs?
• Should I check with the user before proceeding?

CHECK IN with users when:

• Multiple valid methodologies exist
• Tradeoffs between precision and practicality arise
• Findings are surprising or counterintuitive
• Scope might need adjustment

Related Skills - When to Load

Core Workflow Skills (Load Together):

• polars - Required for DataFrame operations; data-scientist provides methodology, polars provides syntax
• marimo - Required for creating validated notebooks; data-scientist defines validation patterns, marimo provides implementation

For Data Analysis Workflows:

In the research pipeline, data-scientist methodology is applied within the file-first execution pattern:

• Write script files FIRST (to scripts/stage{N}_{type}/)
• Execute via Bash with automatic output capture wrapper script
• Validation results get automatically embedded in scripts as comments
• Marimo notebook assembles validated scripts for interactive review

Closely read agent_reference/SCRIPT_EXECUTION_REFERENCE.md for the mandatory file-first execution protocol covering complete code file writing, output capture, and file versioning rules.

Load for Specific Needs:

What task are you performing?
├─ Data visualization (any kind)
│   └─ Stage 8.2 — FIRST read visualization reference files below:
│       ├─ ./references/visualization-design.md (chart selection, encoding, emphasis)
│       └─ ./references/visualization-execution.md (color, labeling, accessibility, export)
│       THEN load the tool-specific skill:
│       ├─ Static plots → Load `plotnine` skill for grammar of graphics
│       └─ Interactive plots → Load `plotly` skill for interactive charts
├─ Descriptive analysis (subgroups, distributions, decompositions, trends)
│   └─ Stage 8.1 — FIRST read ./references/descriptive-analysis.md
│       THEN use polars for implementation (some methods may also need
│       `statsmodels` for weighted SEs/formal tests or `pyfixest` for descriptive FE regressions)
├─ Statistical modeling (regression, robustness checks)
│   └─ Stage 8.1 — FIRST read ./references/statistical-modeling.md
│       THEN load library skill:
│       ├─ Standard regression (OLS, logistic, GLM) → Load `statsmodels` skill
│       │   (Note: for OLS with clustered SEs, prefer `pyfixest` — native cluster support)
│       ├─ Fixed effects, IV with FE, or DiD → Load `pyfixest` skill
│       ├─ Random effects, between, first difference, Fama-MacBeth → Load `linearmodels` skill
│       ├─ IV without FE (LIML, GMM) → Load `linearmodels` skill
│       ├─ System estimation (SUR, 3SLS) → Load `linearmodels` skill
│       └─ Spatial regression (spatial lag, spatial error, GWR) → Load `geopandas` skill
│           (spatial regression uses PySAL/spreg via geopandas; also read geospatial refs)
├─ Supervised ML (prediction, classification, risk scoring)
│   ├─ Methodology (when to use ML, how to validate, interpret, report)
│   │   → Read supervised-ml.md
│   ├─ Implementation (algorithms, syntax, evaluation)
│   │   → Load `scikit-learn` skill
│   ├─ Model interpretation (SHAP, feature importance)
│   │   → Read supervised-ml.md "Interpreting ML Models" + scikit-learn interpretation.md
│   └─ Fairness assessment
│       → Read supervised-ml.md "Fairness" + scikit-learn fairness.md
├─ Unsupervised analysis (clustering, dimensionality reduction, pattern discovery)
│   └─ Stage 8.1 — FIRST read ./references/exploratory-unsupervised.md
│       THEN load `scikit-learn` skill for implementation
│       ├─ Clustering → clustering.md, evaluation-unsupervised.md
│       ├─ Dimensionality reduction → decomposition.md, manifold.md
│       └─ Index construction via PCA → also read ./references/descriptive-analysis.md
├─ Causal / quasi-experimental analysis
│   └─ FIRST read ./references/causal-inference.md
│       THEN load appropriate library skill (pyfixest for DiD/IV/FE, linearmodels for panel RE/IV-GMM, statsmodels for RD/matching)
├─ Complex survey data analysis (NHANES, ACS PUMS, CPS, ECLS-K, MEPS, etc.)
│   └─ FIRST read ./references/survey-analysis.md (methodology, pitfalls, weight selection)
│       THEN load `svy` skill for implementation syntax
│       ├─ Survey-weighted descriptive statistics → svy estimation.md
│       ├─ Survey-weighted regression (OLS, logistic, Poisson) → svy regression.md
│       ├─ Survey design setup / replicate weights → svy design-weights.md
│       └─ Advanced models not in svy (ordinal, survival, IV) → rpy2 + R survey package
│           (see svy skill "rpy2 Bridge" section)
├─ Communicating to non-technical audiences
│   └─ Load `science-communication` skill
├─ Geospatial / spatial analysis (any kind)
│   └─ FIRST read methodology reference files:
│       ├─ ./references/geospatial-analysis.md (spatial thinking, methods, interpretation)
│       └─ ./references/geospatial-operations.md (joins, weights, interpolation, operations)
│       THEN load `geopandas` skill for implementation syntax
├─ Not currently covered by DAAF skills:
│   ├─ Bayesian modeling (PyMC, bambi) → escalate to orchestrator
│   ├─ Survival / time-to-event analysis → escalate to orchestrator
│   └─ Deep learning (PyTorch, TensorFlow) → escalate to orchestrator

Visualization loading order matters: The reference files provide design principles (what chart to use, how to direct attention, how to handle color accessibly). The tool skills provide syntax (how to code it). Read the design guidance first so implementation choices are principled, not ad-hoc.

For Domain-Specific Analysis (e.g., CCD Education Data):

• Load relevant *-data-source-* skill first to understand domain-specific data caveats
• Then apply data-scientist methodology with that context

Prerequisite Knowledge: This skill assumes familiarity with:

• Python programming basics
• DataFrame concepts (rows, columns, filtering)
• Basic statistical concepts (mean, distribution, correlation)

Important: This skill provides the METHODOLOGY. The specialized skills provide TOOL KNOWLEDGE. Use both together.

Reference File Structure

Validation Tracking

For multi-step transformations, track validation state with a simple dict:

validation_log = {}

# After each transformation step:
validation_log["Filter to high schools"] = {
    "pre_rows": pre_rows,
    "post_rows": result.shape[0],
    "status": "PASSED" if result.shape[0] > 0 else "FAILED",
}

# Print summary at end:
for step, info in validation_log.items():
    print(f"  [{info['status']}] {step}: {info['pre_rows']:,} → {info['post_rows']:,}")

This is inline code, not a separate module. Never create a validation.py or import a validation class.

Quick Decision Trees

"I'm starting a new analysis"

Starting new analysis?
├─ Do I have data documentation?
│   ├─ Yes → Read it thoroughly first
│   │         → ./references/data-documentation.md
│   └─ No → Create it as you explore
│           → ./references/data-documentation.md
├─ Have I profiled the data?
│   └─ No → Run full EDA checklist
│           → ./references/eda-checklist.md
├─ Do I understand the research question?
│   └─ Unclear → Clarify with stakeholder
│                → ./references/research-questions.md
└─ Ready to analyze → Document as you go
                      → ./references/code-documentation.md

"I have unfamiliar data"

Unfamiliar data?
├─ Step 1: Basic inspection
│   └─ Shape, types, head/tail/sample
│      → ./references/eda-checklist.md
│      IF data contains geometry column, lat/lon, GEOID, or FIPS codes:
│      → also read ./references/geospatial-analysis.md
├─ Step 2: Understand granularity
│   └─ What does each row represent?
│   └─ What columns uniquely identify a row?
├─ Step 3: Check data quality
│   └─ Missing values, duplicates, outliers
│      → ./references/eda-checklist.md
├─ Step 4: Seek documentation
│   └─ Data dictionary, schema, provenance
│      → ./references/data-documentation.md
└─ Step 5: Document findings
    └─ Create documentation if none exists

"I need to transform data"

Transforming data?
├─ Before transformation:
│   ├─ Document current state (shape, sample)
│   ├─ Identify what SHOULD change
│   └─ Identify what should NOT change
│      → ./references/transformation-validation.md
├─ After transformation:
│   ├─ Verify shape changes are expected
│   ├─ Check random sample of results
│   ├─ Validate invariants (sums, counts)
│   └─ Document what you verified
│      → ./references/transformation-validation.md
└─ For joins specifically:
    ├─ Check for unintended row duplication
    ├─ Check for unintended data loss
    └─ Validate join keys match expectations

"I need to communicate findings"

Communicating findings?
├─ Have I documented limitations?
│   └─ No → List caveats and assumptions
│           → ./references/research-questions.md
├─ Am I making causal claims?
│   └─ Yes → Ensure justified; prefer correlational language
│            → ./references/research-questions.md
├─ Is uncertainty quantified?
│   └─ No → Add confidence intervals or ranges
└─ Have I checked in with stakeholder?
    └─ No → Validate findings align with expectations

"I need to create a visualization"

What kind of visualization task?
├─ Choosing what chart to make
│   └─ → ./references/visualization-design.md
├─ Directing attention / emphasis strategy
│   └─ → ./references/visualization-design.md
├─ Selecting colors or ensuring accessibility
│   └─ → ./references/visualization-execution.md
├─ Labeling, titling, or annotating
│   └─ → ./references/visualization-execution.md
├─ Making it publication-ready (export, DPI, fonts)
│   └─ → ./references/visualization-execution.md
├─ Ensuring project consistency (theme, palette)
│   └─ → ./references/visualization-execution.md
├─ Mapping geographic data (choropleth, dot density, proportional symbols)
│   └─ → ./references/geospatial-analysis.md (map design, classification)
│       THEN → ./references/visualization-execution.md (color, accessibility)
│       THEN load `geopandas` skill for implementation
└─ Tool-specific syntax (geoms, traces, themes)
    ├─ Static plots → Load `plotnine` skill
    └─ Interactive plots → Load `plotly` skill

"I need to analyze patterns in this data"

Am I trying to describe or explain?
├─ Describe (characterize what exists)
│   └─ → ./references/descriptive-analysis.md
│       ├─ Subgroup comparisons → Stratification section
│       ├─ Distribution shape → Distributional analysis section
│       ├─ Trends over time → Trend analysis section
│       ├─ Gaps between groups → Decomposition methods section
│       ├─ Composite measure → Index construction section
│       ├─ Inequality → Inequality measurement section
│       └─ Weighted estimates → Weighted analysis section
├─ Model (regression, hypothesis testing)
│   └─ → ./references/statistical-modeling.md
│       ├─ Choose model by outcome type → Model selection framework
│       ├─ Check assumptions → Assumption checking protocol
│       ├─ Choose standard errors → SE type decision table
│       └─ Interpret coefficients → Interpretation guide
└─ Explain causally
    └─ → ./references/causal-inference.md
        └─ Select method per Method Selection Guide

"I need to establish a causal relationship"

What variation identifies the causal effect?
├─ Random assignment → RCT analysis
│   → ./references/causal-inference.md
├─ I can control for all confounders → Regression / matching
│   → ./references/causal-inference.md
├─ There's a valid instrument → IV / 2SLS
│   → ./references/causal-inference.md
├─ There's a score cutoff → Regression discontinuity
│   → ./references/causal-inference.md
├─ Policy changed for some groups → Difference-in-differences
│   → ./references/causal-inference.md
├─ Few treated units, long pre-period → Synthetic control
│   → ./references/causal-inference.md
└─ Not sure → Start with a DAG
    → ./references/causal-inference.md

"I need to discover structure or groupings in data"

What kind of structure am I looking for?
├─ Groups of similar observations (typology, classification)
│   ├─ Know number of groups → K-means or GMM (scikit-learn)
│   ├─ Don't know number → Try multiple k + validation (scikit-learn)
│   ├─ Arbitrary shapes / noise → DBSCAN or HDBSCAN (scikit-learn)
│   └─ Uncertain → Read exploratory-unsupervised.md "Algorithm Selection" table
├─ Reducing a large variable set
│   ├─ Linear reduction → PCA (scikit-learn)
│   └─ Visualizing structure → t-SNE or UMAP (scikit-learn / umap-learn)
│       └─ CAUTION: visualization only — not for analysis
│           → ./references/exploratory-unsupervised.md
├─ Using unsupervised results in subsequent regression
│   └─ Read exploratory-unsupervised.md "The Classify-Analyze Problem"
└─ Predicting outcomes with ML methods
    └─ Load scikit-learn skill → classification.md or regression-ml.md

"I'm working with geographic/spatial data"

Geospatial analysis task?
├─ Understanding spatial concepts, methods, or statistical theory
│   └─ (MAUP, CRS, autocorrelation, spatial regression)
│       → ./references/geospatial-analysis.md
├─ Choosing a spatial analysis method
│   └─ → ./references/geospatial-analysis.md (decision guide)
├─ Performing spatial joins, overlays, or weights construction
│   └─ → ./references/geospatial-operations.md
│       THEN load `geopandas` skill for syntax
├─ Interpreting Moran's I, LISA, or spatial regression results
│   └─ → ./references/geospatial-operations.md (interpretation sections)
├─ Interpolation or areal interpolation
│   └─ → ./references/geospatial-operations.md
├─ Extracting raster values into polygons (zonal statistics)
│   └─ → ./references/geospatial-operations.md
├─ Debugging spatial operation failures or geometry errors
│   └─ → ./references/geospatial-operations.md (geometry validity)
├─ Making maps or choosing classification schemes
│   └─ → ./references/geospatial-analysis.md (map design)
│       THEN → ./references/visualization-execution.md (color, accessibility)
└─ Implementation syntax (geopandas, PySAL, rasterio)
    └─ Load `geopandas` skill

"I need to predict an outcome or classify observations"

Am I predicting or explaining?
├─ Explaining (estimating a causal or associational parameter)
│   └─ Use pyfixest or statsmodels — see statistical-modeling.md
├─ Predicting (minimizing prediction error on new data)
│   ├─ Read supervised-ml.md for methodology
│   ├─ Load scikit-learn skill for implementation
│   ├─ Tabular data → Start with logistic regression baseline,
│   │   then try HistGradientBoosting or LightGBM
│   ├─ Text data → See supervised-ml.md "When Deep Learning Methods Are Appropriate"
│   ├─ Need to explain predictions → scikit-learn interpretation.md (SHAP)
│   └─ Need fairness assessment → scikit-learn fairness.md
└─ Not sure → Read supervised-ml.md "Prediction vs. Inference"

Essential Workflows

New Data Workflow

When you receive new data, ALWAYS follow this sequence:

1. Load and inspect (do not transform yet)

   # Load data
   df = pl.read_csv("data.csv")  # or scan_csv for lazy
   
   # Immediate inspection
   print(f"Shape: {df.shape}")
   print(f"Columns: {df.columns}")
   print(f"Types:\n{df.dtypes}")
   print(f"First 5 rows:\n{df.head()}")
   print(f"Last 5 rows:\n{df.tail()}")
   print(f"Random sample:\n{df.sample(5)}")
   

2. Check data quality

   # Missing values
   print(f"Null counts:\n{df.null_count()}")
   print(f"Null percentages:\n{df.null_count() / len(df) * 100}")
   
   # Duplicates
   print(f"Duplicate rows: {len(df) - len(df.unique())}")
   
   # Unique values per column
   for col in df.columns:
       print(f"{col}: {df[col].n_unique()} unique values")
   

3. Understand distributions

   # Numerical columns
   print(df.describe())
   
   # Categorical columns - value counts
   for col in df.select(pl.col(pl.String)).columns:
       print(f"\n{col}:\n{df[col].value_counts().head(10)}")
   

4. Identify granularity

   # What uniquely identifies a row?
   # Test candidate keys
   candidate_keys = ["id", "user_id", ["user_id", "date"]]
   for key in candidate_keys:
       cols = [key] if isinstance(key, str) else key
       unique_count = df.select(cols).n_unique()
       print(f"{cols}: {unique_count} unique vs {len(df)} rows")
   

5. Document findings before proceeding

Transformation Workflow

For ANY data transformation:

1. Document pre-state

   # Record state before transformation
   pre_shape = df.shape
   pre_columns = df.columns.copy()
   pre_sample = df.sample(10, seed=42)  # Reproducible sample
   pre_sum = df.select(pl.col("amount").sum()).item()  # If applicable
   

2. Perform transformation with comments

   # GOAL: Filter to active users and calculate total spend
   # REASONING: We only want users who logged in within 30 days
   # EXPECTED: Fewer rows, same columns, preserved sum for included rows
   result = (
       df
       .filter(pl.col("last_login") > cutoff_date)  # Remove inactive
       .group_by("user_id")
       .agg(pl.col("amount").sum().alias("total_spend"))
   )
   

3. Validate post-state

   # Verify transformation results
   post_shape = result.shape
   print(f"Shape: {pre_shape} -> {post_shape}")
   
   # Check sample of results
   sample_ids = pre_sample["user_id"].to_list()[:3]
   print(f"Sample before:\n{pre_sample.filter(pl.col('user_id').is_in(sample_ids))}")
   print(f"Sample after:\n{result.filter(pl.col('user_id').is_in(sample_ids))}")
   
   # Validate invariants where applicable
   # (e.g., sum should be preserved or explainably different)
   

4. Document what you verified

Analysis Workflow

From question to answer:

1. Clarify the question

   • What decision will this inform?
   • What would a "good" answer look like?
   • What level of rigor is required?

2. Assess data fitness

   • Does the data contain what we need?
   • What are the limitations?
   • Are there gaps or quality issues?

3. Choose methodology

   • What approaches are valid?
   • What are the tradeoffs?
   • CHECK WITH USER if multiple valid options

4. Execute with verification

   • Follow transformation workflow
   • Document each step thoroughly

5. Validate findings

   • Do results make sense?
   • Cross-check with known facts
   • Identify limitations and caveats

6. Communicate with appropriate uncertainty

Quick Checklists

Initial Data Inspection Checklist

• Loaded data successfully
• Checked shape (rows x columns)
• Reviewed column names
• Checked data types
• Examined head, tail, and random sample
• Counted missing values per column
• Checked for duplicate rows
• Identified unique value counts per column
• Generated summary statistics
• Identified granularity (what uniquely identifies a row)
• Documented findings

Pre-Transformation Checklist

• Documented current shape and columns
• Saved sample of data for comparison
• Recorded relevant aggregates (sums, counts)
• Stated what SHOULD change
• Stated what should NOT change
• Explained WHY this transformation is needed

Post-Transformation Checklist

• Verified shape change matches expectations
• Compared sample before/after
• Validated invariants are preserved
• Checked for unintended nulls
• Checked for unintended duplicates
• Documented what was verified and results

Documentation Checklist

• Data source documented
• Each column defined
• Missing value conventions explained
• Granularity/unit of observation stated
• Known quality issues noted
• Transformation history recorded

Marimo Integration

When working in marimo notebooks:

Cell Organization Pattern

# Cell 1: Imports and setup
import marimo as mo
import polars as pl

# Cell 2: Data loading (separate cell for reactivity)
df = pl.read_csv("data.csv")

# Cell 3: Data inspection (markdown + code)
mo.md("## Data Inspection")
# ... inspection code ...

# Cell 4: Data quality checks
mo.md("## Data Quality")
# ... quality checks ...

# Cell 5+: Analysis cells, each with:
# - Markdown explaining goal
# - Code with thorough comments
# - Validation of results

Using Reactivity for Validation

# Create interactive validators
validation_column = mo.ui.dropdown(
    options=df.columns,
    label="Select column to validate"
)

# Reactive validation display
mo.md(f"""
### Validation for `{validation_column.value}`
- Null count: {df[validation_column.value].null_count()}
- Unique values: {df[validation_column.value].n_unique()}
- Sample values: {df[validation_column.value].head(5).to_list()}
""")

Documentation Cells

Use markdown cells liberally:

• Before code: explain what you're about to do and why
• After code: summarize findings and implications
• At decision points: document choices made

Topic Index

Citation Responsibility

When analytical methods from this skill's reference materials are used in DAAF analyses, the research-executor includes relevant citations in its structured output. Focus on primary citations — the papers and tools that directly enable the analytical results, not every background reference mentioned in the reference files.

Each citation must include a brief rationale explaining why it is included, so the researcher can make informed decisions about what to keep in the final report.

For the master citation index and inclusion thresholds, consult agent_reference/CITATION_REFERENCE.md.