Research Project Coding Guidelines

Version: 1.0 Last Updated: January 2026 Purpose: Standardized coding practices for empirical research projects

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Table of Contents

1. Project Structure
2. Python Guidelines
3. Stata Guidelines
4. General Best Practices
5. Quick Reference Templates

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Project Structure

Directory Organization

ProjectName/
├── Code/                           # All analysis scripts
│   ├── [Number]_[Name].py         # Data processing (Python)
│   ├── AN_[Number]_[Name].do      # Analysis scripts (Stata)
│   ├── AN_[Number]_[Name].py      # Analysis scripts (Python)
│   ├── LogFiles/                  # Stata log files
│   └── README.md                  # Project documentation
├── Data/
│   ├── Raw/                       # Original data (never modify)
│   ├── Intermediate/              # Partial processing
│   └── Clean/                     # Analysis-ready data
└── Results/
    ├── Tables/                    # Regression tables
    └── Figures/                   # Visualizations

Script Numbering Convention

• 0: Initial data extraction
• 1a, 1b, 1c: Data cleaning and preparation
• 2a, 2b: Data merging and linking
• 3a, 3b: Feature extraction and engineering
• 4a, 4b: Final data preparation
• 5a, 5b: Descriptive analysis
• AN_1, AN_2: Formal analysis and regressions

Use letter suffixes (a, b, c) for parallel steps Use number suffixes (1, 2, 3) for sequential substeps

Tool Preferences by Task

Task	Preferred Tool	Rationale
Figures/Visualizations	Python	Better control, publication-quality with matplotlib/seaborn
Regression Tables	Stata	More efficient with outreg2/esttab, standard in economics
Data Cleaning	Python	Better for large datasets, flexible transformations
Panel Regressions	Stata	reghdfe package is gold standard

---

Python Guidelines

1. Script Template

#!/usr/bin/env python3
"""
ScriptName.py

Brief description of what this script does.

Input files:
- Data/Raw/input1.csv
- Data/Intermediate/input2.csv

Output files:
- Data/Clean/output.csv (description)

Author: Your Name
Date: YYYY-MM-DD
"""

import pandas as pd
import numpy as np
from pathlib import Path
import matplotlib.pyplot as plt
import seaborn as sns

def get_project_root():
    """Automatically detect the project root directory."""
    return Path(__file__).parent.absolute()


def main():
    """Main processing function."""
    print("=" * 70)
    print("SCRIPT TITLE")
    print("=" * 70)

    # Setup paths
    base_dir = get_project_root()
    data_clean_dir = base_dir / ".." / "Data" / "Clean"

    # Your code here

    print("\n" + "=" * 70)
    print("PROCESSING COMPLETE")
    print("=" * 70)


if __name__ == "__main__":
    main()

2. Path Management (CRITICAL)

Always use this pattern for portability:

def get_project_root():
    """Automatically detect the project root directory."""
    return Path(__file__).parent.absolute()

# Then use relative paths
base_dir = get_project_root()
data_raw_dir = base_dir / ".." / "Data" / "Raw"
data_clean_dir = base_dir / ".." / "Data" / "Clean"
data_intermediate_dir = base_dir / ".." / "Data" / "Intermediate"
results_tables_dir = base_dir / ".." / "Results" / "Tables"
results_figures_dir = base_dir / ".." / "Results" / "Figures"

# Create directories if they don't exist
data_intermediate_dir.mkdir(parents=True, exist_ok=True)

3. Data Loading & Saving

# Loading with error handling
if not input_file.exists():
    raise FileNotFoundError(f"Input file not found: {input_file}")

try:
    df = pd.read_csv(input_file, low_memory=False)
    print(f"Loaded {len(df):,} records")
except Exception as e:
    print(f"Error reading file: {e}")
    return

# Saving with confirmation
df_sorted = df.sort_values(['company', 'year'])
df_sorted.to_csv(output_file, index=False)
print(f"Saved {len(df_sorted):,} records to: {output_file}")

4. Progress Reporting

Use consistent formatting for readability:

# Section headers
print("\n" + "=" * 70)
print("DATA PROCESSING")
print("=" * 70)

# Progress with comma formatting
print(f"\nLoaded {len(df):,} records")
print(f"  After filtering: {len(df_filtered):,} ({len(df_filtered)/len(df)*100:.1f}%)")

# Summary statistics
print("\n=== SUMMARY ===")
print(f"Total companies: {df['company'].nunique():,}")
print(f"Date range: {df['date'].min()} to {df['date'].max()}")
print(f"Match rate: {match_rate*100:.1f}%")

5. Function Documentation

def clean_company_name(name_str):
    """
    Clean and standardize company names for matching.

    Parameters:
    - name_str: Raw company name string

    Returns:
    - Cleaned company name (uppercase, no punctuation)
    """
    if pd.isna(name_str):
        return ""

    # Remove common suffixes
    name = str(name_str).upper()
    name = re.sub(r'\b(INC|CORP|LTD|LLC)\b', '', name)
    name = re.sub(r'[^\w\s]', '', name)  # Remove punctuation

    return name.strip()

6. Data Validation

# Check for required columns
required_cols = ['company', 'year', 'value']
missing_cols = [col for col in required_cols if col not in df.columns]
if missing_cols:
    raise ValueError(f"Missing required columns: {missing_cols}")

# Report data quality
print("\nData Quality Checks:")
print(f"  Missing values in key column: {df['key_col'].isna().sum():,}")
print(f"  Duplicate records: {df.duplicated().sum():,}")
print(f"  Unique companies: {df['company'].nunique():,}")

7. Merging Pattern

# Prepare keys
df1['merge_key'] = df1['company'].astype(str).str.strip().str.upper()
df2['merge_key'] = df2['company'].astype(str).str.strip().str.upper()

# Merge with reporting
print(f"\nMerging datasets:")
print(f"  Dataset 1: {len(df1):,} records")
print(f"  Dataset 2: {len(df2):,} records")

df_merged = df1.merge(df2, on='merge_key', how='inner', indicator=True)

print(f"  Merged: {len(df_merged):,} records")
print(f"  Match rate: {len(df_merged)/len(df1)*100:.1f}%")

# Check merge results
print("\nMerge indicator breakdown:")
print(df_merged['_merge'].value_counts())

8. Visualization Standards

# Setup (at top of script)
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_style("whitegrid")
plt.rcParams['figure.figsize'] = (12, 7)

# Create publication-quality figures
fig, ax = plt.subplots(figsize=(14, 8))

ax.plot(x, y, marker='o', linewidth=2, markersize=8,
        color='#2E86AB', label='Series Name')

ax.set_xlabel('X-axis Label', fontsize=12, fontweight='bold')
ax.set_ylabel('Y-axis Label', fontsize=12, fontweight='bold')
ax.set_title('Figure Title', fontsize=14, fontweight='bold', pad=20)

# Format y-axis with commas
ax.yaxis.set_major_formatter(plt.FuncFormatter(lambda x, p: f'{int(x):,}'))

ax.legend(loc='best', frameon=True, fancybox=True, shadow=True)
ax.grid(True, alpha=0.3)

plt.tight_layout()
plt.savefig(output_path, dpi=300, bbox_inches='tight')
plt.close()

print(f"Saved figure to: {output_path}")

9. Variable Naming Conventions

Type	Convention	Examples
DataFrames	df_ prefix	df, df_filtered, df_merged, df_agg
Paths	_dir or _file suffix	base_dir, input_file, output_path
Functions	snake_case verbs	clean_data(), load_files(), calculate_returns()
Variables	snake_case	company_name, year_founded, total_assets
Constants	UPPER_CASE	START_YEAR, MIN_OBSERVATIONS

---

Stata Guidelines

1. Script Template

/*
================================================================================
ScriptName.do

Description of the analysis performed in this script.

Inputs:
- ../Data/Clean/input_data.csv

Outputs:
- ../Results/Tables/Table1_MainResults.xls
- ../Code/LogFiles/ScriptName.log

Author: Your Name
Date: YYYY-MM-DD
================================================================================
*/

*** Set up paths
global repodir "/Users/zrsong/MIT Dropbox/Zirui Song/Research Projects/PROJECT_NAME"
global datadir "$repodir/Data"
global cleandir "$datadir/Clean"
global intdir "$datadir/Intermediate"
global tabdir "$repodir/Results/Tables"
global figdir "$repodir/Results/Figures"
global logdir "$repodir/Code/LogFiles"

*** Start log
log using "$logdir/ScriptName.log", text replace

/*==============================================================================
    Data Preparation
==============================================================================*/

import delimited "$cleandir/input_data.csv", clear

[Your code here]

*** Close log
log close

2. Global Path Setup (CRITICAL)

Always define these at the top:

global repodir "/Full/Path/To/Project"
global datadir "$repodir/Data"
global cleandir "$datadir/Clean"
global intdir "$datadir/Intermediate"
global rawdir "$datadir/Raw"
global tabdir "$repodir/Results/Tables"
global figdir "$repodir/Results/Figures"
global logdir "$repodir/Code/LogFiles"

Note: Update repodir for each user/computer

3. Regression Structure

/*==============================================================================
    Main Regressions - Table 1
==============================================================================*/

*** Define variable lists
local borr_controls "log_assets leverage tangibility profitability"
local loan_controls "log_amount maturity"
local all_controls "`borr_controls' `loan_controls'"

*** Column 1: No controls
reghdfe outcome treatment_var, ///
    absorb(industry year) ///
    vce(cluster firm_id)

outreg2 using "$tabdir/Table1_MainResults.xls", replace excel ///
    ctitle("(1) No Controls") label dec(3) ///
    addtext(Industry FE, YES, Year FE, YES) ///
    keep(treatment_var)

*** Column 2: With controls
reghdfe outcome treatment_var `all_controls', ///
    absorb(industry year) ///
    vce(cluster firm_id)

outreg2 using "$tabdir/Table1_MainResults.xls", append excel ///
    ctitle("(2) Full Controls") label dec(3) ///
    addtext(Industry FE, YES, Year FE, YES, Controls, YES) ///
    keep(treatment_var `all_controls')

4. Output Table Conventions

Two output workflows:

Stage	Command	Output Format	Use Case
Working/Exploratory	outreg2	Excel (.xls)	Quick iteration, reviewing results
Final Paper	esttab	LaTeX (.tex)	Publication-ready tables

---

A. Working Tables: outreg2 with Excel

Use outreg2 with the excel option for exploratory analysis and quick iterations:

outreg2 using "$tabdir/TableName.xls", [replace/append] excel ///
    ctitle("Column Title") ///              // Column header
    label ///                                // Use variable labels
    dec(3) ///                              // 3 decimal places
    keep(vars_to_show) ///                  // Variables to display
    addtext(Industry FE, YES, ///           // Notes for fixed effects
            Year FE, YES, ///
            Controls, YES)

Working table naming:

• Table1_MainResults.xls
• Table2_Robustness.xls
• TableA1_DescriptiveStats.xls (appendix)

---

B. Final Paper Tables: esttab for LaTeX

Use esttab to generate publication-ready LaTeX tables:

*** Store regression results
eststo clear

eststo m1: reghdfe outcome treatment, absorb(industry year) vce(cluster firm_id)
eststo m2: reghdfe outcome treatment `controls', absorb(industry year) vce(cluster firm_id)
eststo m3: reghdfe outcome treatment `controls', absorb(firm_id year) vce(cluster firm_id)

*** Output LaTeX table
esttab m1 m2 m3 using "$tabdir/Table1_MainResults.tex", replace ///
    b(3) se(3) ///                          // 3 decimal places for coef and SE
    star(* 0.10 ** 0.05 *** 0.01) ///       // Significance stars
    label ///                                // Use variable labels
    booktabs ///                            // Professional table formatting
    nomtitles ///                           // No model titles (use column numbers)
    mgroups("Dependent Variable: Outcome", pattern(1 0 0) ///
            prefix(\multicolumn{@span}{c}{) suffix(}) span erepeat(\cmidrule(lr){@span})) ///
    keep(treatment `controls') ///           // Variables to display
    order(treatment `controls') ///          // Variable order
    stats(r2 N, fmt(3 0) labels("R-squared" "Observations")) ///
    indicate("Industry FE = *industry*" "Year FE = *year*" "Firm FE = *firm_id*") ///
    addnotes("Standard errors clustered by firm in parentheses." ///
             "* p<0.10, ** p<0.05, *** p<0.01")

Simplified esttab for quick LaTeX output:

esttab m1 m2 m3 using "$tabdir/Table1.tex", replace ///
    b(3) se(3) star(* 0.10 ** 0.05 *** 0.01) ///
    label booktabs ///
    keep(treatment) ///
    stats(r2 N, fmt(3 0) labels("R\$^2\$" "N")) ///
    addnotes("Clustered SEs in parentheses.")

Final table naming:

• Table1_MainResults.tex
• Table2_Robustness.tex
• TableA1_Appendix.tex

5. Fixed Effects Patterns

*** Firm and year fixed effects with clustering
reghdfe outcome treatment controls, ///
    absorb(firm_id year) ///
    vce(cluster firm_id)

*** Industry and year fixed effects
reghdfe outcome treatment controls, ///
    absorb(industry year) ///
    vce(cluster firm_id)

*** Fama-French 12 industry classification
sicff sic, ind(12) gen(ff12)
reghdfe outcome treatment controls, ///
    absorb(ff12 year) ///
    vce(cluster firm_id)

6. Subsample Analysis

/*==============================================================================
    Subsample Analysis - Large Firms
==============================================================================*/

preserve

*** Keep only observations meeting criteria
keep if total_assets > median_assets

*** Run regressions for subsample
reghdfe outcome treatment controls, ///
    absorb(industry year) ///
    vce(cluster firm_id)

outreg2 using "$tabdir/Table2_Subsamples.xls", append excel ///
    ctitle("Large Firms") label dec(3)

restore

7. Variable Generation

*** Generate dummy variables
gen high_leverage = (leverage > 0.3)
replace high_leverage = 0 if missing(high_leverage)
label variable high_leverage "Leverage > 30%"

*** Generate interaction terms
gen treat_x_post = treatment * post
label variable treat_x_post "Treatment × Post"

*** Generate time trends
gen year_trend = year - 2000
gen year_trend_sq = year_trend^2

8. Summary Statistics Table

/*==============================================================================
    Table 1: Descriptive Statistics
==============================================================================*/

*** Summary statistics
estpost tabstat outcome treatment control1 control2, ///
    statistics(count mean sd min p25 p50 p75 max) ///
    columns(statistics)

esttab using "$tabdir/Table1_Descriptives.csv", ///
    cells("count mean sd min p25 p50 p75 max") ///
    replace noobs nomtitle nonumber

*** Alternative: Use outreg2
outreg2 using "$tabdir/Table1_Descriptives.xls", replace sum(log) ///
    keep(outcome treatment control1 control2) ///
    eqkeep(N mean sd min max)

9. Section Headers

/*==============================================================================
    Section Title
==============================================================================*/

*** Subsection description
[Code for subsection]

*** Another subsection
[More code]

---

General Best Practices

1. File Naming Conventions

Type	Convention	Examples
Data cleaning	[N]_[Action][Dataset].py	1a_CleanIPO.py, 2_MergeCompustat.py
Analysis	AN_[N]_[Description].[ext]	AN_1_DescriptiveStats.py, AN_2_MainReg.do
Data files	Descriptive names	comp_crspa_merged.csv, loan_panel_final.csv

2. Workflow Checklist

Before running any script:

• Input files exist in specified locations
• Output directories are created
• Paths are correctly specified

After running any script:

• Check output file was created
• Verify record counts make sense
• Review summary statistics
• Check for unexpected missing values

3. Documentation Requirements

Every script must include:

• Docstring/header comment with purpose
• List of input files
• List of output files
• Date last modified

Every analysis must document:

• Sample selection criteria
• Variable construction
• Outlier treatment
• Missing data handling

4. Code Organization

Within a script, follow this order:

1. Imports/library loading
2. Path setup
3. Helper functions
4. Main processing function
5. Execution block (if __name__ == "__main__":)

5. Error Prevention

# Check before processing
assert df['key'].notna().all(), "Key column has missing values"
assert df['year'].between(1990, 2025).all(), "Year outside expected range"
assert not df.duplicated(subset=['key']).any(), "Duplicate keys found"

# Validate merge results
assert len(df_merged) > 0, "Merge produced no matches"
assert '_merge' in df_merged.columns, "Merge indicator missing"

6. Reproducibility

Always include:

• Random seeds when using randomization: np.random.seed(42)
• Package versions in README
• Data processing workflow diagram
• Clear execution order in README

Never:

• Hardcode absolute paths (except Stata global repodir)
• Modify raw data files
• Delete intermediate files until project complete
• Use undocumented manual data adjustments

7. Version Control

Git best practices:

• Commit after completing each script
• Use descriptive commit messages
• Don't commit large data files
• Include .gitignore for:

  __pycache__/
  *.pyc
  .DS_Store
  LogFiles/
  *.log
  .ipynb_checkpoints/
  

---

Quick Reference Templates

Python: Basic Data Cleaning

#!/usr/bin/env python3
"""Brief description."""

import pandas as pd
from pathlib import Path

def get_project_root():
    return Path(__file__).parent.absolute()

def main():
    # Paths
    base_dir = get_project_root()
    input_file = base_dir / ".." / "Data" / "Raw" / "input.csv"
    output_file = base_dir / ".." / "Data" / "Clean" / "output.csv"

    # Load
    df = pd.read_csv(input_file)
    print(f"Loaded {len(df):,} records")

    # Process
    df_clean = df.dropna(subset=['key_col'])
    df_clean = df_clean[df_clean['year'] >= 2000].copy()

    # Save
    df_clean.to_csv(output_file, index=False)
    print(f"Saved {len(df_clean):,} records")

if __name__ == "__main__":
    main()

Python: Data Merging

def merge_datasets(df1, df2, merge_key, how='inner'):
    """Merge with reporting."""
    print(f"\nMerging datasets:")
    print(f"  Left: {len(df1):,} records")
    print(f"  Right: {len(df2):,} records")

    merged = df1.merge(df2, on=merge_key, how=how, indicator=True)

    print(f"  Result: {len(merged):,} records")
    print(f"\nMerge breakdown:")
    print(merged['_merge'].value_counts())

    return merged

Stata: Standard Regression Table

*** Table X: Main Results

local controls "control1 control2 control3"

*** Column 1
reghdfe outcome treatment, absorb(fe1 fe2) vce(cluster id)
outreg2 using "$tabdir/TableX.xls", replace excel ///
    ctitle("(1)") label dec(3) ///
    addtext(FE1, YES, FE2, YES) keep(treatment)

*** Column 2
reghdfe outcome treatment `controls', absorb(fe1 fe2) vce(cluster id)
outreg2 using "$tabdir/TableX.xls", append excel ///
    ctitle("(2)") label dec(3) ///
    addtext(FE1, YES, FE2, YES, Controls, YES) keep(treatment `controls')

Stata: Summary Statistics

*** Generate summary statistics
estpost tabstat var1 var2 var3, ///
    statistics(count mean sd min max) columns(statistics)

esttab using "$tabdir/Summary.csv", ///
    cells("count mean sd min max") replace noobs

---

Common Pitfalls to Avoid

Python

1. SettingWithCopyWarning: Always use .copy() after filtering

   df_subset = df[df['year'] >= 2000].copy()  # Good
   df_subset = df[df['year'] >= 2000]         # Bad
   

2. Path issues: Use Path objects, not string concatenation

   file = base_dir / "Data" / "file.csv"  # Good
   file = base_dir + "/Data/file.csv"     # Bad
   

3. Memory issues: Use low_memory=False for large CSV files

   df = pd.read_csv(file, low_memory=False)
   

Stata

1. Path separators: Use forward slashes even on Windows

   global dir "C:/Users/Name/Project"  // Good
   global dir "C:\Users\Name\Project"  // Bad
   

2. Missing absorb(): Don't forget to include absorb when using reghdfe

   reghdfe y x, absorb(fe1 fe2) vce(cluster id)  // Good
   reghdfe y x, vce(cluster id)                   // Bad - will error
   

3. Log file conflicts: Always use replace option

   log using "$logdir/script.log", text replace  // Good
   log using "$logdir/script.log", text          // Bad - will error if exists
   

---

Checklist for New Projects

Initial Setup

• Create directory structure (Code/, Data/, Results/)
• Create subdirectories (Raw/, Intermediate/, Clean/, Tables/, Figures/)
• Initialize git repository
• Create README.md with project description
• Create .gitignore file
• Document data sources and access methods

For Each Script

• Include header docstring with inputs/outputs
• Use standardized path management
• Include progress reporting
• Validate input files exist
• Check output makes sense
• Document any manual decisions

Before Finalizing

• All scripts run without errors
• Results reproduce from raw data
• Tables and figures saved to Results/
• README documents full workflow
• Code is commented appropriately
• No hardcoded paths (except Stata repodir)