Survival Curve Risk Table

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Data Analytics/survival-curve-risk-table"
python -m py_compile scripts/main.py
python scripts/main.py --help

Example run plan:

1. Confirm the user input, output path, and any required config values.
2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
3. Run python scripts/main.py with the validated inputs.
4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related details.

• Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
• Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
• Primary implementation surface: scripts/main.py.
• Reference guidance: references/ contains supporting rules, prompts, or checklists.
• Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
• Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py

# Example invocation: python scripts/main.py --help

# Example invocation: python scripts/main.py --input "Audit validation sample with explicit symptoms, history, assessment, and next-step plan."

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Function Overview

Automatically add "Number at risk" tables to Kaplan-Meier survival curves that meet clinical oncology journal standards. Automatically align time points and generate publication-quality combined figures.

Usage Trigger Conditions

• Need to add number at risk tables to KM survival curves
• Generate survival plots that meet journal requirements such as NEJM, Lancet, JCO
• Risk tables needed in clinical trial reports
• Medical paper chart standardization before submission
• Precise alignment of risk tables with survival curve time axis

Core Functions

1. Automatic Number at Risk Calculation

• Automatically calculate number at risk at each time point from survival data
• Support right-censored data processing
• Count remaining observed subjects by group
• Automatic handling of censoring events

2. Journal Standard Formats

• NEJM Standard: Clean time axis, groups arranged horizontally
• Lancet Standard: Complete statistical information, vertical alignment
• JCO Standard: Censoring symbols marked, group comparison
• Support custom journal templates

3. Precise Alignment

• Time axis precisely aligned with curve X-axis
• Automatic adjustment of table spacing and font size
• Responsive layout adapts to different image sizes
• Support horizontal/vertical layouts

4. Output Formats

• High-quality PNG/JPEG images
• PDF vector graphics
• SVG editable format
• PowerPoint embeddable format

Usage

Example 1: Basic Risk Table Generation

# Example invocation: python scripts/main.py \
    --input survival_data.csv \
    --time-col time \
    --event-col event \
    --group-col treatment \
    --output risk_table.png

Example 2: Specify Journal Style

# Example invocation: python scripts/main.py \
    --input survival_data.csv \
    --time-col time \
    --event-col status \
    --group-col arm \
    --style NEJM \
    --time-points 0,6,12,18,24,30,36 \
    --output figure_1a.pdf

Example 3: Combined Figure Generation (Curve + Risk Table)

# Example invocation: python scripts/main.py \
    --input survival_data.csv \
    --time-col months \
    --event-col death \
    --group-col group \
    --km-plot km_curve.png \
    --combine \
    --output combined_figure.png

Example 4: Batch Generate Multi-Timepoint Tables

# Example invocation: python scripts/main.py \
    --input survival_data.csv \
    --time-col time \
    --event-col event \
    --group-col treatment \
    --time-points 0,12,24,36,48,60 \
    --format both \
    --output-dir ./output/

Example 5: Using Existing Survival Data (Python API)

from scripts.main import RiskTableGenerator

# Initialize generator
generator = RiskTableGenerator(
    style="JCO",
    time_points=[0, 6, 12, 18, 24, 30],
    figure_size=(8, 6)
)

# Load survival data
generator.load_data(
    df=survival_df,
    time_col="time",
    event_col="event",
    group_col="treatment_arm"
)

# Generate risk table
generator.generate_risk_table(
    output_path="risk_table.png",
    show_censored=True
)

# Generate combined figure (KM curve + risk table)
generator.generate_combined_plot(
    km_plot_path="km_curve.png",
    output_path="combined_figure.pdf"
)

Input Data Format

CSV Format Example

time,event,treatment_arm
0,0,Experimental
3.2,1,Experimental
5.1,0,Experimental
12.3,1,Control
18.7,0,Control
24.0,1,Experimental
...

Required Columns

Supported Data Formats

• CSV (.csv)
• Excel (.xlsx, .xls)
• SAS (.sas7bdat)
• RData (.rda, .rds)
• Python pickle (.pkl)

Journal Style Configuration

NEJM Style

{
  "style": "NEJM",
  "font_family": "Helvetica",
  "font_size": 8,
  "time_points": [0, 6, 12, 18, 24, 30, 36],
  "table_height": 0.15,
  "show_grid": false,
  "separator_lines": true
}

Lancet Style

{
  "style": "Lancet",
  "font_family": "Times New Roman",
  "font_size": 9,
  "time_points": [0, 12, 24, 36, 48, 60],
  "table_height": 0.18,
  "show_grid": true,
  "header_bold": true
}

JCO Style

{
  "style": "JCO",
  "font_family": "Arial",
  "font_size": 8,
  "time_points": [0, 6, 12, 18, 24, 30],
  "table_height": 0.16,
  "show_censored": true,
  "censor_symbol": "+"
}

Command Line Parameters

Required Parameters

Optional Parameters

Output Format

Standalone Risk Table

┌─────────────────────────────────────────────────────────┐
│  Number at risk                                         │
├─────────┬─────┬─────┬─────┬─────┬─────┬─────┬───────────┤
│ Group   │  0  │ 12  │ 24  │ 36  │ 48  │ 60  │ 72 (mo)   │
├─────────┼─────┼─────┼─────┼─────┼─────┼─────┼───────────┤
│ Exp     │ 150 │ 142 │ 128 │ 105 │  89 │  72 │  58       │
│ Control │ 148 │ 135 │ 118 │  92 │  76 │  61 │  45       │
└─────────┴─────┴─────┴─────┴─────┴─────┴─────┴───────────┘

Combined Figure Layout

┌─────────────────────────────────────┐
│                                     │
│     Kaplan-Meier Survival Curve     │
│                                     │
│    ━━━━━━━━━  Experimental         │
│    ─ ─ ─ ─ ─  Control              │
│                                     │
└─────────────────────────────────────┘
┌─────────────────────────────────────┐
│ Number at risk                      │
│ Exp    150  142  128  105   89   72 │
│ Ctrl   148  135  118   92   76   61 │
│         0   12   24   36   48   60  │
└─────────────────────────────────────┘

Algorithm Description

Number at Risk Calculation

For each time point t:
    For each group g:
        N_at_risk(t, g) = N_total(g) 
                          - Σ(patients with events occurring ≤ t)
                          - Σ(patients censored occurring < t)

Time Point Selection Strategy

1. Auto Mode: Automatically select equally spaced time points based on data distribution
2. Fixed Interval: Select at specified intervals (e.g., every 6 months)
3. Custom: User-specified specific time points
4. Event-driven: Select based on event occurrence density

Quality Checklist

• Time axis precisely aligned with X-axis
• Number at risk calculations correct (can manually spot-check)
• Group labels clear and readable
• Font size meets journal requirements (≥8pt)
• Image resolution ≥300 DPI
• Color contrast meets accessibility standards
• Censoring marks (if present) clearly distinguishable
• Export format meets submission requirements

Journal-Specific Notes

NEJM

• Minimum font size 8pt
• Recommended time unit: months
• Fixed spacing between risk table and curve

Lancet

• Minimum font size 9pt
• Support multi-group display (max 4 groups)
• Table grid lines optional

JCO

• Need to label censoring information
• Support risk table + censoring table double-layer structure
• Recommend labeling median follow-up time

FAQ

Q: How are time points automatically determined?

A: Default uses quantiles in the data (0%, 25%, 50%, 75%, 100%) or fixed intervals (e.g., every 12 months)

Q: How to handle multiple groups?

A: Automatically detect group column, support up to 6 groups. Exceeding automatically uses pagination or reduced font

Q: Can it work with KM curves generated by Python/R?

A: Yes, supports importing external KM curve images for combination

Dependency Requirements

numpy >= 1.20.0
pandas >= 1.3.0
matplotlib >= 3.4.0
seaborn >= 0.11.0
lifelines >= 0.27.0  (optional, for survival analysis)
Pillow >= 8.0.0      (image processing)

Related Tools

• lifelines: Python survival analysis library
• survminer: R survival curve visualization
• ggsurvplot: ggplot2 survival plot extension

Risk Assessment

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues: None
• Planned Improvements:
  • Performance optimization
  • Additional feature support

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of survival-curve-risk-table and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

survival-curve-risk-table only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.

Inputs to Collect

• Required inputs: the user goal, the primary data or source file, and the requested output format.
• Optional inputs: output directory, formatting preferences, and validation constraints.
• If a required input is unavailable, return a short clarification request before continuing.

Output Contract

• Return a short summary, the main deliverables, and any assumptions that materially affect interpretation.
• If execution is partial, label what succeeded, what failed, and the next safe recovery step.
• Keep the final answer within the documented scope of the skill.

Validation and Safety Rules

• Validate identifiers, file paths, and user-provided parameters before execution.
• Do not fabricate results, metrics, citations, or downstream conclusions.
• Use safe fallback behavior when dependencies, credentials, or required inputs are missing.
• Surface any execution failure with a concise diagnosis and recovery path.