survival 1.0.10

A high-performance survival analysis library written in Rust with Python bindings
Documentation 
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import os
import sys

sys.path.insert(0, os.path.dirname(__file__))

try:
    from helpers import setup_survival_import

    survival = setup_survival_import()
    print(" Successfully imported survival module")

    print("\n=== Testing agsurv4 ===")
    ndeath: list[int] = [1, 1, 0, 1, 0]
    risk: list[float] = [1.0, 1.0, 1.0, 1.0, 1.0]
    wt: list[float] = [1.0, 1.0, 1.0, 1.0]
    sn: int = 5
    denom: list[float] = [5.0, 4.0, 3.0, 2.0, 1.0]

    result = survival.agsurv4(ndeath, risk, wt, sn, denom)
    print(" agsurv4 executed successfully")
    print(f"   Result: {result}")
    assert isinstance(result, list), "Should return a list"
    assert len(result) == sn, "Should return same length as sn"

    print("\n=== Testing agsurv5 ===")
    n: int = 5
    nvar: int = 2
    dd: list[int] = [1, 1, 2, 1, 1]
    x1: list[float] = [10.0, 9.0, 8.0, 7.0, 6.0]
    x2: list[float] = [5.0, 4.0, 3.0, 2.0, 1.0]
    xsum: list[float] = [10.0, 9.0, 8.0, 7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0]
    xsum2: list[float] = [5.0, 4.0, 3.0, 2.0, 1.0, 2.5, 2.0, 1.5, 1.0, 0.5]

    result = survival.agsurv5(n, nvar, dd, x1, x2, xsum, xsum2)
    print(" agsurv5 executed successfully")
    print(f"   Result type: {type(result)}")
    assert isinstance(result, dict), "Should return a dictionary"
    assert "sum1" in result, "Should have 'sum1' key"
    assert "sum2" in result, "Should have 'sum2' key"
    assert "xbar" in result, "Should have 'xbar' key"
    print(f"   sum1: {result['sum1']}")
    print(f"   sum2: {result['sum2']}")

    print("\n=== Testing agmart ===")
    n: int = 5
    method: int = 0
    start: list[float] = [0.0, 0.0, 1.0, 1.0, 2.0]
    stop: list[float] = [1.0, 2.0, 2.0, 3.0, 3.0]
    event: list[int] = [1, 0, 1, 0, 1]
    score: list[float] = [1.0, 1.0, 1.0, 1.0, 1.0]
    wt: list[float] = [1.0, 1.0, 1.0, 1.0, 1.0]
    strata: list[int] = [1, 0, 0, 0, 0]

    result = survival.agmart(n, method, start, stop, event, score, wt, strata)
    print(" agmart executed successfully")
    print(f"   Result: {result}")
    assert isinstance(result, list), "Should return a list"
    assert len(result) == n, "Should return same length as n"

    print("\n=== Testing survfitkm ===")
    time: list[float] = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0]
    status: list[float] = [1.0, 1.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0]

    result = survival.survfitkm(
        time=time,
        status=status,
        weights=None,
        entry_times=None,
        position=None,
        reverse=False,
        computation_type=0,
    )
    print(" survfitkm executed successfully")
    assert hasattr(result, "time"), "Should have time attribute"
    assert hasattr(result, "estimate"), "Should have estimate attribute"
    assert hasattr(result, "std_err"), "Should have std_err attribute"
    assert len(result.time) > 0, "Should have time points"
    assert len(result.estimate) == len(result.time), "Estimate should match time length"
    print(f"   Time points: {len(result.time)}")
    print(f"   First estimate: {result.estimate[0]:.4f}")

    print("\n=== Testing survdiff2 ===")
    time: list[float] = [1.0, 2.0, 3.0, 4.0, 5.0, 1.5, 2.5, 3.5, 4.5, 5.5]
    status: list[int] = [1, 1, 0, 1, 0, 1, 1, 1, 0, 1]
    group: list[int] = [1, 1, 1, 1, 1, 2, 2, 2, 2, 2]

    result = survival.survdiff2(
        time=time,
        status=status,
        group=group,
        strata=None,
        rho=0.0,
    )
    print(" survdiff2 executed successfully")
    assert hasattr(result, "observed"), "Should have observed attribute"
    assert hasattr(result, "expected"), "Should have expected attribute"
    assert hasattr(result, "chi_squared"), "Should have chi_squared attribute"
    assert len(result.observed) > 0, "Should have observed values"
    print(f"   Observed: {result.observed}")
    print(f"   Expected: {result.expected}")
    print(f"   Chi-squared: {result.chi_squared:.4f}")

    print("\n All survival analysis tests passed!")

except ImportError as e:
    print(f" Failed to import survival module: {e}")
    print("Make sure to build the project first with: maturin build")
    sys.exit(1)
except Exception as e:
    print(f" Error in survival analysis tests: {e}")
    import traceback

    traceback.print_exc()
    sys.exit(1)