Use this Skill for epidemiological survival analysis: Kaplan-Meier with log-rank test, Cox PH (time-varying covariates, Schoenfeld residuals), AFT models, and competing risks.
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SKILL.md
Instructions source · Aperçu en lecture seule
name
survival-epi
description
Use this Skill for epidemiological survival analysis: Kaplan-Meier with log-rank test, Cox PH (time-varying covariates, Schoenfeld residuals), AFT models, and competing risks.
Covariates (X): Baseline or time-varying predictors
Right censoring (most common): Subject's event time is unknown because
follow-up ended before the event (lost to follow-up, study end, withdrawal).
The survival time is known to exceed the observed time.
Kaplan-Meier Estimator
The KM estimator is the non-parametric maximum likelihood estimator of the
survival function S(t) = P(T > t):
S(t) = Π_{t_i ≤ t} (1 - d_i / n_i)
Plus depuis ce dépôt
where d_i = number of events at time t_i, n_i = number at risk just before t_i.
exp(βⱼ): hazard ratio for a one-unit increase in Xⱼ
Partial likelihood: estimates β without specifying h_0(t)
Proportional hazards assumption: The hazard ratio between any two subjects
is constant over time. Test via scaled Schoenfeld residuals (should be uncorrelated
with time under PH).
Competing Risks
When multiple event types can occur and one prevents observation of others:
Cause-specific hazard: Rate of cause-k events among those still at risk
(ignoring other causes)
Cumulative Incidence Function (CIF): Probability of cause-k event by time t
accounting for competing risks: CIF_k(t) = ∫ S(s-) × h_k(s) ds
Fine-Gray model (subdistribution hazard): Directly models the CIF by treating
subjects who experienced competing events as permanently at risk
import numpy as np
import pandas as pd
defgenerate_survival_data(
n: int = 500,
seed: int = 42,
competing_risks: bool = False,
) -> pd.DataFrame:
"""
Generate synthetic right-censored survival data.
Args:
n: Number of subjects.
seed: Random seed for reproducibility.
competing_risks: If True, generate two event types (1=primary, 2=competing).
Returns:
DataFrame with: id, time, event, group, age, sex, treatment.
"""
rng = np.random.default_rng(seed)
group = rng.binomial(1, 0.5, n) # 0=control, 1=exposed
treatment = rng.binomial(1, 0.4, n) # 0=no treatment, 1=treated
age = rng.normal(55, 12, n).clip(18, 90)
sex = rng.binomial(1, 0.5, n) # 0=female, 1=male# True hazard: group doubles hazard, treatment halves it
lam = np.exp(0.6 * group - 0.5 * treatment + 0.02 * (age - 55))
true_time = rng.exponential(1.0 / lam)
censor_time = rng.uniform(1.0, 10.0, n)
time = np.minimum(true_time, censor_time)
event = (true_time <= censor_time).astype(int)
df = pd.DataFrame({
'id': range(n),
'time': time.round(3),
'event': event,
'group': group,
'age': age.round(1),
'sex': sex,
'treatment': treatment,
})
if competing_risks:
# Assign competing event type: 1=primary, 2=competing
comp_time = rng.exponential(2.0, n) # competing event has lower rate
has_comp = (comp_time < censor_time) & (comp_time < true_time)
df['event_type'] = 0
df.loc[event == 1, 'event_type'] = 1
df.loc[has_comp, 'event_type'] = 2# Recalculate time as minimum of all three
df['time'] = np.minimum.reduce([true_time, comp_time, censor_time]).round(3)
return df
Core Workflow
Step 1 — Kaplan-Meier Curves by Exposure Group and Log-Rank Test
import matplotlib.pyplot as plt
import pandas as pd
from lifelines import KaplanMeierFitter
from lifelines.statistics import logrank_test, multivariate_logrank_test
defkm_analysis(
df: pd.DataFrame,
time_col: str = 'time',
event_col: str = 'event',
group_col: str = 'group',
group_labels: dict = None,
alpha: float = 0.05,
output_path: str = 'km_curves.png',
) -> dict:
"""
Plot Kaplan-Meier survival curves stratified by group and perform log-rank test.
Args:
df: DataFrame with time, event, and group columns.
time_col: Name of the time-to-event column.
event_col: Name of the event indicator (1=event, 0=censored).
group_col: Column to stratify by.
group_labels: Dict mapping group values to display names.
alpha: Significance level for CI.
output_path: File path to save the plot.
Returns:
Dict with median survival per group and log-rank test results.
"""
groups = sorted(df[group_col].unique())
if group_labels isNone:
group_labels = {g: str(g) for g in groups}
fig, ax = plt.subplots(figsize=(9, 5))
results = {}
kmfs = {}
for grp in groups:
mask = df[group_col] == grp
T = df.loc[mask, time_col]
E = df.loc[mask, event_col]
kmf = KaplanMeierFitter(alpha=alpha)
kmf.fit(T, E, label=group_labels[grp])
kmf.plot_survival_function(ax=ax, ci_show=True)
kmfs[grp] = kmf
results[group_labels[grp]] = {
'n': int(mask.sum()),
'events': int(E.sum()),
'median_survival': float(kmf.median_survival_time_),
'median_ci_lower': float(kmf.confidence_interval_median_['KM_estimate_lower_0.95'].iloc[0])
ifhasattr(kmf, 'confidence_interval_median_') elseNone,
}
# Log-rank test (pairwise for 2 groups)iflen(groups) == 2:
g0, g1 = groups
lrt = logrank_test(
df.loc[df[group_col] == g0, time_col],
df.loc[df[group_col] == g1, time_col],
event_observed_A=df.loc[df[group_col] == g0, event_col],
event_observed_B=df.loc[df[group_col] == g1, event_col],
)
results['log_rank_p'] = float(lrt.p_value)
results['log_rank_stat'] = float(lrt.test_statistic)
ax.set_title(f'Kaplan-Meier Curves\nLog-rank p = {lrt.p_value:.4f}')
else:
mlrt = multivariate_logrank_test(
df[time_col], df[group_col], event_observed=df[event_col]
)
results['log_rank_p'] = float(mlrt.p_value)
ax.set_title(f'Kaplan-Meier Curves\nLog-rank p = {mlrt.p_value:.4f}')
ax.set_xlabel('Time')
ax.set_ylabel('Survival probability S(t)')
ax.set_ylim(0, 1.05)
ax.grid(True, alpha=0.3)
fig.tight_layout()
fig.savefig(output_path, dpi=150)
plt.close(fig)
for label, r in results.items():
ifisinstance(r, dict):
print(f" {label}: n={r['n']}, events={r['events']}, median={r['median_survival']:.2f}")
if'log_rank_p'in results:
print(f" Log-rank p-value: {results['log_rank_p']:.4f}")
return results
# --- Demo ---
df = generate_survival_data(n=500)
km_results = km_analysis(df, group_labels={0: 'Unexposed', 1: 'Exposed'})
Step 2 — Cox PH Model and Schoenfeld PH Assumption Test
import matplotlib.pyplot as plt
from lifelines import CoxPHFitter
from lifelines.statistics import proportional_hazard_test
defcox_ph_analysis(
df: pd.DataFrame,
time_col: str = 'time',
event_col: str = 'event',
covariates: list = None,
penalizer: float = 0.0,
output_path: str = 'schoenfeld_residuals.png',
) -> dict:
"""
Fit a Cox PH model and test the proportional hazards assumption using
scaled Schoenfeld residuals.
Args:
df: DataFrame containing time, event, and covariate columns.
time_col: Time column name.
event_col: Event indicator column name.
covariates: List of covariate names. If None, use all columns except time/event.
penalizer: L2 penalty for coefficient shrinkage (0 = no penalty).
output_path: Path to save Schoenfeld residual plots.
Returns:
Dict with hazard ratios, CIs, p-values, and PH test results.
"""if covariates isNone:
covariates = [c for c in df.columns if c notin (time_col, event_col, 'id')]
data = df[[time_col, event_col] + covariates].dropna()
cph = CoxPHFitter(penalizer=penalizer)
cph.fit(data, duration_col=time_col, event_col=event_col)
print("Cox PH Summary:")
cph.print_summary()
# Extract HR table
summary = cph.summary.copy()
hr_table = summary[['coef', 'exp(coef)', 'exp(coef) lower 95%',
'exp(coef) upper 95%', 'p']].round(4)
hr_table.columns = ['log_hr', 'hr', 'hr_lower95', 'hr_upper95', 'pvalue']
# PH assumption: scaled Schoenfeld residualstry:
ph_test = proportional_hazard_test(cph, data, time_transform='rank')
print("\nProportional Hazards Test (Schoenfeld residuals):")
print(ph_test.summary)
ph_results = ph_test.summary[['test_statistic', 'p']].to_dict(orient='index')
except Exception as e:
print(f"PH test unavailable: {e}")
ph_results = {}
# Plot Schoenfeld residuals for first covariateif covariates:
fig, ax = plt.subplots(figsize=(8, 4))
try:
cph.check_assumptions(data, show_plots=False)
residuals = cph.compute_residuals(data, kind='scaled_schoenfeld')
ax.scatter(residuals.index, residuals[covariates[0]],
alpha=0.5, s=10, color='steelblue')
ax.axhline(0, color='red', linestyle='--')
ax.set_title(f'Scaled Schoenfeld Residuals — {covariates[0]}')
ax.set_xlabel('Time')
ax.set_ylabel('Scaled residual')
except Exception:
ax.text(0.5, 0.5, 'Residuals unavailable', ha='center', va='center',
transform=ax.transAxes)
fig.tight_layout()
fig.savefig(output_path, dpi=150)
plt.close(fig)
return {
'concordance_index': float(cph.concordance_index_),
'hr_table': hr_table,
'ph_test_results': ph_results,
}
# --- Demo ---
df = generate_survival_data(n=500)
cox_results = cox_ph_analysis(df, covariates=['group', 'age', 'sex', 'treatment'])
print(f"\nConcordance index: {cox_results['concordance_index']:.3f}")
print(cox_results['hr_table'])
Step 3 — Competing Risks: Fine-Gray vs Cause-Specific
import matplotlib.pyplot as plt
import pandas as pd
from lifelines import AalenJohansenFitter, CoxPHFitter
import numpy as np
defcompeting_risks_analysis(
df: pd.DataFrame,
time_col: str = 'time',
event_type_col: str = 'event_type',
group_col: str = 'group',
primary_event: int = 1,
competing_event: int = 2,
output_path: str = 'competing_risks_cif.png',
) -> dict:
"""
Estimate Cumulative Incidence Functions (CIF) for primary and competing events
using the Aalen-Johansen estimator. Compare CIF between groups.
Args:
df: DataFrame with time and event_type columns.
time_col: Time column.
event_type_col: Event type column (0=censored, 1=primary, 2=competing).
group_col: Group stratification column.
primary_event: Integer code for primary event.
competing_event: Integer code for competing event.
output_path: Path to save CIF plot.
Returns:
Dict with CIF estimates at key time points by group and event type.
"""
groups = sorted(df[group_col].unique())
fig, axes = plt.subplots(1, 2, figsize=(12, 5))
event_types = {primary_event: 'Primary event', competing_event: 'Competing event'}
results = {}
for ax_idx, (etype, elabel) inenumerate(event_types.items()):
ax = axes[ax_idx]
for grp in groups:
mask = df[group_col] == grp
T = df.loc[mask, time_col].values
E = df.loc[mask, event_type_col].values
ajf = AalenJohansenFitter(calculate_variance=True)
ajf.fit(T, E, event_of_interest=etype)
ajf.plot(ax=ax, label=f'Group {grp}')
# CIF at median time
med_time = np.median(T)
cif_at_med = float(ajf.predict(med_time))
results[f'group{grp}_{elabel}_CIF@median'] = round(cif_at_med, 4)
ax.set_title(f'CIF — {elabel}')
ax.set_xlabel('Time')
ax.set_ylabel('Cumulative incidence')
ax.set_ylim(0, 1)
ax.legend()
ax.grid(True, alpha=0.3)
fig.suptitle('Competing Risks: Cumulative Incidence Functions', fontsize=13)
fig.tight_layout()
fig.savefig(output_path, dpi=150)
plt.close(fig)
# Cause-specific Cox PH for primary event (treating competing as censored)
df_cs = df.copy()
df_cs['event_cs'] = (df_cs[event_type_col] == primary_event).astype(int)
data_cs = df_cs[[time_col, 'event_cs', group_col, 'age', 'sex']].dropna()
cph_cs = CoxPHFitter()
cph_cs.fit(data_cs, duration_col=time_col, event_col='event_cs')
hr_group_cs = float(cph_cs.summary.loc[group_col, 'exp(coef)'])
results['cause_specific_HR_group'] = round(hr_group_cs, 4)
print("Competing risks results:")
for k, v in results.items():
print(f" {k}: {v}")
return results
# --- Demo ---
df_cr = generate_survival_data(n=600, competing_risks=True)
cr_results = competing_risks_analysis(
df_cr,
time_col='time',
event_type_col='event_type',
group_col='group',
)
Advanced Usage
Time-Varying Covariates (Long Format)
import pandas as pd
from lifelines import CoxPHFitter
defcox_time_varying_covariates(
df_long: pd.DataFrame,
start_col: str = 'start',
stop_col: str = 'stop',
event_col: str = 'event',
covariates: list = None,
) -> CoxPHFitter:
"""
Fit a Cox PH model with time-varying covariates using start/stop interval format.
Long format: each row is a time interval [start, stop) for one subject.
The event column is 1 only in the last interval if the event occurred.
Args:
df_long: Long-format DataFrame with start/stop intervals.
start_col: Start of interval.
stop_col: End of interval.
event_col: Event indicator (1 = event in this interval).
covariates: List of covariate columns.
Returns:
Fitted CoxPHFitter object.
"""if covariates isNone:
exclude = {start_col, stop_col, event_col, 'id'}
covariates = [c for c in df_long.columns if c notin exclude]
cols = [start_col, stop_col, event_col] + covariates
data = df_long[cols].dropna()
cph = CoxPHFitter()
cph.fit(data, duration_col=stop_col, event_col=event_col,
start_col=start_col, show_progress=False)
cph.print_summary()
return cph
IPW-Adjusted Kaplan-Meier
defipw_km_curve(
df: pd.DataFrame,
time_col: str = 'time',
event_col: str = 'event',
treatment_col: str = 'treatment',
confounder_cols: list = None,
) -> pd.DataFrame:
"""
Inverse probability weighted Kaplan-Meier estimator.
Weights balance confounders between treatment groups.
Returns:
DataFrame with columns: time, survival_treated, survival_control.
"""from sklearn.linear_model import LogisticRegression
import numpy as np
if confounder_cols isNone:
confounder_cols = ['age', 'sex']
X = df[confounder_cols].fillna(df[confounder_cols].mean())
A = df[treatment_col].values
lr = LogisticRegression(max_iter=500)
lr.fit(X, A)
ps = lr.predict_proba(X)[:, 1] # propensity scores# IPW: treated = 1/ps, control = 1/(1-ps)
weights = np.where(A == 1, 1.0 / ps, 1.0 / (1.0 - ps))
df = df.copy()
df['ipw'] = weights
print("IPW summary: min={:.2f}, max={:.2f}, mean={:.2f}".format(
weights.min(), weights.max(), weights.mean()))
return df # pass df with 'ipw' column to weighted KM estimator
Troubleshooting
Error
Cause
Fix
ConvergenceError in Cox model
Collinear covariates or complete separation
Drop correlated variables; add penalizer=0.1
Negative median survival time
All subjects are censored
Increase follow-up time or check event coding
ValueError: Observed and expected must be >= 1 in log-rank
