survival 1.1.5__cp314-cp314-macosx_10_12_x86_64.whl

survival-1.1.5.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: survival
+Version: 1.1.5
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Typing :: Typed
+Requires-Dist: pre-commit==4.5.1 ; extra == 'dev'
+Requires-Dist: pytest==9.0.2 ; extra == 'dev'
+Requires-Dist: numpy==2.4.0 ; extra == 'dev'
+Requires-Dist: pytest==9.0.2 ; extra == 'test'
+Requires-Dist: numpy==2.4.0 ; extra == 'test'
+Requires-Dist: pandas==2.3.3 ; extra == 'test'
+Requires-Dist: polars==1.36.1 ; extra == 'test'
+Provides-Extra: dev
+Provides-Extra: test
+License-File: LICENSE
+Summary: A high-performance survival analysis library written in Rust with Python bindings
+Keywords: survival-analysis,kaplan-meier,cox-regression,statistics,biostatistics,rust
+Author-email: Cameron Lyons <cameron.lyons2@gmail.com>
+Maintainer-email: Cameron Lyons <cameron.lyons2@gmail.com>
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Repository, https://github.com/Cameron-Lyons/survival
+Project-URL: Documentation, https://github.com/Cameron-Lyons/survival#readme
+Project-URL: Issues, https://github.com/Cameron-Lyons/survival/issues
+
+# survival
+
+[![Crates.io](https://img.shields.io/crates/v/survival.svg)](https://crates.io/crates/survival)
+[![PyPI version](https://img.shields.io/pypi/v/survival.svg)](https://pypi.org/project/survival/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+A high-performance survival analysis library written in Rust, with a Python API powered by [PyO3](https://github.com/PyO3/pyo3) and [maturin](https://github.com/PyO3/maturin).
+
+## Features
+
+- Core survival analysis routines
+- Cox proportional hazards models with frailty
+- Kaplan-Meier and Aalen-Johansen (multi-state) survival curves
+- Nelson-Aalen estimator
+- Parametric accelerated failure time models
+- Fine-Gray competing risks model
+- Penalized splines (P-splines) for smooth covariate effects
+- Concordance index calculations
+- Person-years calculations
+- Score calculations for survival models
+- Residual analysis (martingale, Schoenfeld, score residuals)
+- Bootstrap confidence intervals
+- Cross-validation for model assessment
+- Statistical tests (log-rank, likelihood ratio, Wald, score, proportional hazards)
+- Sample size and power calculations
+- RMST (Restricted Mean Survival Time) analysis
+- Landmark analysis
+- Calibration and risk stratification
+- Time-dependent AUC
+- Conditional logistic regression
+- Time-splitting utilities
+
+## Installation
+
+### From PyPI (Recommended)
+
+```sh
+pip install survival
+```
+
+### From Source
+
+#### Prerequisites
+
+- Python 3.9+
+- Rust (see [rustup.rs](https://rustup.rs/))
+- [maturin](https://github.com/PyO3/maturin)
+
+Install maturin:
+```sh
+pip install maturin
+```
+
+#### Build and Install
+
+Build the Python wheel:
+```sh
+maturin build --release
+```
+
+Install the wheel:
+```sh
+pip install target/wheels/survival-*.whl
+```
+
+For development:
+```sh
+maturin develop
+```
+
+## Usage
+
+### Aalen's Additive Regression Model
+
+```python
+from survival import AaregOptions, aareg
+
+data = [
+    [1.0, 0.0, 0.5],
+    [2.0, 1.0, 1.5],
+    [3.0, 0.0, 2.5],
+]
+variable_names = ["time", "event", "covariate1"]
+
+# Create options with required parameters (formula, data, variable_names)
+options = AaregOptions(
+    formula="time + event ~ covariate1",
+    data=data,
+    variable_names=variable_names,
+)
+
+# Optional: modify default values via setters
+# options.weights = [1.0, 1.0, 1.0]
+# options.qrtol = 1e-8
+# options.dfbeta = True
+
+result = aareg(options)
+print(result)
+```
+
+### Penalized Splines (P-splines)
+
+```python
+from survival import PSpline
+
+x = [0.1 * i for i in range(100)]
+pspline = PSpline(
+    x=x,
+    df=10,
+    theta=1.0,
+    eps=1e-6,
+    method="GCV",
+    boundary_knots=(0.0, 10.0),
+    intercept=True,
+    penalty=True,
+)
+pspline.fit()
+```
+
+### Concordance Index
+
+```python
+from survival import perform_concordance1_calculation
+
+time_data = [1.0, 2.0, 3.0, 4.0, 5.0, 1.0, 2.0, 3.0, 4.0, 5.0]
+weights = [1.0, 1.0, 1.0, 1.0, 1.0]
+indices = [0, 1, 2, 3, 4]
+ntree = 5
+
+result = perform_concordance1_calculation(time_data, weights, indices, ntree)
+print(f"Concordance index: {result['concordance_index']}")
+```
+
+### Cox Regression with Frailty
+
+```python
+from survival import perform_cox_regression_frailty
+
+result = perform_cox_regression_frailty(
+    time_data=[...],
+    status_data=[...],
+    covariates=[...],
+    # ... other parameters
+)
+```
+
+### Person-Years Calculation
+
+```python
+from survival import perform_pyears_calculation
+
+result = perform_pyears_calculation(
+    time_data=[...],
+    weights=[...],
+    # ... other parameters
+)
+```
+
+### Kaplan-Meier Survival Curves
+
+```python
+from survival import survfitkm, SurvFitKMOutput
+
+# Example survival data
+time = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0]
+status = [1.0, 1.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0]  # 1 = event, 0 = censored
+weights = [1.0] * len(time)  # Optional: equal weights
+
+result = survfitkm(
+    time=time,
+    status=status,
+    weights=weights,
+    entry_times=None,  # Optional: entry times for left-truncation
+    position=None,     # Optional: position flags
+    reverse=False,     # Optional: reverse time order
+    computation_type=0 # Optional: computation type
+)
+
+print(f"Time points: {result.time}")
+print(f"Survival estimates: {result.estimate}")
+print(f"Standard errors: {result.std_err}")
+print(f"Number at risk: {result.n_risk}")
+```
+
+### Fine-Gray Competing Risks Model
+
+```python
+from survival import finegray, FineGrayOutput
+
+# Example competing risks data
+tstart = [0.0, 0.0, 0.0, 0.0]
+tstop = [1.0, 2.0, 3.0, 4.0]
+ctime = [0.5, 1.5, 2.5, 3.5]  # Cut points
+cprob = [0.1, 0.2, 0.3, 0.4]  # Cumulative probabilities
+extend = [True, True, False, False]  # Whether to extend intervals
+keep = [True, True, True, True]      # Which cut points to keep
+
+result = finegray(
+    tstart=tstart,
+    tstop=tstop,
+    ctime=ctime,
+    cprob=cprob,
+    extend=extend,
+    keep=keep
+)
+
+print(f"Row indices: {result.row}")
+print(f"Start times: {result.start}")
+print(f"End times: {result.end}")
+print(f"Weights: {result.wt}")
+```
+
+### Parametric Survival Regression (Accelerated Failure Time Models)
+
+```python
+from survival import survreg, SurvivalFit, DistributionType
+
+# Example survival data
+time = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0]
+status = [1.0, 1.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0]  # 1 = event, 0 = censored
+covariates = [
+    [1.0, 2.0],
+    [1.5, 2.5],
+    [2.0, 3.0],
+    [2.5, 3.5],
+    [3.0, 4.0],
+    [3.5, 4.5],
+    [4.0, 5.0],
+    [4.5, 5.5],
+]
+
+# Fit parametric survival model
+result = survreg(
+    time=time,
+    status=status,
+    covariates=covariates,
+    weights=None,          # Optional: observation weights
+    offsets=None,          # Optional: offset values
+    initial_beta=None,     # Optional: initial coefficient values
+    strata=None,           # Optional: stratification variable
+    distribution="weibull",  # "extreme_value", "logistic", "gaussian", "weibull", or "lognormal"
+    max_iter=20,          # Optional: maximum iterations
+    eps=1e-5,             # Optional: convergence tolerance
+    tol_chol=1e-9,        # Optional: Cholesky tolerance
+)
+
+print(f"Coefficients: {result.coefficients}")
+print(f"Log-likelihood: {result.log_likelihood}")
+print(f"Iterations: {result.iterations}")
+print(f"Variance matrix: {result.variance_matrix}")
+print(f"Convergence flag: {result.convergence_flag}")
+```
+
+### Cox Proportional Hazards Model
+
+```python
+from survival import CoxPHModel, Subject
+
+# Create a Cox PH model
+model = CoxPHModel()
+
+# Or create with data
+covariates = [[1.0, 2.0], [2.0, 3.0], [1.5, 2.5]]
+event_times = [1.0, 2.0, 3.0]
+censoring = [1, 1, 0]  # 1 = event, 0 = censored
+
+model = CoxPHModel.new_with_data(covariates, event_times, censoring)
+
+# Fit the model
+model.fit(n_iters=10)
+
+# Get results
+print(f"Baseline hazard: {model.baseline_hazard}")
+print(f"Risk scores: {model.risk_scores}")
+print(f"Coefficients: {model.get_coefficients()}")
+
+# Predict on new data
+new_covariates = [[1.0, 2.0], [2.0, 3.0]]
+predictions = model.predict(new_covariates)
+print(f"Predictions: {predictions}")
+
+# Calculate Brier score
+brier = model.brier_score()
+print(f"Brier score: {brier}")
+
+# Compute survival curves for new covariates
+new_covariates = [[1.0, 2.0], [2.0, 3.0]]
+time_points = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0]  # Optional: specific time points
+times, survival_curves = model.survival_curve(new_covariates, time_points)
+print(f"Time points: {times}")
+print(f"Survival curves: {survival_curves}")  # One curve per covariate set
+
+# Create and add subjects
+subject = Subject(
+    id=1,
+    covariates=[1.0, 2.0],
+    is_case=True,
+    is_subcohort=True,
+    stratum=0
+)
+model.add_subject(subject)
+```
+
+### Cox Martingale Residuals
+
+```python
+from survival import coxmart
+
+# Example survival data
+time = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0]
+status = [1, 1, 0, 1, 0, 1, 1, 0]  # 1 = event, 0 = censored
+score = [0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2]  # Risk scores
+
+# Calculate martingale residuals
+residuals = coxmart(
+    time=time,
+    status=status,
+    score=score,
+    weights=None,      # Optional: observation weights
+    strata=None,       # Optional: stratification variable
+    method=0,          # Optional: method (0 = Breslow, 1 = Efron)
+)
+
+print(f"Martingale residuals: {residuals}")
+```
+
+### Survival Difference Tests (Log-Rank Test)
+
+```python
+from survival import survdiff2, SurvDiffResult
+
+# Example: Compare survival between two groups
+time = [1.0, 2.0, 3.0, 4.0, 5.0, 1.5, 2.5, 3.5, 4.5, 5.5]
+status = [1, 1, 0, 1, 0, 1, 1, 1, 0, 1]
+group = [1, 1, 1, 1, 1, 2, 2, 2, 2, 2]  # Group 1 and Group 2
+
+# Perform log-rank test (rho=0 for standard log-rank)
+result = survdiff2(
+    time=time,
+    status=status,
+    group=group,
+    strata=None,  # Optional: stratification variable
+    rho=0.0,      # 0.0 = log-rank, 1.0 = Wilcoxon, other = generalized
+)
+
+print(f"Observed events: {result.observed}")
+print(f"Expected events: {result.expected}")
+print(f"Chi-squared statistic: {result.chi_squared}")
+print(f"Degrees of freedom: {result.degrees_of_freedom}")
+print(f"Variance matrix: {result.variance}")
+```
+
+## API Reference
+
+### Classes
+
+**Core Models:**
+- `AaregOptions`: Configuration options for Aalen's additive regression model
+- `PSpline`: Penalized spline class for smooth covariate effects
+- `CoxPHModel`: Cox proportional hazards model class
+- `Subject`: Subject data structure for Cox PH models
+- `ConditionalLogisticRegression`: Conditional logistic regression model
+- `ClogitDataSet`: Dataset for conditional logistic regression
+
+**Survival Curves:**
+- `SurvFitKMOutput`: Output from Kaplan-Meier survival curve fitting
+- `SurvFitAJ`: Output from Aalen-Johansen survival curve fitting
+- `NelsonAalenResult`: Output from Nelson-Aalen estimator
+- `StratifiedKMResult`: Output from stratified Kaplan-Meier
+
+**Parametric Models:**
+- `SurvivalFit`: Output from parametric survival regression
+- `DistributionType`: Distribution types for parametric models (extreme_value, logistic, gaussian, weibull, lognormal)
+- `FineGrayOutput`: Output from Fine-Gray competing risks model
+
+**Statistical Tests:**
+- `SurvDiffResult`: Output from survival difference tests
+- `LogRankResult`: Output from log-rank test
+- `TrendTestResult`: Output from trend tests
+- `TestResult`: General test result output
+- `ProportionalityTest`: Output from proportional hazards test
+
+**Validation:**
+- `BootstrapResult`: Output from bootstrap confidence interval calculations
+- `CVResult`: Output from cross-validation
+- `CalibrationResult`: Output from calibration analysis
+- `PredictionResult`: Output from prediction functions
+- `RiskStratificationResult`: Output from risk stratification
+- `TdAUCResult`: Output from time-dependent AUC calculation
+
+**RMST and Survival Metrics:**
+- `RMSTResult`: Output from RMST calculation
+- `RMSTComparisonResult`: Output from RMST comparison between groups
+- `MedianSurvivalResult`: Output from median survival calculation
+- `CumulativeIncidenceResult`: Output from cumulative incidence calculation
+- `NNTResult`: Number needed to treat result
+
+**Landmark Analysis:**
+- `LandmarkResult`: Output from landmark analysis
+- `ConditionalSurvivalResult`: Output from conditional survival calculation
+- `HazardRatioResult`: Output from hazard ratio calculation
+- `SurvivalAtTimeResult`: Output from survival at specific times
+- `LifeTableResult`: Output from life table calculation
+
+**Power and Sample Size:**
+- `SampleSizeResult`: Output from sample size calculations
+- `AccrualResult`: Output from accrual calculations
+
+**Utilities:**
+- `CoxCountOutput`: Output from Cox counting functions
+- `SplitResult`: Output from time-splitting
+- `LinkFunctionParams`: Link function parameters
+- `CchMethod`: Case-cohort method specification
+- `CohortData`: Cohort data structure
+
+### Functions
+
+**Model Fitting:**
+- `aareg(options)`: Fit Aalen's additive regression model
+- `survreg(...)`: Fit parametric accelerated failure time models
+- `perform_cox_regression_frailty(...)`: Fit Cox proportional hazards model with frailty
+
+**Survival Curves:**
+- `survfitkm(...)`: Fit Kaplan-Meier survival curves
+- `survfitaj(...)`: Fit Aalen-Johansen survival curves (multi-state)
+- `nelson_aalen_estimator(...)`: Calculate Nelson-Aalen estimator
+- `stratified_kaplan_meier(...)`: Calculate stratified Kaplan-Meier curves
+- `agsurv4(...)`: Anderson-Gill survival calculations (version 4)
+- `agsurv5(...)`: Anderson-Gill survival calculations (version 5)
+
+**Statistical Tests:**
+- `survdiff2(...)`: Perform survival difference tests (log-rank, Wilcoxon, etc.)
+- `logrank_test(...)`: Perform log-rank test
+- `fleming_harrington_test(...)`: Perform Fleming-Harrington weighted test
+- `logrank_trend(...)`: Perform log-rank trend test
+- `lrt_test(...)`: Likelihood ratio test
+- `wald_test_py(...)`: Wald test
+- `score_test_py(...)`: Score test
+- `ph_test(...)`: Proportional hazards assumption test
+
+**Residuals:**
+- `coxmart(...)`: Calculate Cox martingale residuals
+- `agmart(...)`: Calculate Anderson-Gill martingale residuals
+- `schoenfeld_residuals(...)`: Calculate Schoenfeld residuals
+- `cox_score_residuals(...)`: Calculate Cox score residuals
+
+**Concordance:**
+- `perform_concordance1_calculation(...)`: Calculate concordance index (version 1)
+- `perform_concordance3_calculation(...)`: Calculate concordance index (version 3)
+- `perform_concordance_calculation(...)`: Calculate concordance index (version 5)
+- `concordance(...)`: General concordance calculation
+
+**Validation:**
+- `bootstrap_cox_ci(...)`: Bootstrap confidence intervals for Cox models
+- `bootstrap_survreg_ci(...)`: Bootstrap confidence intervals for parametric models
+- `cv_cox_concordance(...)`: Cross-validation for Cox model concordance
+- `cv_survreg_loglik(...)`: Cross-validation for parametric model log-likelihood
+- `calibration(...)`: Model calibration assessment
+- `predict_cox(...)`: Predictions from Cox models
+- `risk_stratification(...)`: Risk group stratification
+- `td_auc(...)`: Time-dependent AUC calculation
+- `brier(...)`: Calculate Brier score
+- `integrated_brier(...)`: Calculate integrated Brier score
+
+**RMST and Survival Metrics:**
+- `rmst(...)`: Calculate restricted mean survival time
+- `rmst_comparison(...)`: Compare RMST between groups
+- `survival_quantile(...)`: Calculate survival quantiles (median, etc.)
+- `cumulative_incidence(...)`: Calculate cumulative incidence
+- `number_needed_to_treat(...)`: Calculate NNT
+
+**Landmark Analysis:**
+- `landmark_analysis(...)`: Perform landmark analysis
+- `landmark_analysis_batch(...)`: Perform batch landmark analysis at multiple time points
+- `conditional_survival(...)`: Calculate conditional survival
+- `hazard_ratio(...)`: Calculate hazard ratios
+- `survival_at_times(...)`: Calculate survival at specific time points
+- `life_table(...)`: Generate life table
+
+**Power and Sample Size:**
+- `sample_size_survival(...)`: Calculate required sample size
+- `sample_size_survival_freedman(...)`: Sample size using Freedman's method
+- `power_survival(...)`: Calculate statistical power
+- `expected_events(...)`: Calculate expected number of events
+
+**Utilities:**
+- `finegray(...)`: Fine-Gray competing risks model data preparation
+- `perform_pyears_calculation(...)`: Calculate person-years of observation
+- `perform_pystep_calculation(...)`: Perform step calculations
+- `perform_pystep_simple_calculation(...)`: Perform simple step calculations
+- `perform_score_calculation(...)`: Calculate score statistics
+- `perform_agscore3_calculation(...)`: Calculate score statistics (version 3)
+- `survsplit(...)`: Split survival data at specified times
+- `tmerge(...)`: Merge time-dependent covariates
+- `tmerge2(...)`: Merge time-dependent covariates (version 2)
+- `tmerge3(...)`: Merge time-dependent covariates (version 3)
+- `collapse(...)`: Collapse survival data
+- `coxcount1(...)`: Cox counting process calculations
+- `coxcount2(...)`: Cox counting process calculations (version 2)
+- `agexact(...)`: Exact Anderson-Gill calculations
+- `norisk(...)`: No-risk calculations
+- `cipoisson(...)`: Poisson confidence intervals
+- `cipoisson_exact(...)`: Exact Poisson confidence intervals
+- `cipoisson_anscombe(...)`: Anscombe Poisson confidence intervals
+- `cox_callback(...)`: Cox model callback for iterative fitting
+
+## PSpline Options
+
+The `PSpline` class provides penalized spline smoothing:
+
+**Constructor Parameters:**
+- `x`: Covariate vector (list of floats)
+- `df`: Degrees of freedom (integer)
+- `theta`: Roughness penalty (float)
+- `eps`: Accuracy for degrees of freedom (float)
+- `method`: Penalty method for tuning parameter selection. Supported methods:
+  - `"GCV"` - Generalized Cross-Validation
+  - `"UBRE"` - Unbiased Risk Estimator
+  - `"REML"` - Restricted Maximum Likelihood
+  - `"AIC"` - Akaike Information Criterion
+  - `"BIC"` - Bayesian Information Criterion
+- `boundary_knots`: Tuple of (min, max) for the spline basis
+- `intercept`: Whether to include an intercept in the basis
+- `penalty`: Whether to apply the penalty
+
+**Methods:**
+- `fit()`: Fit the spline model, returns coefficients
+- `predict(new_x)`: Predict values at new x points
+
+**Properties:**
+- `coefficients`: Fitted coefficients (None if not fitted)
+- `fitted`: Whether the model has been fitted
+- `df`: Degrees of freedom
+- `eps`: Convergence tolerance
+
+## Development
+
+Build the Rust library:
+```sh
+cargo build
+```
+
+Run tests:
+```sh
+cargo test
+```
+
+Format code:
+```sh
+cargo fmt
+```
+
+The codebase is organized with:
+- Core routines in `src/`
+- Tests and examples in `test/`
+- Python bindings using PyO3
+
+## Dependencies
+
+- [PyO3](https://github.com/PyO3/pyo3) - Python bindings
+- [ndarray](https://github.com/rust-ndarray/ndarray) - N-dimensional arrays
+- [faer](https://github.com/sarah-ek/faer-rs) - Pure-Rust linear algebra
+- [itertools](https://github.com/rust-itertools/itertools) - Iterator utilities
+- [rayon](https://github.com/rayon-rs/rayon) - Parallel computation
+
+## Compatibility
+
+- This build is for Python only. R/extendr bindings are currently disabled.
+- macOS users: Ensure you are using the correct Python version and have Homebrew-installed Python if using Apple Silicon.
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+

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+Tag: cp314-cp314-macosx_10_12_x86_64

survival-1.1.5.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Cameron Lyons
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.