scitex 2.0.0__py2.py3-none-any.whl

scitex/stats/tests/__corr_test_multi.py

@@ -0,0 +1,343 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Time-stamp: "2024-10-07 22:59:12 (ywatanabe)"
+
+from bisect import bisect_right
+import numpy as np
+import scitex
+from scipy import stats
+from typing import Any, Literal, Dict, Callable
+from ...decorators import numpy_fn
+import multiprocessing as mp
+from functools import partial
+import pandas as pd
+
+# def _compute_surrogate(args):
+#     data1, data2, corr_func, seed = args
+#     np.random.seed(seed)
+
+#     data1 = data1
+#     data2 = np.random.permutation(data2)
+
+#     non_nan_indices = ~(np.isnan(data1) | np.isnan(data2))
+#     data1, data2 = data1[non_nan_indices], data2[non_nan_indices]
+
+
+#     return corr_func(data1, data2)[0]
+def _compute_surrogate(args):
+    data1, data2, corr_func, seed = args
+    np.random.seed(seed)
+
+    data2 = np.random.permutation(data2)
+
+    if corr_func == stats.spearmanr:
+        return corr_func(data1, data2)[0]
+    else:
+        non_nan_indices = ~(np.isnan(data1) | np.isnan(data2))
+        return corr_func(data1[non_nan_indices], data2[non_nan_indices])[0]
+
+
+def _corr_test_base(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    only_significant: bool,
+    n_perm: int,
+    seed: int,
+    corr_func: Callable,
+    test_name: str,
+    n_jobs: int = -1,
+) -> Dict[str, Any]:
+    np.random.seed(seed)
+    seeds = np.random.randint(0, n_perm * 100, size=n_perm)
+
+    if corr_func != stats.spearmanr:
+        # Convert to numeric, replacing non-numeric values with NaN
+        data1 = pd.to_numeric(data1, errors="coerce")
+        data2 = pd.to_numeric(data2, errors="coerce")
+
+        # Remove NaN values
+        mask = ~(np.isnan(data1) | np.isnan(data2))
+        data1 = data1[mask]
+        data2 = data2[mask]
+
+    if len(data1) < 2 or len(data2) < 2:
+        raise ValueError("Not enough valid numeric data points for correlation.")
+
+    corr_obs, _ = corr_func(data1, data2)
+
+    # def _corr_test_base(
+    #     data1: np.ndarray,
+    #     data2: np.ndarray,
+    #     only_significant: bool,
+    #     n_perm: int,
+    #     seed: int,
+    #     corr_func: Callable,
+    #     test_name: str,
+    #     n_jobs: int = -1
+    # ) -> Dict[str, Any]:
+    #     # Random seed
+    #     np.random.seed(seed)
+    #     seeds = np.random.randint(0, n_perm*100, size=n_perm)
+
+    #     # Convert data to numeric type and handle non-numeric values
+    #     data1 = np.asarray(data1, dtype=float)
+    #     data2 = np.asarray(data2, dtype=float)
+
+    #     # Remove NaN values
+    #     mask = ~(np.isnan(data1) | np.isnan(data2))
+    #     data1 = data1[mask]
+    #     data2 = data2[mask]
+
+    #     corr_obs, _ = corr_func(data1, data2)
+
+    if n_jobs != 1:
+        n_jobs = mp.cpu_count() if n_jobs == -1 else n_jobs
+        with mp.Pool(n_jobs) as pool:
+            surrogate = np.array(
+                pool.map(
+                    _compute_surrogate, [(data1, data2, corr_func, s) for s in seeds]
+                )
+            )
+    else:
+        surrogate = np.array(
+            [_compute_surrogate((data1, data2, corr_func, s)) for s in seeds]
+        )
+
+    # Add normality test for surrogate distribution
+    _, p_normal = stats.normaltest(surrogate)
+    if not p_normal > 0.05:
+        print(f"Warning: Surrogate distribution may not be normal (p={p_normal:.3f})")
+
+    rank = bisect_right(sorted(surrogate), corr_obs)
+    pvalue = min(rank, n_perm - rank) / n_perm * 2
+
+    stars = scitex.stats.p2stars(pvalue)
+    sample_size = len(data1)
+    effect_size = np.abs(corr_obs)
+
+    result_string = (
+        f"{test_name} Corr. = {corr_obs:.3f}; p-value = {pvalue:.3f} "
+        f"(n={sample_size:,}, eff={effect_size:.3f}) {stars}"
+    )
+
+    if not only_significant or (only_significant and pvalue < 0.05):
+        print(result_string)
+
+    return {
+        "p_value": round(pvalue, 3),
+        "stars": stars,
+        "effsize": round(effect_size, 3),
+        "corr": round(corr_obs, 3),
+        "surrogate": surrogate,
+        "n": sample_size,
+        "test_name": f"Permutation-based {test_name} correlation test",
+        "statistic": round(corr_obs, 3),
+        "H0": f"There is no {test_name.lower()} correlation between the two variables",
+    }
+
+
+@numpy_fn
+def corr_test_spearman(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    only_significant: bool = False,
+    n_perm: int = 1_000,
+    seed: int = 42,
+) -> Dict[str, Any]:
+    return _corr_test_base(
+        data1, data2, only_significant, n_perm, seed, stats.spearmanr, "Spearman"
+    )
+
+
+@numpy_fn
+def corr_test_pearson(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    only_significant: bool = False,
+    n_perm: int = 1_000,
+    seed: int = 42,
+) -> Dict[str, Any]:
+    return _corr_test_base(
+        data1, data2, only_significant, n_perm, seed, stats.pearsonr, "Pearson"
+    )
+
+
+@numpy_fn
+def corr_test(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    test: Literal["pearson", "spearman"] = "pearson",
+    only_significant: bool = False,
+    n_perm: int = 1_000,
+    seed: int = 42,
+) -> Dict[str, Any]:
+    """
+    Performs a correlation test between two datasets using permutation.
+
+    Parameters
+    ----------
+    data1 : np.ndarray
+        First dataset for correlation.
+    data2 : np.ndarray
+        Second dataset for correlation.
+    test : {"pearson", "spearman"}, optional
+        Type of correlation test to perform. Default is "pearson".
+    only_significant : bool, optional
+        If True, only prints significant results. Default is False.
+    n_perm : int, optional
+        Number of permutations for the test. Default is 1,000.
+    seed : int, optional
+        Random seed for reproducibility. Default is 42.
+
+    Returns
+    -------
+    Dict[str, Any]
+        Contains 'p_value', 'stars', 'effsize', 'corr', 'surrogate', 'n', 'test_name', 'statistic', and 'H0'.
+
+    Example
+    -------
+    >>> xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+    >>> yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+    >>> results = corr_test(xx, yy, test="pearson")
+    """
+    if test == "spearman":
+        return corr_test_spearman(data1, data2, only_significant, n_perm, seed)
+    elif test == "pearson":
+        return corr_test_pearson(data1, data2, only_significant, n_perm, seed)
+    else:
+        raise ValueError("Invalid test type. Choose 'pearson' or 'spearman'.")
+
+
+if __name__ == "__main__":
+    xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+    yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+    results_pearson = corr_test(xx, yy)
+    results_spearman = corr_test(xx, yy, test="spearman")
+    print("Pearson results:", results_pearson)
+    print("Spearman results:", results_spearman)
+# #!/usr/bin/env python3
+# # -*- coding: utf-8 -*-
+# # Time-stamp: "2024-10-06 12:02:18 (ywatanabe)"
+
+# from bisect import bisect_right
+# import numpy as np
+# import scitex
+# from scipy import stats
+# from typing import Any, Literal, Dict, List
+
+# def _corr_test_base(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     only_significant: bool,
+#     n_perm: int,
+#     seed: int,
+#     corr_func: callable,
+#     test_name: str
+# ) -> Dict[str, Any]:
+#     np.random.seed(seed)
+
+#     non_nan_indices = ~(np.isnan(data1) | np.isnan(data2))
+#     data1, data2 = data1[non_nan_indices], data2[non_nan_indices]
+
+#     corr_obs, _ = corr_func(data1, data2)
+#     surrogate = [
+#         corr_func(data1, np.random.permutation(data2))[0]
+#         for _ in range(n_perm)
+#     ]
+
+#     rank = bisect_right(sorted(surrogate), corr_obs)
+#     pvalue = min(rank, n_perm - rank) / n_perm * 2
+
+#     stars = scitex.stats.p2stars(pvalue)
+#     sample_size = len(data1)
+#     effect_size = np.abs(corr_obs)
+
+#     # result_string = (
+#     #     f"{test_name} Corr. = {corr_obs:.3f}; p-value = {pvalue:.3f} "
+#     #     f"(n={sample_size:,}, eff={effect_size:.3f}) {stars}"
+#     # )
+
+#     if not only_significant or (only_significant and pvalue < 0.05):
+#         print(result_string)
+
+#     return {
+#         "p_value": round(pvalue, 3),
+#         "stars": stars,
+#         "effsize": round(effect_size, 3),
+#         "corr": round(corr_obs, 3),
+#         "surrogate": np.array(surrogate),
+#         "n": sample_size,
+#         "test_name": f"Permutation-based {test_name} correlation",
+#         "statistic": round(corr_obs, 3),
+#         "H0": f"There is no {test_name.lower()} correlation between the two variables",
+#     }
+
+# def corr_test_spearman(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     only_significant: bool = False,
+#     n_perm: int = 1_000,
+#     seed: int = 42,
+# ) -> Dict[str, Any]:
+#     return _corr_test_base(data1, data2, only_significant, n_perm, seed, stats.spearmanr, "Spearman")
+
+# def corr_test_pearson(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     only_significant: bool = False,
+#     n_perm: int = 1_000,
+#     seed: int = 42,
+# ) -> Dict[str, Any]:
+#     return _corr_test_base(data1, data2, only_significant, n_perm, seed, stats.pearsonr, "Pearson")
+
+# def corr_test(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     test: Literal["pearson", "spearman"] = "pearson",
+#     only_significant: bool = False,
+#     n_perm: int = 1_000,
+#     seed: int = 42,
+# ) -> Dict[str, Any]:
+#     """
+#     Performs a correlation test between two datasets using permutation.
+
+#     Parameters
+#     ----------
+#     data1 : np.ndarray
+#         First dataset for correlation.
+#     data2 : np.ndarray
+#         Second dataset for correlation.
+#     test : {"pearson", "spearman"}, optional
+#         Type of correlation test to perform. Default is "pearson".
+#     only_significant : bool, optional
+#         If True, only prints significant results. Default is False.
+#     n_perm : int, optional
+#         Number of permutations for the test. Default is 1,000.
+#     seed : int, optional
+#         Random seed for reproducibility. Default is 42.
+
+#     Returns
+#     -------
+#     Dict[str, Any]
+#         Contains 'p_value', 'stars', 'effsize', 'corr', 'surrogate', 'n', 'test_name', 'statistic', and 'H0'.
+
+#     Example
+#     -------
+#     >>> xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+#     >>> yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+#     >>> results = corr_test(xx, yy, test="pearson")
+#     """
+#     if test == "spearman":
+#         return corr_test_spearman(data1, data2, only_significant, n_perm, seed)
+#     elif test == "pearson":
+#         return corr_test_pearson(data1, data2, only_significant, n_perm, seed)
+#     else:
+#         raise ValueError("Invalid test type. Choose 'spearman' or 'pearson'.")
+
+# if __name__ == "__main__":
+#     xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+#     yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+#     results_spearman = corr_test(xx, yy)
+#     results_pearson = corr_test(xx, yy, test="pearson")
+#     print("Spearman results:", results_spearman)
+#     print("Pearson results:", results_pearson)

scitex/stats/tests/__corr_test_single.py

@@ -0,0 +1,277 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Time-stamp: "2024-10-06 12:04:31 (ywatanabe)"
+
+from bisect import bisect_right
+import numpy as np
+import scitex
+from scipy import stats
+from typing import Any, Literal, Dict, Callable
+
+
+def _corr_test_base(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    only_significant: bool,
+    num_permutations: int,
+    seed: int,
+    corr_func: Callable,
+    test_name: str,
+) -> Dict[str, Any]:
+    np.random.seed(seed)
+
+    non_nan_indices = ~(np.isnan(data1) | np.isnan(data2))
+    data1, data2 = data1[non_nan_indices], data2[non_nan_indices]
+
+    corr_obs, _ = corr_func(data1, data2)
+    surrogate = np.array(
+        [
+            corr_func(data1, np.random.permutation(data2))[0]
+            for _ in range(num_permutations)
+        ]
+    )
+
+    rank = bisect_right(sorted(surrogate), corr_obs)
+    pvalue = min(rank, num_permutations - rank) / num_permutations * 2
+
+    stars = scitex.stats.p2stars(pvalue)
+    sample_size = len(data1)
+    effect_size = np.abs(corr_obs)
+
+    result_string = (
+        f"{test_name} Corr. = {corr_obs:.3f}; p-value = {pvalue:.3f} "
+        f"(n={sample_size:,}, eff={effect_size:.3f}) {stars}"
+    )
+
+    if not only_significant or (only_significant and pvalue < 0.05):
+        print(result_string)
+
+    return {
+        "p_value": round(pvalue, 3),
+        "stars": stars,
+        "effsize": round(effect_size, 3),
+        "corr": round(corr_obs, 3),
+        "surrogate": surrogate,
+        "n": sample_size,
+        "test_name": f"Permutation-based {test_name} correlation",
+        "statistic": round(corr_obs, 3),
+        "H0": f"There is no {test_name.lower()} correlation between the two variables",
+    }
+
+
+def corr_test_spearman(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    only_significant: bool = False,
+    num_permutations: int = 1_000,
+    seed: int = 42,
+) -> Dict[str, Any]:
+    return _corr_test_base(
+        data1,
+        data2,
+        only_significant,
+        num_permutations,
+        seed,
+        stats.spearmanr,
+        "Spearman",
+    )
+
+
+def corr_test_pearson(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    only_significant: bool = False,
+    num_permutations: int = 1_000,
+    seed: int = 42,
+) -> Dict[str, Any]:
+    return _corr_test_base(
+        data1,
+        data2,
+        only_significant,
+        num_permutations,
+        seed,
+        stats.pearsonr,
+        "Pearson",
+    )
+
+
+def corr_test(
+    data1: np.ndarray,
+    data2: np.ndarray,
+    test: Literal["pearson", "spearman"] = "pearson",
+    only_significant: bool = False,
+    num_permutations: int = 1_000,
+    seed: int = 42,
+) -> Dict[str, Any]:
+    """
+    Performs a correlation test between two datasets using permutation.
+
+    Parameters
+    ----------
+    data1 : np.ndarray
+        First dataset for correlation.
+    data2 : np.ndarray
+        Second dataset for correlation.
+    test : {"pearson", "spearman"}, optional
+        Type of correlation test to perform. Default is "pearson".
+    only_significant : bool, optional
+        If True, only prints significant results. Default is False.
+    num_permutations : int, optional
+        Number of permutations for the test. Default is 1,000.
+    seed : int, optional
+        Random seed for reproducibility. Default is 42.
+
+    Returns
+    -------
+    Dict[str, Any]
+        Contains 'p_value', 'stars', 'effsize', 'corr', 'surrogate', 'n', 'test_name', 'statistic', and 'H0'.
+
+    Example
+    -------
+    >>> xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+    >>> yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+    >>> results = corr_test(xx, yy, test="pearson")
+    """
+    if test == "spearman":
+        return corr_test_spearman(
+            data1, data2, only_significant, num_permutations, seed
+        )
+    elif test == "pearson":
+        return corr_test_pearson(data1, data2, only_significant, num_permutations, seed)
+    else:
+        raise ValueError("Invalid test type. Choose 'pearson' or 'spearman'.")
+
+
+if __name__ == "__main__":
+    xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+    yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+    results_pearson = corr_test(xx, yy)
+    results_spearman = corr_test(xx, yy, test="spearman")
+    print("Pearson results:", results_pearson)
+    print("Spearman results:", results_spearman)
+# #!/usr/bin/env python3
+# # -*- coding: utf-8 -*-
+# # Time-stamp: "2024-10-06 12:02:18 (ywatanabe)"
+
+# from bisect import bisect_right
+# import numpy as np
+# import scitex
+# from scipy import stats
+# from typing import Any, Literal, Dict, List
+
+# def _corr_test_base(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     only_significant: bool,
+#     num_permutations: int,
+#     seed: int,
+#     corr_func: callable,
+#     test_name: str
+# ) -> Dict[str, Any]:
+#     np.random.seed(seed)
+
+#     non_nan_indices = ~(np.isnan(data1) | np.isnan(data2))
+#     data1, data2 = data1[non_nan_indices], data2[non_nan_indices]
+
+#     corr_obs, _ = corr_func(data1, data2)
+#     surrogate = [
+#         corr_func(data1, np.random.permutation(data2))[0]
+#         for _ in range(num_permutations)
+#     ]
+
+#     rank = bisect_right(sorted(surrogate), corr_obs)
+#     pvalue = min(rank, num_permutations - rank) / num_permutations * 2
+
+#     stars = scitex.stats.p2stars(pvalue)
+#     sample_size = len(data1)
+#     effect_size = np.abs(corr_obs)
+
+#     # result_string = (
+#     #     f"{test_name} Corr. = {corr_obs:.3f}; p-value = {pvalue:.3f} "
+#     #     f"(n={sample_size:,}, eff={effect_size:.3f}) {stars}"
+#     # )
+
+#     if not only_significant or (only_significant and pvalue < 0.05):
+#         print(result_string)
+
+#     return {
+#         "p_value": round(pvalue, 3),
+#         "stars": stars,
+#         "effsize": round(effect_size, 3),
+#         "corr": round(corr_obs, 3),
+#         "surrogate": np.array(surrogate),
+#         "n": sample_size,
+#         "test_name": f"Permutation-based {test_name} correlation",
+#         "statistic": round(corr_obs, 3),
+#         "H0": f"There is no {test_name.lower()} correlation between the two variables",
+#     }
+
+# def corr_test_spearman(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     only_significant: bool = False,
+#     num_permutations: int = 1_000,
+#     seed: int = 42,
+# ) -> Dict[str, Any]:
+#     return _corr_test_base(data1, data2, only_significant, num_permutations, seed, stats.spearmanr, "Spearman")
+
+# def corr_test_pearson(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     only_significant: bool = False,
+#     num_permutations: int = 1_000,
+#     seed: int = 42,
+# ) -> Dict[str, Any]:
+#     return _corr_test_base(data1, data2, only_significant, num_permutations, seed, stats.pearsonr, "Pearson")
+
+# def corr_test(
+#     data1: np.ndarray,
+#     data2: np.ndarray,
+#     test: Literal["pearson", "spearman"] = "pearson",
+#     only_significant: bool = False,
+#     num_permutations: int = 1_000,
+#     seed: int = 42,
+# ) -> Dict[str, Any]:
+#     """
+#     Performs a correlation test between two datasets using permutation.
+
+#     Parameters
+#     ----------
+#     data1 : np.ndarray
+#         First dataset for correlation.
+#     data2 : np.ndarray
+#         Second dataset for correlation.
+#     test : {"pearson", "spearman"}, optional
+#         Type of correlation test to perform. Default is "pearson".
+#     only_significant : bool, optional
+#         If True, only prints significant results. Default is False.
+#     num_permutations : int, optional
+#         Number of permutations for the test. Default is 1,000.
+#     seed : int, optional
+#         Random seed for reproducibility. Default is 42.
+
+#     Returns
+#     -------
+#     Dict[str, Any]
+#         Contains 'p_value', 'stars', 'effsize', 'corr', 'surrogate', 'n', 'test_name', 'statistic', and 'H0'.
+
+#     Example
+#     -------
+#     >>> xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+#     >>> yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+#     >>> results = corr_test(xx, yy, test="pearson")
+#     """
+#     if test == "spearman":
+#         return corr_test_spearman(data1, data2, only_significant, num_permutations, seed)
+#     elif test == "pearson":
+#         return corr_test_pearson(data1, data2, only_significant, num_permutations, seed)
+#     else:
+#         raise ValueError("Invalid test type. Choose 'spearman' or 'pearson'.")
+
+# if __name__ == "__main__":
+#     xx = np.array([3, 4, 4, 5, 7, 8, 10, 12, 13, 15])
+#     yy = np.array([2, 4, 4, 5, 4, 7, 8, 19, 14, 10])
+#     results_spearman = corr_test(xx, yy)
+#     results_pearson = corr_test(xx, yy, test="pearson")
+#     print("Spearman results:", results_spearman)
+#     print("Pearson results:", results_pearson)

scitex/stats/tests/__init__.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+"""Scitex tests module."""
+
+from .__corr_test import corr_test, corr_test_pearson, corr_test_spearman
+from .__corr_test_multi import corr_test as corr_test_multi
+from .__corr_test_single import corr_test as corr_test_single, _corr_test_base
+from ._brunner_munzel_test import brunner_munzel_test
+from ._nocorrelation_test import calc_partial_corrcoef, nocorrelation_test
+from ._smirnov_grubbs import smirnov_grubbs
+
+__all__ = [
+    "brunner_munzel_test",
+    "calc_partial_corrcoef",
+    "corr_test",
+    "corr_test_multi",
+    "corr_test_single",
+    "corr_test_pearson",
+    "corr_test_spearman",
+    "_corr_test_base",
+    "nocorrelation_test",
+    "smirnov_grubbs",
+]