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"""Type stubs for scirs2 - Scientific Computing in Rust for Python."""
# =============================================================================
# Clustering Module
# =============================================================================
"""K-Means clustering algorithm."""
:
:
...
...
"""Calculate silhouette score for clustering evaluation."""
...
"""Calculate Davies-Bouldin score for clustering evaluation."""
...
"""Calculate Calinski-Harabasz score for clustering evaluation."""
...
"""Standardize data (zero mean, unit variance)."""
...
"""Normalize data rows (l1, l2, or max norm)."""
...
# =============================================================================
# Time Series Module
# =============================================================================
"""Time series data container."""
...
...
...
...
...
...
...
...
"""ARIMA time series model."""
...
...
...
...
...
...
...
"""Apply differencing to a time series."""
...
"""Apply seasonal differencing to a time series."""
...
"""Perform STL decomposition. Returns dict with trend, seasonal, residual."""
...
"""Augmented Dickey-Fuller test for stationarity."""
...
"""Box-Cox transformation. Returns dict with transformed data and lambda."""
...
"""Inverse Box-Cox transformation."""
...
# =============================================================================
# Linear Algebra Module
# =============================================================================
"""Compute matrix determinant."""
...
"""Compute matrix inverse."""
...
"""Compute matrix trace."""
...
"""LU decomposition. Returns dict with L, U, P matrices."""
...
"""QR decomposition. Returns dict with Q, R matrices."""
...
"""SVD decomposition. Returns dict with U, S, Vt matrices."""
...
"""Cholesky decomposition for positive definite matrices."""
...
"""Eigenvalue decomposition. Returns dict with eigenvalues and eigenvectors."""
...
"""Eigenvalue decomposition for symmetric/Hermitian matrices."""
...
"""Compute eigenvalues only."""
...
"""Solve linear system Ax = b."""
...
"""Least squares solution to Ax = b."""
...
"""Compute matrix norm (fro, 1, inf)."""
...
"""Compute vector norm."""
...
"""Compute matrix condition number."""
...
"""Compute matrix rank."""
...
"""
Compute the Moore-Penrose pseudoinverse of a matrix.
The pseudoinverse of a matrix A, denoted A⁺, is defined as the
matrix that satisfies the Moore-Penrose conditions:
- A A⁺ A = A
- A⁺ A A⁺ = A⁺
- (A A⁺)ᵀ = A A⁺
- (A⁺ A)ᵀ = A⁺ A
Parameters:
a: Input matrix (m × n)
rcond: Cutoff threshold for small singular values.
Singular values smaller than rcond are treated as zero.
If None, uses machine precision * max(m, n) * largest_singular_value
Returns:
Pseudoinverse of the matrix (n × m)
Notes:
- For invertible square matrices, pinv(A) = inv(A)
- For rank-deficient matrices, provides the minimum-norm least-squares solution
- Computed using SVD: A⁺ = V Σ⁺ Uᵀ where A = U Σ Vᵀ
Examples:
>>> a = np.array([[1, 2], [3, 4], [5, 6]])
>>> a_pinv = scirs2.pinv_py(a)
>>> # Verify A A⁺ A = A
>>> np.allclose(a @ a_pinv @ a, a)
True
"""
...
# =============================================================================
# Statistics Module
# =============================================================================
"""Compute descriptive statistics (mean, std, var, min, max, median, count)."""
...
"""Compute mean."""
...
"""Compute standard deviation."""
...
"""Compute variance."""
...
"""Compute percentile (0-100)."""
...
"""Compute median."""
...
"""Compute interquartile range."""
...
"""Compute Pearson correlation coefficient."""
...
"""Compute covariance."""
...
# Statistical tests
"""
One-sample t-test.
Parameters:
data: Sample data
popmean: Population mean for null hypothesis
alternative: 'two-sided', 'less', or 'greater'
Returns:
Dict with 'statistic', 'pvalue', 'df'
"""
...
"""
Two-sample independent t-test.
Parameters:
a: First sample
b: Second sample
equal_var: If True, assume equal variance
alternative: 'two-sided', 'less', or 'greater'
Returns:
Dict with 'statistic', 'pvalue', 'df'
"""
...
"""
Paired (related samples) t-test.
Tests whether the means of two related/paired samples differ. This is a
parametric test for paired observations (e.g., before/after measurements,
matched pairs, repeated measures on the same subjects).
The paired t-test works by computing the differences between paired
observations (d_i = a_i - b_i), then performing a one-sample t-test on
these differences to test if the mean difference is significantly different
from zero.
Parameters:
a: First array of observations (e.g., before treatment)
b: Second array of observations (e.g., after treatment)
Must be same length as a (paired observations)
alternative: Alternative hypothesis (default: "two-sided")
- "two-sided" or "two_sided": Test if means differ (μ_d ≠ 0)
- "less": Test if a < b (μ_d < 0)
- "greater": Test if a > b (μ_d > 0)
Returns:
Dictionary with:
- statistic: t-statistic computed from the differences
- pvalue: P-value for the hypothesis test
- df: Degrees of freedom (n - 1, where n is number of pairs)
Examples:
>>> # Before and after treatment measurements
>>> before = np.array([140, 145, 138, 142, 147], dtype=np.float64)
>>> after = np.array([125, 130, 122, 128, 132], dtype=np.float64)
>>> result = scirs2.ttest_rel_py(before, after)
>>> print(f"t={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Test if treatment reduced values (one-sided test)
>>> result = scirs2.ttest_rel_py(before, after, alternative="greater")
>>> if result['pvalue'] < 0.05:
... print("Treatment significantly reduced values")
>>> # Matched pairs design (e.g., twins)
>>> twin1 = np.array([75, 82, 79, 85, 88], dtype=np.float64)
>>> twin2 = np.array([78, 85, 82, 89, 92], dtype=np.float64)
>>> result = scirs2.ttest_rel_py(twin1, twin2)
Notes:
- **Assumptions**:
1. Paired observations (each a_i paired with corresponding b_i)
2. Differences are approximately normally distributed
3. Observations are independent
- **Use cases**:
- Before/after measurements on same subjects
- Matched pairs experimental designs
- Repeated measures on same subjects
- Crossover study designs
- **When NOT to use**:
- For independent samples → use ttest_ind_py instead
- For non-normal differences → consider wilcoxon_py (signed-rank test)
- The test is more powerful than independent t-test when observations
are truly paired, as it accounts for within-pair correlation
- If all differences are identical (zero variance), the test statistic
will be infinite and p-value will be 0
Statistical Background:
The test statistic is computed as:
t = (mean(d) - 0) / (std(d) / sqrt(n))
where d = a - b are the paired differences, and follows a t-distribution
with n-1 degrees of freedom under the null hypothesis (mean difference = 0).
See Also:
- ttest_1samp_py: One-sample t-test
- ttest_ind_py: Independent two-sample t-test
- wilcoxon_py: Non-parametric alternative for paired samples
"""
...
"""
Shapiro-Wilk test for normality.
Tests the null hypothesis that the data was drawn from a normal distribution.
Parameters:
data: Sample data
Returns:
Dictionary with:
- statistic: W statistic
- pvalue: Two-sided p-value
Notes:
- Sample size should be between 3 and 5000
- Higher W values indicate more normality
- Reject normality if pvalue < significance level (e.g., 0.05)
"""
...
"""
Chi-square goodness-of-fit test.
Tests whether observed frequencies differ from expected frequencies.
Parameters:
observed: Observed frequencies
expected: Expected frequencies (optional, defaults to uniform distribution)
Returns:
Dictionary with:
- statistic: Chi-square statistic
- pvalue: Two-sided p-value
- dof: Degrees of freedom
Examples:
>>> observed = np.array([10, 15, 12, 13])
>>> result = scirs2.chisquare_py(observed)
"""
...
"""
Chi-square test for independence in contingency tables.
Tests whether two categorical variables are independent using a contingency
table (cross-tabulation) of observed frequencies. Under the null hypothesis,
the row and column variables are independent.
Parameters:
observed: 2D array of observed frequencies (contingency table)
Must have at least 2 rows and 2 columns
Each cell represents the count for a combination of categories
Returns:
Dictionary with:
- statistic: Chi-square test statistic
- pvalue: P-value for the test
- df: Degrees of freedom ((rows-1) × (columns-1))
- expected: 2D array of expected frequencies under independence
Raises:
RuntimeError: If the table has fewer than 2 rows or 2 columns
Examples:
>>> # Test independence between treatment and outcome (2×2 table)
>>> observed = np.array([
... [10, 20], # Treatment A: Success, Failure
... [15, 25] # Treatment B: Success, Failure
... ], dtype=np.int64)
>>> result = scirs2.chi2_independence_py(observed)
>>> print(f"χ²={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Test independence between education and income (3×3 table)
>>> observed = np.array([
... [20, 30, 10], # High school: Low, Medium, High income
... [15, 25, 20], # Bachelor's: Low, Medium, High income
... [25, 15, 40] # Graduate: Low, Medium, High income
... ], dtype=np.int64)
>>> result = scirs2.chi2_independence_py(observed)
>>> if result['pvalue'] < 0.05:
... print("Variables are dependent (reject independence)")
... else:
... print("Variables appear independent")
Notes:
- This test assumes all expected frequencies are at least 5
- For 2×2 tables with small samples, consider using chi2_yates_py
- Expected frequencies are calculated as:
E[i,j] = (row_i_sum × col_j_sum) / total
- The test statistic is: χ² = Σ[(O - E)² / E]
- Degrees of freedom: df = (rows - 1) × (columns - 1)
- Large χ² values (small p-values) indicate dependence
- The test does not indicate the direction or nature of the association
"""
...
"""
Chi-square test with Yates' continuity correction for 2×2 tables.
Applies Yates' continuity correction to improve the chi-square approximation
for 2×2 contingency tables, especially with small sample sizes. The correction
reduces the chi-square statistic, making the test more conservative.
Parameters:
observed: 2×2 array of observed frequencies
Must be exactly 2 rows and 2 columns
Returns:
Dictionary with:
- statistic: Chi-square test statistic with Yates' correction
- pvalue: P-value for the test
- df: Degrees of freedom (always 1 for 2×2 tables)
- expected: 2×2 array of expected frequencies under independence
Raises:
RuntimeError: If the table is not 2×2
Examples:
>>> # Test with small sample (where Yates' correction is beneficial)
>>> observed = np.array([
... [8, 12], # Group 1: Success, Failure
... [10, 15] # Group 2: Success, Failure
... ], dtype=np.int64)
>>> result = scirs2.chi2_yates_py(observed)
>>> print(f"χ²={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Compare with standard chi-square test
>>> yates_result = scirs2.chi2_yates_py(observed)
>>> chi2_result = scirs2.chi2_independence_py(observed)
>>> print(f"Yates: χ²={yates_result['statistic']:.3f}")
>>> print(f"Standard: χ²={chi2_result['statistic']:.3f}")
>>> # Yates gives lower (more conservative) statistic
Notes:
- **Only for 2×2 tables** - use chi2_independence_py for larger tables
- Recommended when expected frequencies are between 5 and 10
- The correction subtracts 0.5 from |O - E| before squaring:
χ²_Yates = Σ[(|O - E| - 0.5)² / E]
- Makes the test more conservative (higher p-values)
- More accurate p-values for small samples than uncorrected test
- For very small samples (expected < 5), consider Fisher's exact test
- Degrees of freedom is always 1 for 2×2 tables
"""
...
# Contingency table analysis
"""
Fisher's exact test for 2×2 contingency tables.
Performs Fisher's exact test, which calculates the exact probability of
observing a table at least as extreme as the one given, under the null
hypothesis of independence. Particularly useful for small sample sizes
where chi-square approximation may not be valid.
Fisher's exact test is based on the hypergeometric distribution and
provides exact p-values without relying on large-sample approximations.
Parameters:
table: 2×2 array of observed frequencies
Must be exactly 2 rows and 2 columns
[[a, b],
[c, d]]
where a, b, c, d are counts (frequencies)
alternative: Alternative hypothesis (default: "two-sided")
- "two-sided": Test if association exists (OR ≠ 1)
- "less": Test if odds ratio < 1
- "greater": Test if odds ratio > 1
Returns:
Dictionary with:
- odds_ratio: Odds ratio (a*d)/(b*c)
Measure of association strength
- pvalue: Exact p-value for the test
Examples:
>>> # Example: Treatment effectiveness study
>>> # Rows: Treatment (Yes/No), Cols: Improved (Yes/No)
>>> table = np.array([[8, 2], # Treated: 8 improved, 2 not
... [1, 5]], # Control: 1 improved, 5 not
... dtype=np.float64)
>>> result = scirs2.fisher_exact_py(table)
>>> print(f"OR={result['odds_ratio']:.2f}, p={result['pvalue']:.4f}")
>>> if result['pvalue'] < 0.05:
... print("Significant association found")
>>> # Example: Small sample case (where chi-square wouldn't be valid)
>>> table = np.array([[2, 1], [1, 2]], dtype=np.float64)
>>> result = scirs2.fisher_exact_py(table)
>>> # One-sided test for increased odds
>>> result = scirs2.fisher_exact_py(table, alternative="greater")
Notes:
- **Use when**:
* Sample size is small (expected frequencies < 5)
* Need exact p-values (not approximations)
* 2×2 contingency table analysis
- **Assumptions**:
* Fixed row and column margins (hypergeometric model)
* Independent observations
* All values must be non-negative counts
- **Interpretation**:
* Odds ratio = 1: No association
* Odds ratio > 1: Positive association (rows/cols concordant)
* Odds ratio < 1: Negative association (rows/cols discordant)
* Odds ratio = 0 or ∞: Perfect association
- **Comparison with chi-square**:
* Fisher's exact: Always valid, computationally intensive for large tables
* Chi-square: Approximation, requires expected frequencies ≥ 5
* For large samples, both give similar results
- The test is "exact" because it computes the probability directly
using the hypergeometric distribution, not a large-sample approximation
Statistical Background:
Under the null hypothesis of independence, the probability of observing
the table [[a,b],[c,d]] with fixed margins is:
P = [(a+b)!(c+d)!(a+c)!(b+d)!] / [n!a!b!c!d!]
where n = a+b+c+d is the total sample size.
See Also:
- chi2_independence_py: Chi-square test for larger tables
- chi2_yates_py: Chi-square with Yates' correction for 2×2 tables
- odds_ratio_py: Calculate odds ratio only
"""
...
"""
Calculate odds ratio for a 2×2 contingency table.
The odds ratio (OR) is a measure of association between an exposure and
an outcome. It quantifies how strongly the presence of exposure is
associated with the presence of outcome.
For a 2×2 contingency table:
Outcome+ Outcome-
Exposed+ a b
Exposed- c d
Odds Ratio = (a × d) / (b × c)
Parameters:
table: 2×2 array of observed frequencies
Must be exactly 2 rows and 2 columns
Returns:
Odds ratio value (float)
Examples:
>>> # Example: Case-control study
>>> # Rows: Cases/Controls, Cols: Exposed/Not Exposed
>>> table = np.array([[10, 5], # Cases: 10 exposed, 5 not
... [3, 12]], # Controls: 3 exposed, 12 not
... dtype=np.float64)
>>> or_val = scirs2.odds_ratio_py(table)
>>> print(f"Odds Ratio: {or_val:.2f}")
>>> # OR = (10*12)/(5*3) = 120/15 = 8.0
>>> # Exposed individuals have 8× the odds of being cases
>>> # Example: Equal odds (no association)
>>> table = np.array([[10, 10], [10, 10]], dtype=np.float64)
>>> or_val = scirs2.odds_ratio_py(table)
>>> print(f"OR: {or_val:.2f}") # OR = 1.0
>>> # Example: Protective factor (OR < 1)
>>> table = np.array([[2, 10], [10, 5]], dtype=np.float64)
>>> or_val = scirs2.odds_ratio_py(table)
>>> print(f"OR: {or_val:.2f}") # OR = 0.1
Notes:
- **Interpretation**:
* OR = 1: No association (exposure doesn't affect odds)
* OR > 1: Positive association (exposure increases odds)
* OR < 1: Negative association (exposure decreases odds / protective)
* OR = 0: Impossible outcome when exposed
* OR = ∞: Impossible outcome when not exposed
- **Use cases**:
* Case-control studies (preferred over relative risk)
* Cross-sectional studies
* Logistic regression interpretation
- **Relationship to relative risk**:
* For rare outcomes (< 10% incidence): OR ≈ RR
* For common outcomes: OR > RR (overestimates risk)
* OR is always further from 1 than RR
- **Confidence intervals**:
* Use Fisher's exact test to get p-values
* 95% CI can be computed as: exp(ln(OR) ± 1.96 × SE)
* where SE = sqrt(1/a + 1/b + 1/c + 1/d)
- **Continuity correction**:
* For zero cells, add 0.5 to all cells: (a+0.5)(d+0.5)/(b+0.5)(c+0.5)
* This implementation uses exact calculation
Statistical Background:
The odds ratio compares the odds of outcome in the exposed group
(a/b) to the odds in the unexposed group (c/d):
OR = (a/b) / (c/d) = (a×d) / (b×c)
See Also:
- fisher_exact_py: Includes OR with significance test
- relative_risk_py: Alternative measure for cohort studies
"""
...
"""
Calculate relative risk (risk ratio) for a 2×2 contingency table.
The relative risk (RR) or risk ratio is a measure of association between
an exposure and an outcome in cohort studies. It compares the risk of
outcome in the exposed group to the risk in the unexposed group.
For a 2×2 contingency table:
Outcome+ Outcome-
Exposed+ a b
Exposed- c d
Relative Risk = [a/(a+b)] / [c/(c+d)]
Parameters:
table: 2×2 array of observed frequencies
Must be exactly 2 rows and 2 columns
Returns:
Relative risk value (float)
Examples:
>>> # Example: Cohort study
>>> # Rows: Exposed/Unexposed, Cols: Disease+/Disease-
>>> table = np.array([[20, 80], # Exposed: 20 diseased, 80 not
... [10, 90]], # Unexposed: 10 diseased, 90 not
... dtype=np.float64)
>>> rr_val = scirs2.relative_risk_py(table)
>>> print(f"Relative Risk: {rr_val:.2f}")
>>> # RR = (20/100)/(10/100) = 0.2/0.1 = 2.0
>>> # Exposed group has 2× the risk of disease
>>> # Example: No association (RR = 1)
>>> table = np.array([[10, 40], [10, 40]], dtype=np.float64)
>>> rr_val = scirs2.relative_risk_py(table)
>>> print(f"RR: {rr_val:.2f}") # RR = 1.0
>>> # Example: Protective factor (RR < 1)
>>> table = np.array([[5, 45], [20, 30]], dtype=np.float64)
>>> rr_val = scirs2.relative_risk_py(table)
>>> print(f"RR: {rr_val:.2f}") # RR = 0.25
Notes:
- **Interpretation**:
* RR = 1: No association (equal risk in both groups)
* RR > 1: Positive association (exposure increases risk)
* RR < 1: Negative association (exposure decreases risk / protective)
* RR = 0: No cases in exposed group
* RR = ∞: No cases in unexposed group
- **Use cases**:
* Cohort studies (prospective or retrospective)
* Randomized controlled trials
* When disease incidence can be directly measured
- **Comparison with odds ratio**:
* For rare diseases (< 10% incidence): RR ≈ OR
* For common diseases: RR < OR
* RR is always closer to 1 than OR
* RR is more intuitive and easier to interpret
- **When NOT to use**:
* Case-control studies (can't estimate incidence)
* Use odds ratio instead for case-control designs
- **Confidence intervals**:
* 95% CI can be computed as: exp(ln(RR) ± 1.96 × SE)
* where SE = sqrt(1/a - 1/(a+b) + 1/c - 1/(c+d))
- **Attributable risk**:
* AR = [a/(a+b)] - [c/(c+d)] = incidence difference
* AR% = [(RR-1)/RR] × 100 = attributable risk percent
Statistical Background:
The relative risk compares the probability (risk) of outcome in the
exposed group to the probability in the unexposed group:
RR = P(Outcome|Exposed) / P(Outcome|Unexposed)
= [a/(a+b)] / [c/(c+d)]
See Also:
- odds_ratio_py: Alternative measure for case-control studies
- fisher_exact_py: Significance test with odds ratio
"""
...
# Linear regression
"""
Calculate a simple linear regression.
Performs ordinary least squares (OLS) linear regression to fit a line
y = slope × x + intercept to the data. Computes the correlation coefficient,
p-value for testing H₀: slope = 0, and standard error of the slope estimate.
This function uses the method of least squares to estimate the parameters
of a linear model. It minimizes the sum of squared residuals between the
observed values and the values predicted by the linear model.
Parameters:
x: Independent variable (predictor), 1D array
y: Dependent variable (response), 1D array
Must be same length as x
Returns:
Dictionary with:
- slope: Slope of the regression line (b₁)
Interpretation: change in y per unit change in x
- intercept: Y-intercept of the regression line (b₀)
Interpretation: predicted y when x = 0
- rvalue: Pearson correlation coefficient (r)
Ranges from -1 to 1, measures linear association strength
- pvalue: Two-sided p-value for testing H₀: slope = 0
Tests whether the slope is significantly different from zero
- stderr: Standard error of the slope estimate
Measures uncertainty in the slope estimate
Examples:
>>> # Example: Perfect linear relationship
>>> x = np.array([1, 2, 3, 4, 5], dtype=np.float64)
>>> y = np.array([2, 4, 6, 8, 10], dtype=np.float64) # y = 2x
>>> result = scirs2.linregress_py(x, y)
>>> print(f"y = {result['slope']:.2f}x + {result['intercept']:.2f}")
>>> print(f"R = {result['rvalue']:.4f}, p = {result['pvalue']:.6f}")
>>> # Example: Temperature conversion (Celsius to Fahrenheit)
>>> celsius = np.array([0, 10, 20, 30, 40], dtype=np.float64)
>>> fahrenheit = np.array([32, 50, 68, 86, 104], dtype=np.float64)
>>> result = scirs2.linregress_py(celsius, fahrenheit)
>>> # F = 1.8C + 32
>>> print(f"Conversion: F = {result['slope']:.1f}C + {result['intercept']:.1f}")
>>> # Example: Prediction
>>> x = np.array([1, 2, 3, 4, 5], dtype=np.float64)
>>> y = np.array([2.1, 3.9, 6.1, 7.9, 10.2], dtype=np.float64)
>>> result = scirs2.linregress_py(x, y)
>>> # Predict y for new x value
>>> x_new = 6.0
>>> y_pred = result['slope'] * x_new + result['intercept']
>>> print(f"Predicted y at x={x_new}: {y_pred:.2f}")
>>> # Example: Check significance
>>> if result['pvalue'] < 0.05:
... print("Relationship is statistically significant")
... print(f"95% CI for slope: {result['slope']} ± {1.96 * result['stderr']:.4f}")
Notes:
- **Model**: y = slope × x + intercept + ε, where ε ~ N(0, σ²)
- **Assumptions**:
* Linearity: True relationship between x and y is linear
* Independence: Observations are independent
* Homoscedasticity: Constant variance of residuals
* Normality: Residuals are approximately normally distributed (for inference)
- **Interpretation**:
* slope: Amount y changes for one-unit increase in x
* intercept: Expected value of y when x = 0
* r²: Proportion of variance in y explained by x (r² = rvalue²)
* pvalue: Probability of observing data if true slope were zero
* stderr: Uncertainty in slope estimate (use for confidence intervals)
- **When to use**:
* Simple bivariate relationship
* Quick exploratory analysis
* Single predictor variable
- **Limitations**:
* Only for linear relationships (use nonlinear regression for curves)
* Sensitive to outliers (consider robust regression)
* Only one predictor (use multiple regression for >1 predictor)
* Assumes fixed x, random y (use ODR if both have error)
- **Perfect correlation** (|r| = 1):
* pvalue may be NaN due to division by zero in t-statistic
* stderr = 0 (perfect fit)
* This is expected behavior for exact linear relationships
- **Goodness of fit**:
* R² (coefficient of determination) = rvalue²
* R² = 1: Perfect fit
* R² = 0: No linear relationship
* Closer to 1 indicates better fit
Statistical Background:
The slope is estimated as:
slope = Cov(x, y) / Var(x) = Σ[(xᵢ - x̄)(yᵢ - ȳ)] / Σ[(xᵢ - x̄)²]
The intercept is:
intercept = ȳ - slope × x̄
The correlation coefficient is:
r = Cov(x, y) / [SD(x) × SD(y)]
The p-value is computed from the t-statistic:
t = r × √(n-2) / √(1 - r²)
which follows a t-distribution with n-2 degrees of freedom.
See Also:
- pearsonr_py: Compute correlation without regression
- For multiple predictors: Use dedicated regression libraries
- For robust regression: Consider specialized robust methods
- For nonlinear fits: Consider polynomial or nonlinear regression
"""
...
"""
One-way ANOVA (Analysis of Variance).
Tests whether the means of multiple groups are equal.
Parameters:
*args: Two or more arrays, each representing a group
Returns:
Dictionary with:
- f_statistic: F-statistic
- pvalue: Two-sided p-value
- df_between: Degrees of freedom between groups
- df_within: Degrees of freedom within groups
- ss_between: Sum of squares between groups
- ss_within: Sum of squares within groups
- ms_between: Mean square between groups
- ms_within: Mean square within groups
Examples:
>>> group1 = np.array([85, 82, 78, 88, 91])
>>> group2 = np.array([76, 80, 82, 84, 79])
>>> group3 = np.array([91, 89, 93, 87, 90])
>>> result = scirs2.f_oneway_py(group1, group2, group3)
"""
...
"""
Tukey's Honestly Significant Difference (HSD) post-hoc test.
Performs pairwise comparisons between group means after ANOVA, controlling
the family-wise error rate. This test identifies which specific groups differ
from each other when ANOVA shows a significant overall effect.
Parameters:
*args: Two or more arrays, each representing a group
All groups must have at least 2 observations
alpha: Significance level (default: 0.05)
Supported values: 0.05 or 0.01
Returns:
List of dictionaries, one for each pairwise comparison:
- group1: Index of first group (0-based)
- group2: Index of second group (0-based)
- mean_diff: Difference between group means
- pvalue: P-value for the comparison
- significant: Boolean indicating if difference is significant at alpha level
Raises:
RuntimeError: If fewer than 2 groups provided, or if alpha is not 0.05 or 0.01
Examples:
>>> # Post-hoc test after finding significant ANOVA
>>> group1 = np.array([85.0, 82.0, 78.0, 88.0, 91.0])
>>> group2 = np.array([76.0, 80.0, 82.0, 84.0, 79.0])
>>> group3 = np.array([91.0, 89.0, 93.0, 87.0, 90.0])
>>>
>>> # First, perform ANOVA
>>> anova_result = scirs2.f_oneway_py(group1, group2, group3)
>>> if anova_result['pvalue'] < 0.05:
... # Significant ANOVA, perform post-hoc tests
... comparisons = scirs2.tukey_hsd_py(group1, group2, group3)
... for comp in comparisons:
... print(f"Group {comp['group1']} vs {comp['group2']}: "
... f"diff={comp['mean_diff']:.2f}, p={comp['pvalue']:.4f}, "
... f"sig={comp['significant']}")
>>> # Use custom alpha level
>>> comparisons = scirs2.tukey_hsd_py(group1, group2, group3, alpha=0.01)
>>> # More stringent: fewer comparisons will be significant
>>> # With 4 groups, get 6 pairwise comparisons: C(4,2) = 6
>>> g1 = np.array([5.0, 6.0, 7.0])
>>> g2 = np.array([8.0, 9.0, 10.0])
>>> g3 = np.array([11.0, 12.0, 13.0])
>>> g4 = np.array([14.0, 15.0, 16.0])
>>> comparisons = scirs2.tukey_hsd_py(g1, g2, g3, g4)
>>> print(f"Number of comparisons: {len(comparisons)}") # 6
Notes:
- **Use only after significant ANOVA result** - Tukey HSD is a post-hoc test
- Controls family-wise error rate at the specified alpha level
- More conservative than multiple t-tests (avoids inflated Type I error)
- Based on the studentized range distribution (Q distribution)
- Assumes:
* Independent observations
* Normality within groups
* Homogeneity of variance (equal variances across groups)
- For k groups, performs k(k-1)/2 pairwise comparisons
- All comparisons use pooled within-group variance from all groups
- Alpha = 0.05 or 0.01 supported (uses critical value approximation)
- Groups can have different sample sizes (unequal n)
- If ANOVA is not significant, post-hoc tests may not be appropriate
- Alternative post-hoc tests: Bonferroni, Scheffé, Dunnett
"""
...
# Correlation tests with significance
"""
Pearson correlation coefficient with significance test.
Calculates the Pearson product-moment correlation coefficient between two
arrays and tests for statistical significance. The Pearson correlation measures
linear association between variables.
Parameters:
x: First array of observations
y: Second array of observations (must be same length as x)
alternative: Type of hypothesis test (default: "two-sided")
- "two-sided": Test if correlation is nonzero
- "less": Test if correlation is negative
- "greater": Test if correlation is positive
Returns:
Dictionary with:
- correlation: Pearson correlation coefficient (r) in [-1, 1]
- pvalue: P-value for testing non-correlation
Raises:
RuntimeError: If arrays have different lengths, contain insufficient data,
or have zero variance
Examples:
>>> # Perfect positive linear correlation
>>> x = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> y = np.array([2.0, 4.0, 6.0, 8.0, 10.0])
>>> result = scirs2.pearsonr_py(x, y)
>>> print(f"r={result['correlation']:.3f}, p={result['pvalue']:.4f}")
r=1.000, p=0.0000
>>> # Moderate correlation
>>> x = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
>>> y = np.array([2.1, 3.9, 6.2, 7.8, 10.1, 11.9, 14.2, 15.8, 18.1, 19.9])
>>> result = scirs2.pearsonr_py(x, y)
>>> if result['pvalue'] < 0.05:
... print(f"Significant correlation: r={result['correlation']:.3f}")
>>> # One-sided test for positive correlation
>>> result = scirs2.pearsonr_py(x, y, alternative="greater")
Notes:
- Pearson correlation assumes linear relationship between variables
- Sensitive to outliers
- Requires continuous or interval data
- Test statistic follows t-distribution with n-2 degrees of freedom
- For nonlinear monotonic relationships, consider Spearman correlation
- Range: -1 (perfect negative) to +1 (perfect positive), 0 = no correlation
- P-value tests null hypothesis that true correlation is zero
"""
...
"""
Spearman rank correlation coefficient with significance test.
Calculates the Spearman rank-order correlation coefficient (Spearman's rho)
and tests for statistical significance. Spearman correlation is a nonparametric
measure of monotonic association that works with ranked data.
Parameters:
x: First array of observations
y: Second array of observations (must be same length as x)
alternative: Type of hypothesis test (default: "two-sided")
- "two-sided": Test if correlation is nonzero
- "less": Test if correlation is negative
- "greater": Test if correlation is positive
Returns:
Dictionary with:
- correlation: Spearman rank correlation coefficient (rho) in [-1, 1]
- pvalue: P-value for testing non-correlation
Raises:
RuntimeError: If arrays have different lengths or contain insufficient data
Examples:
>>> # Perfect monotonic relationship (not necessarily linear)
>>> x = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0])
>>> y = x ** 2 # Nonlinear but monotonic
>>> result = scirs2.spearmanr_py(x, y)
>>> print(f"rho={result['correlation']:.3f}, p={result['pvalue']:.4f}")
>>> # With ties in data
>>> x = np.array([1.0, 2.0, 2.0, 3.0, 4.0])
>>> y = np.array([5.0, 6.0, 6.0, 7.0, 8.0])
>>> result = scirs2.spearmanr_py(x, y)
>>> # One-sided test
>>> result = scirs2.spearmanr_py(x, y, alternative="greater")
Notes:
- Nonparametric test (does not assume normality)
- Robust to outliers compared to Pearson
- Works with ordinal (ranked) data
- Detects monotonic relationships (not just linear)
- Converts data to ranks before computing correlation
- Handles tied ranks appropriately
- For n > 10, uses normal approximation for p-value
- Range: -1 (perfect negative monotonic) to +1 (perfect positive monotonic)
- Use when relationship is monotonic but not necessarily linear
- Less powerful than Pearson for truly linear relationships
"""
...
"""
Kendall tau rank correlation coefficient with significance test.
Calculates Kendall's tau correlation coefficient and tests for statistical
significance. Kendall's tau is a nonparametric measure of ordinal association
based on concordant and discordant pairs.
Parameters:
x: First array of observations
y: Second array of observations (must be same length as x)
method: Kendall tau variant (default: "b")
- "b": tau-b, accounts for ties in both variables
- "c": tau-c, more suitable for rectangular contingency tables
alternative: Type of hypothesis test (default: "two-sided")
- "two-sided": Test if correlation is nonzero
- "less": Test if correlation is negative
- "greater": Test if correlation is positive
Returns:
Dictionary with:
- correlation: Kendall tau correlation coefficient in [-1, 1]
- pvalue: P-value for testing non-correlation
Raises:
RuntimeError: If arrays have different lengths, contain insufficient data,
or invalid method specified
Examples:
>>> # Perfect concordance
>>> x = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> y = np.array([2.0, 4.0, 6.0, 8.0, 10.0])
>>> result = scirs2.kendalltau_py(x, y)
>>> print(f"tau={result['correlation']:.3f}, p={result['pvalue']:.4f}")
>>> # With ties, using tau-b
>>> x = np.array([1.0, 2.0, 2.0, 3.0, 4.0])
>>> y = np.array([5.0, 6.0, 6.0, 7.0, 8.0])
>>> result = scirs2.kendalltau_py(x, y, method="b")
>>> # Using tau-c for rectangular tables
>>> result = scirs2.kendalltau_py(x, y, method="c")
>>> # One-sided test
>>> result = scirs2.kendalltau_py(x, y, alternative="greater")
Notes:
- Nonparametric test (does not assume normality)
- Based on concordant and discordant pairs
- More robust to outliers than Pearson
- Tau-b: Accounts for ties in both variables (most common)
- Tau-c: Better for m×n contingency tables where m ≠ n
- Typically has smaller magnitude than Spearman's rho
- For n ≥ 10, uses normal approximation for p-value
- Range: -1 (perfect negative association) to +1 (perfect positive)
- Concordant pair: (x[i] - x[j]) and (y[i] - y[j]) have same sign
- Discordant pair: opposite signs
- tau = (concordant - discordant) / total_pairs
- Less sensitive to errors in rankings than Spearman
- Use when sample size is small or data is ordinal
"""
...
# Nonparametric tests
"""
Wilcoxon signed-rank test for paired samples.
Tests whether two paired samples have different distributions using
ranks instead of actual values. This is a nonparametric alternative
to the paired t-test.
Parameters:
x: First array of observations
y: Second array of observations (paired with x)
zero_method: How to handle zero differences: "wilcox" (default) or "pratt"
correction: Whether to apply continuity correction (default: True)
Returns:
Dictionary with:
- statistic: Wilcoxon signed-rank statistic
- pvalue: Two-sided p-value
Raises:
RuntimeError: If all differences are zero or other test failures
Examples:
>>> before = np.array([120, 135, 128, 140, 125])
>>> after = np.array([115, 130, 125, 138, 120])
>>> result = scirs2.wilcoxon_py(before, after)
>>> print(f"W={result['statistic']:.2f}, p={result['pvalue']:.4f}")
"""
...
"""
Mann-Whitney U test for independent samples.
Tests whether two independent samples have different distributions using
ranks. This is a nonparametric alternative to the independent t-test.
Parameters:
x: First array of observations
y: Second array of observations
alternative: Alternative hypothesis: "two-sided" (default), "less", or "greater"
use_continuity: Whether to apply continuity correction (default: True)
Returns:
Dictionary with:
- statistic: Mann-Whitney U statistic
- pvalue: p-value for the test
Examples:
>>> group1 = np.array([1.2, 2.3, 3.1, 4.5, 5.2])
>>> group2 = np.array([2.1, 3.4, 4.2, 5.5, 6.3])
>>> result = scirs2.mannwhitneyu_py(group1, group2)
>>> print(f"U={result['statistic']:.2f}, p={result['pvalue']:.4f}")
"""
...
"""
Kruskal-Wallis H-test for independent samples.
Tests whether multiple independent samples have different distributions
using ranks. This is a nonparametric alternative to one-way ANOVA.
Parameters:
*args: Two or more arrays, each representing a group
Returns:
Dictionary with:
- statistic: Kruskal-Wallis H statistic
- pvalue: p-value for the test
Raises:
RuntimeError: If fewer than 2 groups are provided
Examples:
>>> group1 = np.array([1.2, 2.3, 3.1, 4.5])
>>> group2 = np.array([5.1, 6.2, 7.3, 8.4])
>>> group3 = np.array([9.5, 10.6, 11.7, 12.8])
>>> result = scirs2.kruskal_py(group1, group2, group3)
>>> print(f"H={result['statistic']:.2f}, p={result['pvalue']:.4f}")
"""
...
# Homogeneity tests
"""
Levene's test for homogeneity of variance.
Tests the null hypothesis that all input samples are from populations
with equal variances. More robust than Bartlett's test when data is
not normally distributed.
Parameters:
*args: Two or more arrays, each representing a group
center: Method to use for center: "mean", "median" (default), or "trimmed"
proportion_to_cut: Proportion to cut from each end when using "trimmed" (default: 0.05)
Returns:
Dictionary with:
- statistic: Levene test statistic (W)
- pvalue: p-value for the test
Raises:
RuntimeError: If fewer than 2 groups are provided or test fails
Examples:
>>> g1 = np.array([8.88, 9.12, 9.04, 8.98, 9.00])
>>> g2 = np.array([8.88, 8.95, 9.29, 9.44, 9.15])
>>> g3 = np.array([8.95, 9.12, 8.95, 8.85, 9.03])
>>> result = scirs2.levene_py(g1, g2, g3)
>>> print(f"W={result['statistic']:.2f}, p={result['pvalue']:.4f}")
>>> # Use mean as center
>>> result = scirs2.levene_py(g1, g2, center="mean")
"""
...
"""
Bartlett's test for homogeneity of variance.
Tests the null hypothesis that all input samples are from populations
with equal variances. More powerful than Levene's test but sensitive
to departures from normality.
Parameters:
*args: Two or more arrays, each representing a group
Returns:
Dictionary with:
- statistic: Bartlett test statistic
- pvalue: p-value for the test
Raises:
RuntimeError: If fewer than 2 groups are provided or test fails
Examples:
>>> g1 = np.array([8.88, 9.12, 9.04, 8.98, 9.00])
>>> g2 = np.array([8.88, 8.95, 9.29, 9.44, 9.15])
>>> result = scirs2.bartlett_test_py(g1, g2)
>>> print(f"T={result['statistic']:.2f}, p={result['pvalue']:.4f}")
"""
...
"""
Brown-Forsythe test for homogeneity of variance.
A modification of Levene's test that uses the median instead of the mean,
making it more robust against non-normality. Equivalent to Levene's test
with center="median".
Parameters:
*args: Two or more arrays, each representing a group
Returns:
Dictionary with:
- statistic: Brown-Forsythe test statistic
- pvalue: p-value for the test
Raises:
RuntimeError: If fewer than 2 groups are provided or test fails
Examples:
>>> g1 = np.array([8.88, 9.12, 9.04, 8.98, 9.00])
>>> g2 = np.array([8.88, 8.95, 9.29, 9.44, 9.15])
>>> g3 = np.array([8.95, 9.12, 8.95, 8.85, 9.03])
>>> result = scirs2.brown_forsythe_py(g1, g2, g3)
>>> print(f"W={result['statistic']:.2f}, p={result['pvalue']:.4f}")
"""
...
# Additional normality tests
"""
Anderson-Darling test for normality.
Tests whether a sample comes from a normal distribution using the
Anderson-Darling statistic. This test is more sensitive to deviations
in the tails of the distribution compared to the Shapiro-Wilk test.
The Anderson-Darling test statistic quantifies how well the data follows
a normal distribution, with smaller values indicating better fit.
Parameters:
x: Array of sample data (minimum 8 observations)
Returns:
Dictionary with:
- statistic: Anderson-Darling test statistic (A²)
- pvalue: Two-sided p-value for the test
Raises:
RuntimeError: If sample size is less than 8 observations
Examples:
>>> data = np.random.normal(0, 1, 100)
>>> result = scirs2.anderson_darling_py(data)
>>> print(f"A²={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Test non-normal data
>>> uniform_data = np.random.uniform(-3, 3, 100)
>>> result = scirs2.anderson_darling_py(uniform_data)
>>> if result['pvalue'] < 0.05:
... print("Data is not normally distributed")
Notes:
The Anderson-Darling test gives more weight to the tails than the
Kolmogorov-Smirnov test, making it better for detecting departures
from normality in the tails of the distribution.
"""
...
"""
D'Agostino's K-squared test for normality.
Tests whether a sample comes from a normal distribution using the
D'Agostino-Pearson K² test. This test combines skewness and kurtosis
to provide a comprehensive test for normality.
The test statistic K² combines standardized measures of skewness and
kurtosis. Under the null hypothesis of normality, K² approximately
follows a chi-square distribution with 2 degrees of freedom.
Parameters:
x: Array of sample data (minimum 20 observations)
Returns:
Dictionary with:
- statistic: K² test statistic
- pvalue: Two-sided p-value for the test
Raises:
RuntimeError: If sample size is less than 20 observations
Examples:
>>> data = np.random.normal(0, 1, 200)
>>> result = scirs2.dagostino_k2_py(data)
>>> print(f"K²={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Test skewed data
>>> skewed_data = np.random.exponential(1.0, 200)
>>> result = scirs2.dagostino_k2_py(skewed_data)
>>> if result['pvalue'] < 0.05:
... print("Data is not normally distributed")
Notes:
This test is particularly sensitive to departures from normality
due to skewness and kurtosis. It requires a larger minimum sample
size (n ≥ 20) compared to some other normality tests.
The test statistic combines:
- Z(skewness): Standardized measure of skewness
- Z(kurtosis): Standardized measure of excess kurtosis
- K² = Z(skewness)² + Z(kurtosis)²
"""
...
"""
Two-sample Kolmogorov-Smirnov test.
Tests whether two independent samples come from the same distribution
using the Kolmogorov-Smirnov statistic. This is a nonparametric test
that makes no assumptions about the underlying distributions.
The test statistic is the maximum absolute difference between the
empirical cumulative distribution functions (ECDFs) of the two samples.
Parameters:
x: First sample array
y: Second sample array
alternative: Type of hypothesis test:
- "two-sided": Test if distributions are different (default)
- "less": Test if x is stochastically less than y
- "greater": Test if x is stochastically greater than y
Returns:
Dictionary with:
- statistic: Kolmogorov-Smirnov test statistic (D)
- pvalue: P-value for the specified alternative hypothesis
Raises:
RuntimeError: If either sample is empty
Examples:
>>> # Test if two samples come from the same distribution
>>> x = np.random.normal(0, 1, 100)
>>> y = np.random.normal(0, 1, 100)
>>> result = scirs2.ks_2samp_py(x, y)
>>> print(f"D={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Test if distributions are different
>>> x = np.random.normal(0, 1, 100)
>>> y = np.random.normal(2, 1, 100) # Different mean
>>> result = scirs2.ks_2samp_py(x, y)
>>> if result['pvalue'] < 0.05:
... print("Distributions are significantly different")
>>> # One-sided test
>>> result = scirs2.ks_2samp_py(x, y, alternative="less")
>>> print(f"One-sided p-value: {result['pvalue']:.4f}")
Notes:
- This is a nonparametric test that does not assume normality
- The test statistic D ranges from 0 to 1
- Works with samples of different sizes
- The test is sensitive to differences in both location and shape
"""
...
# Repeated measures test
"""
Friedman test for repeated measures.
Tests whether k treatments (or conditions) have different effects across
n subjects. This is a nonparametric alternative to repeated measures ANOVA
that does not assume normality.
The test ranks the observations within each subject (row) and compares
the rank sums across treatments (columns). Under the null hypothesis,
all treatments have the same effect.
Parameters:
data: 2D array with shape (n_subjects, k_treatments)
Each row represents one subject's measurements across all treatments
Returns:
Dictionary with:
- statistic: Friedman test statistic (χ²_r)
- pvalue: P-value based on chi-square distribution
Raises:
RuntimeError: If there are fewer than 2 subjects or 2 treatments
Examples:
>>> # Test if 3 treatments have different effects on 5 subjects
>>> data = np.array([
... [5.1, 4.9, 5.3], # Subject 1
... [6.2, 5.8, 6.1], # Subject 2
... [5.7, 5.5, 5.9], # Subject 3
... [4.8, 4.6, 5.0], # Subject 4
... [5.3, 5.1, 5.5] # Subject 5
... ])
>>> result = scirs2.friedman_py(data)
>>> print(f"χ²={result['statistic']:.3f}, p={result['pvalue']:.4f}")
>>> # Interpret results
>>> if result['pvalue'] < 0.05:
... print("Treatments have significantly different effects")
... else:
... print("No significant difference between treatments")
Notes:
- This is a nonparametric test (does not assume normality)
- Requires at least 2 subjects and 2 treatments
- Each row (subject) is ranked independently
- The test statistic follows approximately a chi-square distribution
with k-1 degrees of freedom, where k is the number of treatments
- Use for within-subjects (repeated measures) designs
- If you reject the null hypothesis, consider post-hoc pairwise
comparisons to identify which treatments differ
"""
...
# Additional statistics
"""Compute skewness of data."""
...
"""Compute excess kurtosis of data (Fisher's definition)."""
...
"""Compute mode (most frequent value) of data."""
...
"""Compute geometric mean. All values must be positive."""
...
"""Compute harmonic mean. All values must be positive."""
...
"""Compute z-scores (standard scores) for data."""
...
# Dispersion and variability measures
"""
Compute mean absolute deviation from a center point.
Parameters:
data: Input data array
center: Center point for deviation calculation. If None, uses the mean.
Returns:
Mean absolute deviation
Examples:
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> scirs2.mean_abs_deviation_py(data) # MAD from mean
1.2
>>> scirs2.mean_abs_deviation_py(data, center=3.0) # MAD from center
1.2
"""
...
"""
Compute median absolute deviation (robust measure of variability).
The median absolute deviation is a robust measure of statistical dispersion
that is more resilient to outliers than standard deviation.
Parameters:
data: Input data array
center: Center point for deviation calculation. If None, uses the median.
scale: Scale factor to multiply the MAD. Common values:
- 1.0: Raw MAD (default if None)
- 1.4826: Approximate standard deviation for normal distribution
Returns:
Median absolute deviation (scaled if scale is provided)
Examples:
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> scirs2.median_abs_deviation_py(data)
1.0
>>> scirs2.median_abs_deviation_py(data, scale=1.4826) # Normalized
1.4826
"""
...
"""
Compute the range (max - min) of the data.
Parameters:
data: Input data array
Returns:
Range of the data (maximum value - minimum value)
Examples:
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> scirs2.data_range_py(data)
4.0
"""
...
"""
Compute coefficient of variation (CV = std / mean).
The coefficient of variation is a unitless measure of relative variability,
useful for comparing variability across datasets with different scales or units.
Parameters:
data: Input data array
ddof: Delta degrees of freedom for standard deviation calculation (default: 1)
Returns:
Coefficient of variation
Examples:
>>> data = np.array([10.0, 20.0, 30.0, 40.0, 50.0])
>>> scirs2.coef_variation_py(data) # CV with sample std (ddof=1)
0.527...
>>> scirs2.coef_variation_py(data, ddof=0) # CV with population std
0.471...
"""
...
"""
Compute Gini coefficient (measure of inequality).
The Gini coefficient measures inequality in a distribution. It ranges from
0 (perfect equality) to 1 (maximum inequality). Commonly used for income
and wealth distributions.
Parameters:
data: Input data array (must be non-negative)
Returns:
Gini coefficient in [0, 1]
- 0.0: Perfect equality (all values are the same)
- 1.0: Maximum inequality (one value has everything)
Examples:
>>> # Perfect equality
>>> equal = np.array([1.0, 1.0, 1.0, 1.0])
>>> scirs2.gini_coefficient_py(equal)
0.0
>>> # Some inequality
>>> unequal = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> scirs2.gini_coefficient_py(unequal)
0.266...
"""
...
# Quantile and robust statistics
"""
Compute boxplot statistics (five-number summary and outliers).
Returns quartiles, whiskers, and outliers for creating boxplots and
identifying extreme values in the data.
Parameters:
data: Input data array
whis: Whisker range factor (default: 1.5). Whiskers extend to the most
extreme data point within whis * IQR from the quartiles, where
IQR is the interquartile range (Q3 - Q1).
Returns:
Dictionary containing:
- q1: First quartile (25th percentile)
- median: Second quartile (50th percentile)
- q3: Third quartile (75th percentile)
- whislo: Lower whisker (minimum value within whisker range)
- whishi: Upper whisker (maximum value within whisker range)
- outliers: List of values outside the whisker range
Examples:
>>> data = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 100])
>>> stats = scirs2.boxplot_stats_py(data)
>>> stats["median"]
6.0
>>> 100.0 in stats["outliers"] # Extreme value detected
True
"""
...
"""
Compute quartiles (Q1, Q2, Q3) of the data.
Parameters:
data: Input data array
Returns:
Array of three values [Q1, Q2 (median), Q3]
Examples:
>>> data = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
>>> q = scirs2.quartiles_py(data)
>>> len(q)
3
>>> q[0] < q[1] < q[2] # Q1 < Q2 < Q3
True
"""
...
"""
Compute winsorized mean (robust mean).
The winsorized mean replaces extreme values with less extreme values
before computing the mean, making it more robust to outliers.
Parameters:
data: Input data array
limits: Proportion of values to winsorize at each end (default: 0.1).
For example, limits=0.1 replaces the bottom 10% and top 10%
of values with the values at the 10th and 90th percentiles.
Returns:
Winsorized mean
Examples:
>>> # Data with outlier
>>> data = np.array([1, 2, 3, 4, 5, 100])
>>> regular_mean = np.mean(data) # 19.17
>>> robust_mean = scirs2.winsorized_mean_py(data, limits=0.2)
>>> robust_mean < regular_mean # Less affected by outlier
True
"""
...
"""
Compute winsorized variance (robust variance).
The winsorized variance replaces extreme values with less extreme values
before computing the variance, making it more robust to outliers.
Parameters:
data: Input data array
limits: Proportion of values to winsorize at each end (default: 0.1)
ddof: Delta degrees of freedom (default: 1 for sample variance)
Returns:
Winsorized variance
Examples:
>>> # Data with outlier
>>> data = np.array([1, 2, 3, 4, 5, 100])
>>> regular_var = np.var(data, ddof=1) # Large due to outlier
>>> robust_var = scirs2.winsorized_variance_py(data, limits=0.2, ddof=1)
>>> robust_var < regular_var / 2 # Much smaller
True
"""
...
# Information theory and advanced statistics
"""
Compute Shannon entropy of discrete data.
Entropy measures the uncertainty or information content in a discrete
probability distribution. Higher entropy indicates more uncertainty.
Parameters:
data: Input data array (discrete values, e.g., counts or categories)
base: Logarithm base for entropy calculation (default: e for nats)
- base=2.0 for bits (information theory)
- base=e (default) for nats
- base=10.0 for decimal digits
Returns:
Entropy value (non-negative)
Examples:
>>> # Uniform distribution: maximum entropy
>>> data = np.array([1, 1, 1, 2, 2, 2, 3, 3, 3], dtype=np.int64)
>>> scirs2.entropy_py(data) # Natural log
1.0986...
>>> scirs2.entropy_py(data, base=2.0) # Bits
1.584...
>>> # Deterministic: zero entropy
>>> certain = np.array([1, 1, 1, 1], dtype=np.int64)
>>> scirs2.entropy_py(certain)
0.0
"""
...
"""
Compute Kullback-Leibler (KL) divergence between two probability distributions.
KL divergence measures how one probability distribution (q) diverges from
a reference distribution (p). It's asymmetric: KL(p||q) != KL(q||p).
Parameters:
p: First probability distribution (must sum to 1.0)
q: Second probability distribution (must sum to 1.0)
Returns:
KL divergence value (non-negative, zero when p == q)
Examples:
>>> # Identical distributions: zero divergence
>>> p = np.array([0.3, 0.3, 0.4])
>>> q = np.array([0.3, 0.3, 0.4])
>>> scirs2.kl_divergence_py(p, q)
0.0
>>> # Different distributions: positive divergence
>>> p = np.array([0.5, 0.3, 0.2])
>>> q = np.array([0.4, 0.4, 0.2])
>>> kl = scirs2.kl_divergence_py(p, q)
>>> kl > 0.0
True
>>> # Asymmetric property
>>> kl_pq = scirs2.kl_divergence_py(p, q)
>>> kl_qp = scirs2.kl_divergence_py(q, p)
>>> kl_pq != kl_qp
True
"""
...
"""
Compute cross-entropy between two probability distributions.
Cross-entropy is commonly used as a loss function in machine learning.
It measures the average number of bits needed to encode samples from p
using a code optimized for q.
Parameters:
p: True probability distribution (must sum to 1.0)
q: Predicted probability distribution (must sum to 1.0)
Returns:
Cross-entropy value (non-negative)
Note:
Relationship: H(p,q) = H(p) + KL(p||q)
where H(p) is entropy of p and KL(p||q) is KL divergence
Examples:
>>> # Machine learning classification
>>> true_label = np.array([0.0, 1.0, 0.0]) # One-hot encoded
>>> pred_good = np.array([0.1, 0.8, 0.1]) # Good prediction
>>> pred_poor = np.array([0.6, 0.2, 0.2]) # Poor prediction
>>> loss_good = scirs2.cross_entropy_py(true_label, pred_good)
>>> loss_poor = scirs2.cross_entropy_py(true_label, pred_poor)
>>> loss_good < loss_poor # Lower loss for better prediction
True
"""
...
"""
Compute weighted arithmetic mean.
The weighted mean gives different weights to different values, useful when
some observations are more important or reliable than others.
Parameters:
data: Input data array
weights: Weight array (same length as data, must be non-negative)
Returns:
Weighted mean
Examples:
>>> # Equal weights: same as regular mean
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> weights = np.array([1.0, 1.0, 1.0, 1.0, 1.0])
>>> scirs2.weighted_mean_py(data, weights)
3.0
>>> # Emphasize certain values
>>> data = np.array([10.0, 20.0, 30.0])
>>> weights = np.array([1.0, 2.0, 3.0]) # Weight last value more
>>> wm = scirs2.weighted_mean_py(data, weights)
>>> wm > 20.0 # Closer to 30 than simple mean
True
>>> # Portfolio weighted returns
>>> returns = np.array([5.0, 10.0, -2.0, 8.0]) # Asset returns (%)
>>> portfolio_weights = np.array([0.4, 0.3, 0.1, 0.2]) # Allocations
>>> portfolio_return = scirs2.weighted_mean_py(returns, portfolio_weights)
"""
...
"""
Compute statistical moment of specified order.
Moments are quantitative measures of the shape of a probability distribution.
Special cases:
- 1st moment (uncentered): mean
- 2nd moment (centered): variance
- 3rd moment (centered, normalized): skewness
- 4th moment (centered, normalized): kurtosis
Parameters:
data: Input data array
order: Moment order (positive integer)
center: If True, compute central moment (about the mean).
If False, compute raw moment (about zero).
Returns:
Moment value
Examples:
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> # First uncentered moment is the mean
>>> scirs2.moment_py(data, order=1, center=False)
3.0
>>> # First central moment is always zero
>>> scirs2.moment_py(data, order=1, center=True)
0.0
>>> # Second central moment is variance
>>> m2 = scirs2.moment_py(data, order=2, center=True)
>>> var = np.var(data, ddof=0)
>>> abs(m2 - var) < 0.001
True
>>> # Third central moment (related to skewness)
>>> m3 = scirs2.moment_py(data, order=3, center=True)
>>> # Fourth central moment (related to kurtosis)
>>> m4 = scirs2.moment_py(data, order=4, center=True)
"""
...
"""
Compute quintiles (20th, 40th, 60th, 80th percentiles) of a dataset.
Quintiles divide the dataset into five equal parts, providing finer-grained
information than quartiles. Useful for quality control, performance analysis,
and data stratification.
Parameters:
data: Input data array
Returns:
Array of 4 quintile values: [Q1, Q2, Q3, Q4]
- Q1: 20th percentile
- Q2: 40th percentile
- Q3: 60th percentile
- Q4: 80th percentile
Examples:
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
>>> quintiles = scirs2.quintiles_py(data)
>>> len(quintiles)
4
>>> # quintiles are approximately [2.8, 4.6, 6.4, 8.2]
>>> # Use for quality control zones
>>> measurements = np.random.normal(100, 5, 500)
>>> q = scirs2.quintiles_py(measurements)
>>> # Bottom 20%: below q[0]
>>> # 20-40%: between q[0] and q[1]
>>> # 40-60%: between q[1] and q[2]
>>> # 60-80%: between q[2] and q[3]
>>> # Top 20%: above q[3]
"""
...
"""
Compute skewness with bootstrap confidence interval.
Uses bootstrap resampling to estimate the confidence interval for skewness,
providing uncertainty quantification for distribution asymmetry measurements.
Parameters:
data: Input data array (minimum 3 data points)
bias: If False, compute bias-corrected skewness estimate
confidence: Confidence level (e.g., 0.95 for 95% CI)
n_bootstrap: Number of bootstrap samples (default: 1000)
seed: Random seed for reproducibility (optional)
Returns:
Dictionary with keys:
- 'estimate': Point estimate of skewness
- 'lower': Lower bound of confidence interval
- 'upper': Upper bound of confidence interval
- 'confidence': Confidence level used
Examples:
>>> # Right-skewed data (income distribution)
>>> incomes = np.random.lognormal(mean=10, sigma=0.5, size=200)
>>> result = scirs2.skewness_ci_py(incomes, confidence=0.95, seed=42)
>>> result['estimate'] > 0 # Positive skewness
True
>>> result['lower'] < result['estimate'] < result['upper']
True
>>> # Symmetric data
>>> normal_data = np.random.normal(0, 1, 100)
>>> result = scirs2.skewness_ci_py(normal_data, seed=42)
>>> abs(result['estimate']) < 0.5 # Near zero for symmetric data
True
>>> # Reproducible results with seed
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 10.0])
>>> r1 = scirs2.skewness_ci_py(data, seed=123)
>>> r2 = scirs2.skewness_ci_py(data, seed=123)
>>> r1['estimate'] == r2['estimate']
True
"""
...
"""
Compute kurtosis with bootstrap confidence interval.
Uses bootstrap resampling to estimate the confidence interval for kurtosis,
providing uncertainty quantification for tail heaviness measurements.
Parameters:
data: Input data array (minimum 4 data points)
fisher: If True, compute excess kurtosis (Fisher's definition, subtract 3)
If False, compute raw kurtosis (Pearson's definition)
bias: If False, compute bias-corrected kurtosis estimate
confidence: Confidence level (e.g., 0.95 for 95% CI)
n_bootstrap: Number of bootstrap samples (default: 1000)
seed: Random seed for reproducibility (optional)
Returns:
Dictionary with keys:
- 'estimate': Point estimate of kurtosis
- 'lower': Lower bound of confidence interval
- 'upper': Upper bound of confidence interval
- 'confidence': Confidence level used
Note:
- Fisher's kurtosis (excess kurtosis):
* Normal distribution has kurtosis = 0
* Positive values indicate heavy tails (leptokurtic)
* Negative values indicate light tails (platykurtic)
- Pearson's kurtosis: Normal distribution has kurtosis = 3
Examples:
>>> # Normal-like data
>>> normal_data = np.random.normal(0, 1, 100)
>>> result = scirs2.kurtosis_ci_py(normal_data, fisher=True, seed=42)
>>> abs(result['estimate']) < 1.0 # Near 0 for normal data
True
>>> # Heavy-tailed data (with outliers)
>>> heavy_tail = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 50, -50])
>>> result = scirs2.kurtosis_ci_py(heavy_tail, fisher=True, seed=42)
>>> result['estimate'] > 0 # Positive excess kurtosis
True
>>> # Fisher vs Pearson kurtosis
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
>>> fisher_result = scirs2.kurtosis_ci_py(data, fisher=True, seed=42)
>>> pearson_result = scirs2.kurtosis_ci_py(data, fisher=False, seed=42)
>>> abs((pearson_result['estimate'] - fisher_result['estimate']) - 3.0) < 0.1
True
>>> # Financial returns (often fat-tailed)
>>> returns = np.concatenate([
... np.random.normal(0, 0.01, 180),
... np.random.normal(0, 0.05, 20)
... ])
>>> result = scirs2.kurtosis_ci_py(returns, fisher=True, seed=42)
>>> result['estimate'] > 0 # Fat tails indicated by positive excess kurtosis
True
"""
...
"""
Compute deciles (10th, 20th, 30th, ..., 90th percentiles) of a dataset.
Deciles divide data into 10 equal parts, providing finer granularity than
quartiles (4 parts) or quintiles (5 parts). They are useful for detailed
distribution analysis, performance grading, and quality control.
Parameters:
data: Input data array
Returns:
Array of 9 values representing the 10th through 90th percentiles
Examples:
>>> # Basic deciles
>>> data = np.array([float(i) for i in range(1, 101)]) # 1 to 100
>>> deciles = scirs2.deciles_py(data)
>>> len(deciles)
9
>>> deciles[0] # 10th percentile
10.9
>>> deciles[4] # 50th percentile (median)
50.5
>>> deciles[8] # 90th percentile
90.1
>>> # Deciles provide finer granularity than quintiles
>>> data = np.random.normal(100, 15, 500)
>>> deciles = scirs2.deciles_py(data)
>>> quintiles = scirs2.quintiles_py(data)
>>> # Deciles[1] (20th) matches quintiles[0] (20th)
>>> abs(deciles[1] - quintiles[0]) < 0.5
True
>>> # Performance grading with deciles
>>> scores = np.random.beta(5, 2, 1000) * 100
>>> deciles = scirs2.deciles_py(scores)
>>> # Bottom 10%: needs improvement
>>> # 10-30%: below average
>>> # 30-70%: average
>>> # 70-90%: above average
>>> # Top 10%: excellent
>>> deciles[0] < deciles[4] < deciles[8] # Ascending order
True
"""
...
"""
Compute the standard error of the mean (SEM).
The standard error of the mean measures the variability of the sample mean.
It is computed as: SEM = std / sqrt(n), where std is the standard deviation
and n is the sample size. SEM is crucial for constructing confidence intervals
and hypothesis testing.
Parameters:
data: Input data array
ddof: Degrees of freedom for standard deviation calculation
- 0 for population standard deviation
- 1 for sample standard deviation (default)
Returns:
Standard error of the mean
Notes:
- SEM decreases as sample size increases
- Used to construct confidence intervals: mean ± z * SEM
- For 95% CI: mean ± 1.96 * SEM
- For 99% CI: mean ± 2.576 * SEM
Examples:
>>> # Basic SEM calculation
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> sem = scirs2.sem_py(data, ddof=1)
>>> # SEM ≈ std(data) / sqrt(5) ≈ 1.58 / 2.236 ≈ 0.707
>>> abs(sem - 0.707) < 0.01
True
>>> # SEM decreases with larger sample size
>>> small_sample = np.random.normal(100, 15, 10)
>>> large_sample = np.random.normal(100, 15, 1000)
>>> scirs2.sem_py(large_sample, ddof=1) < scirs2.sem_py(small_sample, ddof=1)
True
>>> # Constructing 95% confidence interval
>>> test_scores = np.array([85.0, 88.0, 92.0, 79.0, 95.0, 87.0, 90.0, 84.0, 91.0, 86.0])
>>> mean = np.mean(test_scores)
>>> sem = scirs2.sem_py(test_scores, ddof=1)
>>> ci_lower = mean - 1.96 * sem
>>> ci_upper = mean + 1.96 * sem
>>> ci_lower < mean < ci_upper # Mean within its own CI
True
>>> # ddof parameter effect
>>> data = np.array([5.0, 10.0, 15.0, 20.0, 25.0, 30.0])
>>> sem_pop = scirs2.sem_py(data, ddof=0) # Population
>>> sem_sample = scirs2.sem_py(data, ddof=1) # Sample
>>> sem_sample > sem_pop # Sample SEM is larger
True
"""
...
"""
Compute the range between two percentiles.
This function calculates the difference between an upper and lower percentile,
providing a measure of spread within a specific portion of the distribution.
It generalizes the interquartile range (IQR), which is the 75th - 25th percentile.
Parameters:
data: Input data array
lower_pct: Lower percentile (0-100)
upper_pct: Upper percentile (0-100)
interpolation: Interpolation method for percentile calculation
- "linear": Linear interpolation (default)
Returns:
Range between the two percentiles (upper - lower)
Notes:
- IQR is equivalent to percentile_range(data, 25, 75)
- Useful for measuring spread while excluding outliers
- Common ranges:
* 10th-90th: Middle 80% spread
* 5th-95th: Middle 90% spread
* 25th-75th: Interquartile range (IQR)
Warning:
Known issue: May overflow with normal distribution data in some cases.
Use with uniform or well-behaved distributions for best results.
Examples:
>>> # Interquartile range (IQR)
>>> data = np.array([float(i) for i in range(1, 101)]) # 1 to 100
>>> iqr_range = scirs2.percentile_range_py(data, 25.0, 75.0)
>>> abs(iqr_range - 50.0) < 1.0 # Should be approximately 50
True
>>> # Custom percentile range
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0])
>>> # Range between 10th and 90th percentile
>>> range_10_90 = scirs2.percentile_range_py(data, 10.0, 90.0)
>>> range_10_90 > 0
True
>>> # Full data range (0th to 100th percentile)
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> full_range = scirs2.percentile_range_py(data, 0.0, 100.0)
>>> abs(full_range - 4.0) < 0.1 # max - min = 5 - 1 = 4
True
>>> # Symmetric distribution ranges
>>> # For symmetric data, 5-50 and 50-95 ranges should be similar
>>> # (Note: Works best with uniform/well-behaved distributions)
>>> # Identical values
>>> constant_data = np.array([42.0, 42.0, 42.0, 42.0, 42.0])
>>> range_const = scirs2.percentile_range_py(constant_data, 25.0, 75.0)
>>> abs(range_const) < 1e-10 # Should be 0
True
"""
...
"""
Compute SIMD-optimized skewness (third standardized moment).
This is a high-performance implementation of skewness calculation using SIMD
(Single Instruction, Multiple Data) acceleration for improved performance on
large datasets. Skewness measures the asymmetry of a distribution around its mean.
The skewness formula is: g₁ = E[(X-μ)³] / σ³
where μ is the mean and σ is the standard deviation.
Parameters:
data: Input data array
bias: If True, use biased estimator (default: False)
If False, apply sample bias correction (requires n >= 3)
Returns:
Skewness value:
- 0: Symmetric distribution (e.g., normal distribution)
- > 0: Positively skewed (right tail longer)
- < 0: Negatively skewed (left tail longer)
Performance:
- Uses SIMD acceleration for arrays larger than threshold
- Significantly faster than regular skew_py for large datasets
- Automatic fallback to scalar computation for small arrays
Examples:
>>> # Symmetric distribution
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> skew = scirs2.skewness_simd_py(data, bias=True)
>>> abs(skew) < 1e-10 # Near zero for symmetric data
True
>>> # Positively skewed (right tail)
>>> right_skewed = np.array([1.0, 2.0, 2.0, 3.0, 10.0])
>>> skew_pos = scirs2.skewness_simd_py(right_skewed)
>>> skew_pos > 0
True
>>> # Negatively skewed (left tail)
>>> left_skewed = np.array([1.0, 8.0, 8.0, 9.0, 10.0])
>>> skew_neg = scirs2.skewness_simd_py(left_skewed)
>>> skew_neg < 0
True
>>> # Large array with SIMD optimization
>>> np.random.seed(42)
>>> large_data = np.random.normal(0, 1, 100000)
>>> skew_large = scirs2.skewness_simd_py(large_data, bias=False)
>>> abs(skew_large) < 0.05 # Near zero for normal distribution
True
"""
...
"""
Compute SIMD-optimized kurtosis (fourth standardized moment).
This is a high-performance implementation of kurtosis calculation using SIMD
acceleration. Kurtosis measures the "tailedness" of a distribution - how prone
it is to producing outliers.
The kurtosis formula is: g₂ = E[(X-μ)⁴] / σ⁴
where μ is the mean and σ is the standard deviation.
Parameters:
data: Input data array
fisher: If True, use Fisher's definition (excess kurtosis: subtract 3)
If False, use Pearson's definition (raw kurtosis)
Default: True
bias: If True, use biased estimator
If False, apply sample bias correction (requires n >= 4)
Default: False
Returns:
Kurtosis value:
- Fisher's (excess kurtosis):
* 0: Normal distribution (mesokurtic)
* > 0: Heavy tails, more outliers (leptokurtic)
* < 0: Light tails, fewer outliers (platykurtic)
- Pearson's (raw kurtosis):
* 3: Normal distribution
* > 3: Heavy tails
* < 3: Light tails
Performance:
- Uses SIMD acceleration for arrays larger than threshold
- Significantly faster than regular kurtosis_py for large datasets
- Automatic fallback to scalar computation for small arrays
Examples:
>>> # Normal-like distribution (Fisher's excess kurtosis ≈ 0)
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0])
>>> kurt_fisher = scirs2.kurtosis_simd_py(data, fisher=True, bias=True)
>>> kurt_fisher < 0 # Uniform has negative excess kurtosis
True
>>> # Pearson's definition (Fisher's + 3)
>>> kurt_pearson = scirs2.kurtosis_simd_py(data, fisher=False, bias=True)
>>> abs(kurt_pearson - (kurt_fisher + 3.0)) < 1e-10
True
>>> # Peaked distribution (high kurtosis)
>>> peaked = np.array([5.0, 5.0, 5.0, 5.0, 5.0, 10.0, 15.0, 5.0, 5.0])
>>> kurt_peaked = scirs2.kurtosis_simd_py(peaked, fisher=True)
>>> kurt_peaked > 0 # Positive excess kurtosis
True
>>> # Large array with SIMD optimization
>>> np.random.seed(42)
>>> large_data = np.random.normal(0, 1, 100000)
>>> kurt_large = scirs2.kurtosis_simd_py(large_data, fisher=True, bias=False)
>>> abs(kurt_large) < 0.2 # Near zero for normal distribution
True
"""
...
"""
Compute SIMD-optimized Pearson correlation coefficient.
This is a high-performance implementation using SIMD acceleration for computing
the Pearson correlation coefficient, which measures the linear relationship
between two variables.
The Pearson correlation formula is:
r = Σ((x-μₓ)(y-μᵧ)) / √(Σ(x-μₓ)² × Σ(y-μᵧ)²)
where μₓ and μᵧ are the means of x and y.
Parameters:
x: First data array
y: Second data array (must have same length as x)
Returns:
Correlation coefficient ranging from -1 to 1:
- 1: Perfect positive correlation
- 0: No linear correlation
- -1: Perfect negative correlation
Raises:
RuntimeError: If arrays have different lengths or zero variance
Performance:
- Uses SIMD acceleration for arrays larger than threshold
- Significantly faster than regular pearsonr_py for large datasets
- Automatic fallback to scalar computation for small arrays
Examples:
>>> # Perfect positive correlation
>>> x = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> y = np.array([2.0, 4.0, 6.0, 8.0, 10.0])
>>> corr = scirs2.pearson_r_simd_py(x, y)
>>> abs(corr - 1.0) < 1e-10
True
>>> # Perfect negative correlation
>>> y_neg = np.array([5.0, 4.0, 3.0, 2.0, 1.0])
>>> corr_neg = scirs2.pearson_r_simd_py(x, y_neg)
>>> abs(corr_neg - (-1.0)) < 1e-10
True
>>> # No correlation
>>> np.random.seed(42)
>>> x_rand = np.random.normal(0, 1, 1000)
>>> y_rand = np.random.normal(0, 1, 1000)
>>> corr_none = scirs2.pearson_r_simd_py(x_rand, y_rand)
>>> abs(corr_none) < 0.1 # Close to zero
True
>>> # Moderate positive correlation
>>> np.random.seed(42)
>>> x_data = np.random.normal(0, 1, 100)
>>> y_data = 0.7 * x_data + np.random.normal(0, 0.5, 100)
>>> corr_mod = scirs2.pearson_r_simd_py(x_data, y_data)
>>> 0.5 < corr_mod < 0.9
True
>>> # Financial data (stock returns)
>>> np.random.seed(42)
>>> stock_a = np.random.normal(0.001, 0.02, 252) # Daily returns
>>> stock_b = 0.6 * stock_a + np.random.normal(0.0005, 0.015, 252)
>>> corr_stocks = scirs2.pearson_r_simd_py(stock_a, stock_b)
>>> 0.4 < corr_stocks < 0.8
True
"""
...
"""
Compute SIMD-optimized covariance.
This is a high-performance implementation using SIMD acceleration for computing
covariance, which measures how two variables change together.
The covariance formula is:
Cov(X,Y) = Σ((x-μₓ)(y-μᵧ)) / (n - ddof)
where μₓ and μᵧ are the means of x and y, and ddof is degrees of freedom.
Parameters:
x: First data array
y: Second data array (must have same length as x)
ddof: Degrees of freedom for bias correction
- 0: Population covariance (biased)
- 1: Sample covariance (unbiased, default)
Returns:
Covariance value:
- > 0: Variables tend to increase together
- 0: No linear relationship
- < 0: Variables move in opposite directions
Raises:
RuntimeError: If arrays have different lengths or insufficient data
Performance:
- Uses SIMD acceleration for arrays larger than threshold
- Significantly faster than regular covariance_py for large datasets
- Automatic fallback to scalar computation for small arrays
Notes:
- Covariance is related to correlation: Cov(X,Y) = r × σₓ × σᵧ
- Units: product of the units of x and y
- Covariance is scale-dependent (unlike correlation)
Examples:
>>> # Positive covariance (variables increase together)
>>> x = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> y = np.array([2.0, 4.0, 6.0, 8.0, 10.0])
>>> cov = scirs2.covariance_simd_py(x, y, ddof=1)
>>> cov > 0
True
>>> # Negative covariance (variables move opposite)
>>> y_neg = np.array([5.0, 4.0, 3.0, 2.0, 1.0])
>>> cov_neg = scirs2.covariance_simd_py(x, y_neg, ddof=1)
>>> cov_neg < 0
True
>>> # Zero covariance (no relationship)
>>> y_const = np.array([5.0, 5.0, 5.0, 5.0, 5.0])
>>> cov_zero = scirs2.covariance_simd_py(x, y_const, ddof=1)
>>> abs(cov_zero) < 1e-10
True
>>> # Formula verification: Cov(X,Y) = E[(X-μₓ)(Y-μᵧ)]
>>> x_data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> y_data = np.array([2.0, 4.0, 6.0, 8.0, 10.0])
>>> cov_result = scirs2.covariance_simd_py(x_data, y_data, ddof=1)
>>> # Manual calculation
>>> mean_x = np.mean(x_data)
>>> mean_y = np.mean(y_data)
>>> manual_cov = np.sum((x_data - mean_x) * (y_data - mean_y)) / 4
>>> abs(cov_result - manual_cov) < 1e-10
True
>>> # ddof=0 (population) vs ddof=1 (sample)
>>> cov_pop = scirs2.covariance_simd_py(x_data, y_data, ddof=0)
>>> cov_sample = scirs2.covariance_simd_py(x_data, y_data, ddof=1)
>>> cov_pop < cov_sample # Population cov is smaller
True
>>> # Large arrays with SIMD optimization
>>> np.random.seed(42)
>>> large_x = np.random.normal(0, 1, 100000)
>>> large_y = 0.7 * large_x + np.random.normal(0, 0.5, 100000)
>>> cov_large = scirs2.covariance_simd_py(large_x, large_y, ddof=1)
>>> cov_large > 0 # Positive relationship
True
"""
...
"""
Compute SIMD-optimized nth statistical moment.
This is a high-performance implementation for calculating any statistical moment
using SIMD acceleration. Moments are fundamental in describing distributions:
- 1st moment (raw): Mean
- 2nd moment (central): Variance (with ddof=0)
- 3rd moment (central): Related to skewness
- 4th moment (central): Related to kurtosis
Formula:
- Raw moment: E[X^n] = Σ(x^n) / N
- Central moment: E[(X-μ)^n] = Σ((x-μ)^n) / N
Parameters:
data: Input data array
moment_order: Order of the moment (0, 1, 2, 3, ...)
center: If True, compute central moment (around mean)
If False, compute raw moment (default: True)
Returns:
The nth moment value
Performance:
- Uses SIMD acceleration for large arrays
- Efficient computation of arbitrary moment orders
- Automatic optimization selection
Examples:
>>> # First raw moment = mean
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> moment1_raw = scirs2.moment_simd_py(data, 1, center=False)
>>> abs(moment1_raw - 3.0) < 1e-10
True
>>> # First central moment = 0
>>> moment1_central = scirs2.moment_simd_py(data, 1, center=True)
>>> abs(moment1_central) < 1e-10
True
>>> # Second central moment = variance (ddof=0)
>>> moment2 = scirs2.moment_simd_py(data, 2, center=True)
>>> variance_pop = np.var(data, ddof=0)
>>> abs(moment2 - variance_pop) < 1e-10
True
>>> # Third central moment (symmetry measure)
>>> moment3 = scirs2.moment_simd_py(data, 3, center=True)
>>> abs(moment3) < 1e-10 # Symmetric data
True
>>> # Fourth central moment (tail heaviness)
>>> moment4 = scirs2.moment_simd_py(data, 4, center=True)
>>> moment4 > 0 # Always positive
True
>>> # Gamma distribution moments
>>> np.random.seed(42)
>>> gamma_data = np.random.gamma(5.0, 2.0, 10000)
>>> m1 = scirs2.moment_simd_py(gamma_data, 1, center=False)
>>> 9.5 < m1 < 10.5 # Mean ≈ k*theta = 10
True
"""
...
"""
Compute SIMD-optimized arithmetic mean.
This is a high-performance implementation of the mean calculation using SIMD
acceleration, providing significant speedup for large datasets while maintaining
numerical accuracy.
Formula: μ = Σx / n
Parameters:
data: Input data array
Returns:
The arithmetic mean of the data
Performance:
- Uses SIMD acceleration for large arrays (typically >1000 elements)
- 2-8x faster than scalar computation depending on CPU
- Automatic fallback for small arrays
- Platform-aware: Leverages SSE, AVX, or NEON instructions
Examples:
>>> # Basic mean
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> mean = scirs2.mean_simd_py(data)
>>> mean == 3.0
True
>>> # Mean with negative values
>>> data_neg = np.array([-5.0, -3.0, -1.0, 1.0, 3.0, 5.0])
>>> mean_neg = scirs2.mean_simd_py(data_neg)
>>> abs(mean_neg) < 1e-10
True
>>> # Large array SIMD optimization
>>> np.random.seed(42)
>>> large_data = np.random.normal(100, 15, 100000)
>>> mean_large = scirs2.mean_simd_py(large_data)
>>> 99 < mean_large < 101
True
>>> # Single value
>>> single = np.array([42.0])
>>> scirs2.mean_simd_py(single)
42.0
>>> # Matches NumPy and regular version
>>> test_data = np.array([10.5, 20.3, 30.7, 40.2, 50.1])
>>> simd_mean = scirs2.mean_simd_py(test_data)
>>> numpy_mean = np.mean(test_data)
>>> regular_mean = scirs2.mean_py(test_data)
>>> abs(simd_mean - numpy_mean) < 1e-10
True
>>> abs(simd_mean - regular_mean) < 1e-10
True
"""
...
"""
Compute SIMD-optimized standard deviation.
This is a high-performance implementation of standard deviation using SIMD
acceleration. Standard deviation measures the amount of variation or dispersion
in a dataset.
Formula: σ = √(Σ(x-μ)² / (n-ddof))
Parameters:
data: Input data array
ddof: Degrees of freedom for bias correction
- 0: Population standard deviation (biased)
- 1: Sample standard deviation (unbiased, default)
Returns:
The standard deviation of the data
Performance:
- Uses SIMD acceleration for large arrays
- 3-8x faster than scalar computation
- Numerically stable Welford-based algorithm
- Automatic optimization selection
Examples:
>>> # Sample standard deviation
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> std_sample = scirs2.std_simd_py(data, ddof=1)
>>> expected = np.std(data, ddof=1)
>>> abs(std_sample - expected) < 1e-10
True
>>> # Population vs sample std
>>> pop_std = scirs2.std_simd_py(data, ddof=0)
>>> sample_std = scirs2.std_simd_py(data, ddof=1)
>>> pop_std < sample_std # Population is smaller
True
>>> # Constant data has zero std
>>> constant = np.array([5.0, 5.0, 5.0, 5.0, 5.0])
>>> std_zero = scirs2.std_simd_py(constant, ddof=1)
>>> abs(std_zero) < 1e-10
True
>>> # Large array optimization
>>> np.random.seed(42)
>>> large_data = np.random.normal(0, 5, 100000)
>>> std_large = scirs2.std_simd_py(large_data, ddof=1)
>>> 4.9 < std_large < 5.1 # Close to true value (5)
True
>>> # Financial volatility
>>> np.random.seed(42)
>>> returns = np.random.normal(0.0005, 0.0127, 252)
>>> volatility = scirs2.std_simd_py(returns, ddof=1)
>>> 0.01 < volatility < 0.02
True
"""
...
"""
Compute SIMD-optimized variance.
This is a high-performance implementation of variance using SIMD acceleration.
Variance measures the average squared deviation from the mean, quantifying
the spread of data.
Formula: σ² = Σ(x-μ)² / (n-ddof)
Parameters:
data: Input data array
ddof: Degrees of freedom for bias correction
- 0: Population variance (biased)
- 1: Sample variance (unbiased, default)
Returns:
The variance of the data
Performance:
- Uses SIMD acceleration for large arrays
- 3-8x faster than scalar computation
- Numerically stable algorithm
- Automatic optimization selection
Notes:
- Variance = std²
- Units: squared units of the data
- Related to 2nd central moment: variance = moment₂ with ddof adjustment
Examples:
>>> # Sample variance
>>> data = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
>>> var_sample = scirs2.variance_simd_py(data, ddof=1)
>>> expected = np.var(data, ddof=1)
>>> abs(var_sample - expected) < 1e-10
True
>>> # Population variance (smaller than sample)
>>> var_pop = scirs2.variance_simd_py(data, ddof=0)
>>> var_pop == 2.0
True
>>> var_sample == 2.5
True
>>> # Variance = std²
>>> variance = scirs2.variance_simd_py(data, ddof=1)
>>> std = scirs2.std_simd_py(data, ddof=1)
>>> abs(variance - std**2) < 1e-10
True
>>> # Constant data has zero variance
>>> constant = np.array([10.0, 10.0, 10.0, 10.0, 10.0])
>>> var_zero = scirs2.variance_simd_py(constant, ddof=1)
>>> abs(var_zero) < 1e-10
True
>>> # Large array optimization
>>> np.random.seed(42)
>>> large_data = np.random.normal(0, 3, 100000)
>>> var_large = scirs2.variance_simd_py(large_data, ddof=1)
>>> 8.8 < var_large < 9.2 # Close to 9 (3²)
True
>>> # Sensor measurement precision
>>> np.random.seed(42)
>>> measurements = np.random.normal(25.0, 0.5, 1000)
>>> var_sensor = scirs2.variance_simd_py(measurements, ddof=1)
>>> 0.20 < var_sensor < 0.30 # Close to 0.25 (0.5²)
True
"""
...
# Statistical Distributions
# =============================================================================
"""
Normal (Gaussian) distribution.
Provides PDF, CDF, PPF, and random variate generation for the normal distribution.
Examples:
>>> # Standard normal distribution (mean=0, std=1)
>>> dist = scirs2.norm()
>>> pdf_value = dist.pdf(0.0) # ~0.3989
>>> cdf_value = dist.cdf(0.0) # 0.5
>>> median = dist.ppf(0.5) # 0.0
>>> samples = dist.rvs(1000) # 1000 random samples
>>>
>>> # Custom normal distribution
>>> dist2 = scirs2.norm(loc=5.0, scale=2.0) # mean=5, std=2
"""
"""
Create a normal distribution.
Parameters:
loc: Mean (location parameter)
scale: Standard deviation (scale parameter), must be > 0
Raises:
RuntimeError: If scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate the PDF
Returns:
PDF value at x
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate the CDF
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
Raises:
RuntimeError: If q not in [0, 1]
"""
...
"""
Random variates.
Parameters:
size: Number of random samples to generate
Returns:
List of random samples from the distribution
"""
...
"""
Binomial distribution.
Models the number of successes in n independent Bernoulli trials,
each with probability p of success.
Examples:
>>> # 10 coin flips, fair coin
>>> dist = scirs2.binom(10, 0.5)
>>> pmf_5 = dist.pmf(5.0) # Probability of exactly 5 heads
>>> cdf_7 = dist.cdf(7.0) # Probability of 7 or fewer heads
>>> median = dist.ppf(0.5) # Median number of successes
>>> samples = dist.rvs(1000) # 1000 random samples
"""
"""
Create a binomial distribution.
Parameters:
n: Number of trials (must be >= 0)
p: Probability of success (must be in [0, 1])
Raises:
RuntimeError: If n < 0 or p not in [0, 1]
"""
...
"""
Probability mass function.
Parameters:
k: Number of successes
Returns:
Probability of exactly k successes
"""
...
"""
Cumulative distribution function.
Parameters:
k: Number of successes
Returns:
Probability of k or fewer successes
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
Smallest k such that CDF(k) >= q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples
"""
...
"""
Poisson distribution.
Models the number of events occurring in a fixed interval when events
occur independently at a constant average rate.
Examples:
>>> # Average 3 events per interval
>>> dist = scirs2.poisson(3.0)
>>> pmf_3 = dist.pmf(3.0) # Probability of exactly 3 events
>>> cdf_5 = dist.cdf(5.0) # Probability of 5 or fewer events
>>> samples = dist.rvs(1000) # 1000 random samples
"""
"""
Create a Poisson distribution.
Parameters:
mu: Expected number of events (lambda parameter), must be > 0
Raises:
RuntimeError: If mu <= 0
"""
...
"""
Probability mass function.
Parameters:
k: Number of events
Returns:
Probability of exactly k events
"""
...
"""
Cumulative distribution function.
Parameters:
k: Number of events
Returns:
Probability of k or fewer events
"""
...
"""
Percent point function (inverse CDF).
Note: Not yet implemented in underlying library.
Parameters:
q: Probability value in [0, 1]
Returns:
Smallest k such that CDF(k) >= q
Raises:
RuntimeError: Currently raises "Not implemented"
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples
"""
...
"""
Exponential distribution.
Models the time between events in a Poisson process (time until next event).
Examples:
>>> # Default: mean=1
>>> dist = scirs2.expon()
>>> pdf_1 = dist.pdf(1.0)
>>> cdf_2 = dist.cdf(2.0)
>>> samples = dist.rvs(1000)
>>>
>>> # Custom scale (mean = scale)
>>> dist2 = scirs2.expon(scale=2.0) # mean=2
"""
"""
Create an exponential distribution.
Parameters:
scale: Scale parameter (mean = scale), must be > 0
Raises:
RuntimeError: If scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value at x
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples
"""
...
"""
Uniform distribution.
Constant probability over the interval [loc, loc+scale).
Examples:
>>> # Standard uniform [0, 1)
>>> dist = scirs2.uniform()
>>> pdf_0_5 = dist.pdf(0.5) # = 1.0
>>> cdf_0_5 = dist.cdf(0.5) # = 0.5
>>> samples = dist.rvs(1000)
>>>
>>> # Custom range [2, 5)
>>> dist2 = scirs2.uniform(loc=2.0, scale=3.0)
"""
"""
Create a uniform distribution over [loc, loc+scale).
Parameters:
loc: Lower bound
scale: Width of the interval, must be > 0
Raises:
RuntimeError: If scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value (1/scale if in [loc, loc+scale), else 0)
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples uniformly distributed over [loc, loc+scale)
"""
...
"""
Beta distribution.
The beta distribution is a continuous probability distribution defined on
the interval [0, 1], parameterized by two positive shape parameters alpha
and beta.
Examples:
>>> # Standard beta distribution
>>> dist = scirs2.beta(2.0, 3.0)
>>> pdf_0_5 = dist.pdf(0.5)
>>> cdf_0_5 = dist.cdf(0.5)
>>> samples = dist.rvs(1000)
>>>
>>> # Shifted and scaled beta
>>> dist2 = scirs2.beta(alpha=2.0, beta=5.0, loc=1.0, scale=2.0)
"""
"""
Create a beta distribution.
Parameters:
alpha: Shape parameter alpha > 0
beta: Shape parameter beta > 0
loc: Location parameter (default: 0.0)
scale: Scale parameter, must be > 0 (default: 1.0)
Raises:
RuntimeError: If alpha <= 0, beta <= 0, or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the beta distribution
"""
...
"""
Gamma distribution.
The gamma distribution is a continuous probability distribution with
shape parameter k and scale parameter theta.
Examples:
>>> # Standard gamma distribution
>>> dist = scirs2.gamma(2.0)
>>> pdf_1 = dist.pdf(1.0)
>>> cdf_1 = dist.cdf(1.0)
>>> samples = dist.rvs(1000)
>>>
>>> # Custom parameters
>>> dist2 = scirs2.gamma(shape=2.0, scale=2.0, loc=0.5)
"""
"""
Create a gamma distribution.
Parameters:
shape: Shape parameter k > 0
scale: Scale parameter theta > 0 (default: 1.0)
loc: Location parameter (default: 0.0)
Raises:
RuntimeError: If shape <= 0 or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the gamma distribution
"""
...
"""
Chi-square distribution.
The chi-square distribution with k degrees of freedom is the distribution
of a sum of the squares of k independent standard normal random variables.
Examples:
>>> # Chi-square with 5 degrees of freedom
>>> dist = scirs2.chi2(5.0)
>>> pdf_3 = dist.pdf(3.0)
>>> cdf_3 = dist.cdf(3.0)
>>> samples = dist.rvs(1000)
>>>
>>> # With location and scale
>>> dist2 = scirs2.chi2(df=10.0, loc=1.0, scale=2.0)
"""
"""
Create a chi-square distribution.
Parameters:
df: Degrees of freedom > 0
loc: Location parameter (default: 0.0)
scale: Scale parameter, must be > 0 (default: 1.0)
Raises:
RuntimeError: If df <= 0 or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Note: Current implementation has known numerical issues.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the chi-square distribution
"""
...
"""
Student's t distribution.
The Student's t distribution is a continuous probability distribution that
arises when estimating the mean of a normally distributed population in
situations where the sample size is small.
Examples:
>>> # Standard t distribution with 5 df
>>> dist = scirs2.t(5.0)
>>> pdf_0 = dist.pdf(0.0) # Symmetric around 0
>>> cdf_0 = dist.cdf(0.0) # = 0.5
>>> samples = dist.rvs(1000)
>>>
>>> # With location and scale
>>> dist2 = scirs2.t(df=10.0, loc=1.0, scale=2.0)
"""
"""
Create a Student's t distribution.
Parameters:
df: Degrees of freedom > 0
loc: Location parameter (default: 0.0)
scale: Scale parameter, must be > 0 (default: 1.0)
Raises:
RuntimeError: If df <= 0 or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the Student's t distribution
"""
...
"""
Cauchy (Lorentz) distribution.
The Cauchy distribution is a continuous probability distribution with
heavy tails. It has no defined mean or variance.
Examples:
>>> # Standard Cauchy distribution
>>> dist = scirs2.cauchy()
>>> pdf_0 = dist.pdf(0.0) # = 1/pi
>>> cdf_0 = dist.cdf(0.0) # = 0.5
>>> samples = dist.rvs(1000)
>>>
>>> # Custom location and scale
>>> dist2 = scirs2.cauchy(loc=1.0, scale=2.0)
"""
"""
Create a Cauchy distribution.
Parameters:
loc: Location parameter (median) (default: 0.0)
scale: Scale parameter, must be > 0 (default: 1.0)
Raises:
RuntimeError: If scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the Cauchy distribution
"""
...
"""
F (Fisher-Snedecor) distribution.
The F distribution is a continuous probability distribution that arises
in the analysis of variance (ANOVA) and in F-tests.
Examples:
>>> # F distribution with 5 and 10 degrees of freedom
>>> dist = scirs2.f(5.0, 10.0)
>>> pdf_1 = dist.pdf(1.0)
>>> cdf_1 = dist.cdf(1.0)
>>> samples = dist.rvs(1000)
>>>
>>> # With location and scale
>>> dist2 = scirs2.f(dfn=2.0, dfd=20.0, loc=0.5, scale=2.0)
"""
"""
Create an F distribution.
Parameters:
dfn: Numerator degrees of freedom > 0
dfd: Denominator degrees of freedom > 0
loc: Location parameter (default: 0.0)
scale: Scale parameter, must be > 0 (default: 1.0)
Raises:
RuntimeError: If dfn <= 0, dfd <= 0, or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Random variates.
Note: PPF (inverse CDF) is not yet implemented for the F distribution.
Parameters:
size: Number of random samples
Returns:
List of random samples from the F distribution
"""
...
"""
Lognormal distribution.
The lognormal distribution is the distribution of a random variable whose
logarithm follows a normal distribution. Commonly used in finance, biology,
and other fields where quantities are multiplicative in nature.
Examples:
>>> # Standard lognormal distribution
>>> dist = scirs2.lognorm()
>>> pdf_1 = dist.pdf(1.0)
>>> cdf_1 = dist.cdf(1.0)
>>> samples = dist.rvs(1000)
>>>
>>> # Custom parameters
>>> dist2 = scirs2.lognorm(mu=0.5, sigma=0.8, loc=0.0)
"""
"""
Create a lognormal distribution.
Parameters:
mu: Mean of underlying normal distribution (default: 0.0)
sigma: Standard deviation of underlying normal distribution > 0 (default: 1.0)
loc: Location parameter (default: 0.0)
Raises:
RuntimeError: If sigma <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value (0 if x <= loc)
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the lognormal distribution
"""
...
"""
Weibull minimum distribution.
The Weibull distribution is widely used in reliability engineering and
failure analysis. It can model a variety of life data behaviors depending
on the value of the shape parameter.
Examples:
>>> # Weibull distribution with shape=2 (Rayleigh-like)
>>> dist = scirs2.weibull_min(2.0)
>>> pdf_1 = dist.pdf(1.0)
>>> cdf_1 = dist.cdf(1.0)
>>> samples = dist.rvs(1000)
>>>
>>> # Custom parameters
>>> dist2 = scirs2.weibull_min(shape=1.5, scale=2.0, loc=0.0)
"""
"""
Create a Weibull distribution.
Parameters:
shape: Shape parameter k > 0
scale: Scale parameter lambda > 0 (default: 1.0)
loc: Location parameter (default: 0.0)
Raises:
RuntimeError: If shape <= 0 or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value (0 if x <= loc)
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the Weibull distribution
"""
...
"""
Laplace (double exponential) distribution.
The Laplace distribution is symmetric with heavier tails than the normal
distribution. Used in robust statistics and signal processing.
Examples:
>>> # Standard Laplace distribution
>>> dist = scirs2.laplace()
>>> pdf_0 = dist.pdf(0.0) # = 0.5
>>> cdf_0 = dist.cdf(0.0) # = 0.5
>>> samples = dist.rvs(1000)
>>>
>>> # Custom location and scale
>>> dist2 = scirs2.laplace(loc=2.0, scale=3.0)
"""
"""
Create a Laplace distribution.
Parameters:
loc: Location parameter (median) (default: 0.0)
scale: Scale parameter > 0 (default: 1.0)
Raises:
RuntimeError: If scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the Laplace distribution
"""
...
"""
Logistic distribution.
The logistic distribution is used in growth models, neural networks, and
logistic regression. It resembles the normal distribution but has heavier
tails.
Examples:
>>> # Standard logistic distribution
>>> dist = scirs2.logistic()
>>> pdf_0 = dist.pdf(0.0) # = 0.25
>>> cdf_0 = dist.cdf(0.0) # = 0.5
>>> samples = dist.rvs(1000)
>>>
>>> # Custom location and scale
>>> dist2 = scirs2.logistic(loc=1.0, scale=2.0)
"""
"""
Create a logistic distribution.
Parameters:
loc: Location parameter (mean, median, mode) (default: 0.0)
scale: Scale parameter > 0 (default: 1.0)
Raises:
RuntimeError: If scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the logistic distribution
"""
...
"""
Pareto distribution.
The Pareto distribution is a power-law distribution commonly used to model
wealth distribution, city populations, and other phenomena following the
"80-20 rule" (Pareto principle).
Examples:
>>> # Pareto distribution with shape=3
>>> dist = scirs2.pareto(3.0)
>>> pdf_2 = dist.pdf(2.0)
>>> cdf_2 = dist.cdf(2.0)
>>> samples = dist.rvs(1000)
>>>
>>> # Custom parameters
>>> dist2 = scirs2.pareto(shape=2.0, scale=2.0, loc=0.0)
"""
"""
Create a Pareto distribution.
Parameters:
shape: Shape parameter alpha > 0
scale: Scale parameter x_m > 0 (default: 1.0)
loc: Location parameter (default: 0.0)
Raises:
RuntimeError: If shape <= 0 or scale <= 0
"""
...
"""
Probability density function.
Parameters:
x: Point at which to evaluate
Returns:
PDF value (0 if x <= scale+loc)
"""
...
"""
Cumulative distribution function.
Parameters:
x: Point at which to evaluate
Returns:
Probability that X <= x
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
x such that CDF(x) = q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples from the Pareto distribution
"""
...
"""
Geometric distribution.
The geometric distribution models the number of failures before the first
success in a sequence of independent Bernoulli trials. Commonly used in
reliability analysis and queuing theory.
Examples:
>>> # Geometric distribution with p=0.3
>>> dist = scirs2.geom(0.3)
>>> pmf_2 = dist.pmf(2.0) # P(X = 2)
>>> cdf_2 = dist.cdf(2.0) # P(X <= 2)
>>> samples = dist.rvs(1000)
>>>
>>> # Geometric with p=0.5 (fair coin)
>>> dist2 = scirs2.geom(0.5)
"""
"""
Create a geometric distribution.
Parameters:
p: Success probability, 0 < p <= 1
Raises:
RuntimeError: If p <= 0 or p > 1
"""
...
"""
Probability mass function.
Parameters:
k: Number of failures before first success (non-negative integer)
Returns:
Probability P(X = k)
"""
...
"""
Cumulative distribution function.
Parameters:
k: Number of failures
Returns:
Probability P(X <= k)
"""
...
"""
Percent point function (inverse CDF).
Parameters:
q: Probability value in [0, 1]
Returns:
k such that CDF(k) >= q
"""
...
"""
Random variates.
Parameters:
size: Number of random samples
Returns:
List of random samples (number of failures before first success)
"""
...
# =============================================================================
# FFT Module
# =============================================================================
"""Compute FFT. Returns dict with real and imag arrays."""
...
"""Compute inverse FFT. Returns dict with real and imag arrays."""
...
"""Compute real FFT. Returns dict with real and imag arrays."""
...
"""Compute inverse real FFT."""
...
"""Compute DCT (type 1, 2, 3, or 4)."""
...
"""Compute inverse DCT."""
...
"""Generate FFT sample frequencies."""
...
"""Generate real FFT sample frequencies."""
...
"""Shift zero-frequency component to center."""
...
"""Inverse of fftshift."""
...
"""Find next fast FFT size."""
...
"""
Compute the 2-D discrete Fourier Transform.
Parameters
----------
data : ndarray of shape (M, N)
Input 2-D array
s : tuple of (int, int), optional
Shape of the output transform; if None, uses input shape
Returns
-------
dict
Dictionary with 'real' and 'imag' arrays of the 2-D FFT result
"""
...
"""
Compute the 2-D real discrete Fourier Transform.
Parameters
----------
data : ndarray of shape (M, N)
Input 2-D real-valued array
s : tuple of (int, int), optional
Shape of the output transform; if None, uses input shape
Returns
-------
dict
Dictionary with 'real' and 'imag' arrays of the 2-D real FFT result
"""
...
"""
Compute the 2-D inverse discrete Fourier Transform.
Parameters
----------
real : ndarray
Real part of the input spectrum
imag : ndarray
Imaginary part of the input spectrum
s : tuple of (int, int), optional
Shape of the output; if None, uses input shape
Returns
-------
dict
Dictionary with 'real' and 'imag' arrays of the reconstructed signal
"""
...
"""
Compute the 2-D inverse real discrete Fourier Transform.
Parameters
----------
real : ndarray
Real part of the rfft2 output
imag : ndarray
Imaginary part of the rfft2 output
s : tuple of (int, int), optional
Shape of the output (required when output shape is ambiguous)
Returns
-------
ndarray
Real-valued 2-D reconstructed signal
"""
...
# =============================================================================
# Optimization Module
# =============================================================================
"""
Minimize a function of one or more variables.
Parameters:
fun: Objective function taking array-like and returning a float
x0: Initial guess
method: Optimization method
- 'nelder-mead': Nelder-Mead simplex
- 'powell': Powell's method
- 'cg': Conjugate gradient
- 'bfgs': BFGS quasi-Newton
- 'lbfgs': Limited-memory BFGS
- 'lbfgsb': L-BFGS-B with bounds
- 'newton-cg': Newton-CG
- 'trust-ncg': Newton trust-region
- 'sr1': SR1 quasi-Newton
- 'dfp': DFP quasi-Newton
options: Dict with 'maxiter', 'ftol', 'gtol'
bounds: Optional list of (min, max) bounds for each variable
Returns:
Dict with 'x' (solution), 'fun' (function value), 'success',
'nit' (iterations), 'nfev' (function evaluations), 'message'
"""
...
"""
Minimize a scalar function.
Parameters:
f: Objective function taking a float and returning a float
bracket: Initial bracket (a, b) where minimum is searched
method: Optimization method ('brent', 'golden', 'bounded')
maxiter: Maximum iterations
tol: Tolerance for termination
Returns:
Dict with 'x' (minimum location), 'fun' (minimum value),
'nfev' (function evaluations), 'success' (bool)
"""
...
"""
Find root of a scalar function using Brent's method.
Parameters:
fun: Function for which to find the root
a: Lower bound of the bracket
b: Upper bound of the bracket
xtol: Absolute tolerance
maxiter: Maximum iterations
Returns:
Dict with 'x' (root location), 'fun' (function value at root),
'iterations', 'success'
"""
...
"""
Global optimization using differential evolution.
Parameters:
f: Objective function taking an array and returning a float
bounds: List of (min, max) bounds for each variable
maxiter: Maximum iterations
popsize: Population size multiplier
tol: Tolerance for convergence
seed: Random seed for reproducibility
Returns:
Dict with 'x' (optimal point), 'fun' (optimal value),
'nfev' (function evaluations), 'success' (bool)
"""
...
"""
Use non-linear least squares to fit a function to data.
Similar to scipy.optimize.curve_fit.
Parameters:
f: Model function f(x, *params) that takes independent variable
and parameters. Example: lambda x, a, b: a * exp(b * x)
xdata: The independent variable where data is measured
ydata: The dependent data to fit
p0: Initial guess for parameters. If None, defaults to [1.0, 1.0]
method: Optimization method - 'lm' (Levenberg-Marquardt),
'trf' (Trust Region Reflective), or 'dogbox'
maxfev: Maximum number of function evaluations
Returns:
Dictionary with:
- popt: Optimized parameters as numpy array
- success: Whether optimization succeeded
- nfev: Number of function evaluations
- message: Status message
Examples:
>>> def model(x, a, b):
... return a * np.exp(b * x)
>>> xdata = [0.0, 1.0, 2.0, 3.0]
>>> ydata = [1.0, 2.7, 7.4, 20.1]
>>> result = scirs2.curve_fit_py(model, xdata, ydata, p0=[1.0, 1.0])
>>> print(result['popt']) # Optimized [a, b]
>>> # Fit quadratic: y = a*x^2 + b*x + c
>>> def quadratic(x, a, b, c):
... return a * x**2 + b * x + c
>>> xdata = [0.0, 1.0, 2.0, 3.0, 4.0]
>>> ydata = [1.0, 3.5, 7.0, 11.5, 17.0]
>>> result = scirs2.curve_fit_py(quadratic, xdata, ydata, p0=[0.5, 2.0, 1.0])
"""
...
# =============================================================================
# Special Functions Module
# =============================================================================
# Gamma functions
"""Compute gamma function Γ(x)."""
...
"""Compute log of gamma function ln(Γ(x))."""
...
"""Compute digamma (psi) function ψ(x) = Γ'(x)/Γ(x)."""
...
"""Compute beta function B(a, b)."""
...
# Bessel functions
"""Bessel function of the first kind, order 0."""
...
"""Bessel function of the first kind, order 1."""
...
"""Bessel function of the first kind, order n."""
...
"""Bessel function of the second kind, order 0."""
...
"""Bessel function of the second kind, order 1."""
...
"""Bessel function of the second kind, order n."""
...
# Modified Bessel functions
"""Modified Bessel function of the first kind, order 0."""
...
"""Modified Bessel function of the first kind, order 1."""
...
"""Modified Bessel function of the second kind, order 0."""
...
"""Modified Bessel function of the second kind, order 1."""
...
# Error functions
"""Compute error function erf(x)."""
...
"""Compute complementary error function erfc(x) = 1 - erf(x)."""
...
"""Compute inverse error function."""
...
"""Compute inverse complementary error function."""
...
"""Compute scaled complementary error function erfcx(x) = exp(x²) * erfc(x)."""
...
"""Compute imaginary error function erfi(x) = -i * erf(ix)."""
...
"""Compute Dawson's integral F(x) = exp(-x²) * ∫₀ˣ exp(t²) dt."""
...
# Combinatorial functions
"""
Compute factorial n!
Parameters:
n: Non-negative integer
Returns:
n! as a float
"""
...
"""
Compute binomial coefficient C(n, k) = n! / (k! * (n-k)!)
Parameters:
n: Total number of items
k: Number of items to choose
Returns:
Binomial coefficient as a float
"""
...
"""
Compute permutations P(n, k) = n! / (n-k)!
Parameters:
n: Total number of items
k: Number of items to arrange
Returns:
Number of permutations as a float
"""
...
# Elliptic integrals
"""
Complete elliptic integral of the first kind K(m).
Parameters:
m: Parameter (0 ≤ m ≤ 1)
Returns:
K(m) = ∫₀^(π/2) dθ / sqrt(1 - m*sin²(θ))
"""
...
"""
Complete elliptic integral of the second kind E(m).
Parameters:
m: Parameter (0 ≤ m ≤ 1)
Returns:
E(m) = ∫₀^(π/2) sqrt(1 - m*sin²(θ)) dθ
"""
...
"""
Incomplete elliptic integral of the first kind F(φ, m).
Parameters:
phi: Amplitude
m: Parameter (0 ≤ m ≤ 1)
Returns:
F(φ, m) = ∫₀^φ dθ / sqrt(1 - m*sin²(θ))
"""
...
"""
Incomplete elliptic integral of the second kind E(φ, m).
Parameters:
phi: Amplitude
m: Parameter (0 ≤ m ≤ 1)
Returns:
E(φ, m) = ∫₀^φ sqrt(1 - m*sin²(θ)) dθ
"""
...
# Vectorized versions
"""Compute gamma function for array of values."""
...
"""Compute error function for array of values."""
...
"""Compute J0 Bessel function for array of values."""
...
# =============================================================================
# Integration Module
# =============================================================================
"""
Integrate using trapezoidal rule.
Parameters:
y: Array of function values
x: Array of sample points (optional)
dx: Sample spacing if x is not provided
"""
...
"""
Integrate using Simpson's rule.
Parameters:
y: Array of function values
x: Array of sample points (optional)
dx: Sample spacing if x is not provided
"""
...
"""
Compute cumulative integral using trapezoidal rule.
Parameters:
y: Array of function values
x: Array of sample points (optional)
dx: Sample spacing if x is not provided
initial: Initial value to prepend to result
"""
...
"""
Integrate using Romberg integration on sampled data.
Parameters:
y: Array of function values (length must be 2^k + 1)
dx: Sample spacing
"""
...
"""
Adaptive quadrature integration.
Parameters:
fun: Function to integrate
a: Lower bound
b: Upper bound
epsabs: Absolute error tolerance
epsrel: Relative error tolerance
maxiter: Maximum function evaluations
Returns:
Dict with 'value' (integral), 'error' (estimated error),
'neval' (function evaluations), 'success' (bool)
"""
...
"""
Solve an initial value problem for a system of ODEs.
Solves dy/dt = f(t, y) with y(t0) = y0.
Parameters:
fun: Function computing dy/dt = f(t, y)
t_span: Integration interval (t0, tf)
y0: Initial state
method: ODE solver method
- 'RK45': Explicit Runge-Kutta 4(5) (default)
- 'RK23': Explicit Runge-Kutta 2(3)
- 'DOP853': Explicit Runge-Kutta 8(5,3)
- 'Radau': Implicit Runge-Kutta (stiff)
- 'BDF': Backward differentiation formula (stiff)
- 'LSODA': Adams/BDF with automatic stiffness detection
rtol: Relative tolerance
atol: Absolute tolerance
max_step: Maximum step size (optional)
Returns:
Dict with 't' (time points), 'y' (solutions as 2D array),
'nfev' (function evaluations), 'success', 'message'
"""
...
# =============================================================================
# Interpolation Module
# =============================================================================
"""1D interpolation class."""
"""
Create 1D interpolator.
Parameters:
x: x coordinates (must be sorted)
y: y coordinates
method: 'linear', 'nearest', 'cubic', or 'pchip'
extrapolate: 'error', 'nearest', or 'extrapolate'
"""
...
"""Evaluate interpolator at new points."""
...
"""Evaluate interpolator at a single point."""
...
"""
Linear interpolation (similar to numpy.interp).
Parameters:
x: x-coordinates at which to evaluate
xp: x-coordinates of data points
fp: y-coordinates of data points
"""
...
"""
Linear interpolation with boundary handling.
Parameters:
x: x-coordinates at which to evaluate
xp: x-coordinates of data points
fp: y-coordinates of data points
left: Value to return for x < xp[0]
right: Value to return for x > xp[-1]
"""
...
"""
Cubic spline interpolation class.
Provides C2-continuous (continuous function, first, and second derivatives)
interpolation through data points using piecewise cubic polynomials.
Examples:
>>> x = np.array([0.0, 1.0, 2.0, 3.0])
>>> y = np.array([0.0, 1.0, 4.0, 9.0])
>>> spline = scirs2.CubicSpline(x, y)
>>>
>>> # Evaluate at new points
>>> x_new = np.array([0.5, 1.5, 2.5])
>>> y_new = spline(x_new)
>>>
>>> # Compute derivatives
>>> dy_dx = spline.derivative(x_new, nu=1) # First derivative
>>> d2y_dx2 = spline.derivative(x_new, nu=2) # Second derivative
>>>
>>> # Integrate
>>> integral = spline.integrate(0.0, 3.0)
"""
"""
Create a cubic spline interpolator.
Parameters:
x: x coordinates (must be strictly increasing)
y: y coordinates
bc_type: Boundary condition type - 'natural', 'not-a-knot', or 'periodic'
'natural': Zero second derivative at endpoints (default)
'not-a-knot': Maximum smoothness at second and second-to-last points
'periodic': Function and derivatives match at endpoints
Raises:
ValueError: If x is not strictly increasing or if x and y have different lengths
"""
...
"""
Evaluate the spline at new points.
Parameters:
x_new: Points at which to evaluate the spline
Returns:
Interpolated values at x_new
"""
...
"""
Evaluate the spline at a single point.
Parameters:
x: Point at which to evaluate
Returns:
Interpolated value at x
"""
...
"""
Compute derivatives of the spline.
Parameters:
x_new: Points at which to evaluate derivatives
nu: Derivative order (1 for first derivative, 2 for second, etc.)
Returns:
Derivative values at x_new
Examples:
>>> spline = scirs2.CubicSpline(x, y)
>>> # First derivative
>>> dy_dx = spline.derivative(x_new, nu=1)
>>> # Second derivative
>>> d2y_dx2 = spline.derivative(x_new, nu=2)
"""
...
"""
Integrate the spline over an interval.
Parameters:
a: Lower bound of integration
b: Upper bound of integration
Returns:
Definite integral from a to b
Examples:
>>> spline = scirs2.CubicSpline(x, y)
>>> area = spline.integrate(0.0, 3.0)
"""
...
"""
2D interpolation on regular grids.
Provides bivariate interpolation for data defined on a 2D rectangular grid.
Similar to scipy.interpolate.interp2d but for regular grids only.
Examples:
>>> # Create a 2D grid
>>> x = np.array([0.0, 1.0, 2.0])
>>> y = np.array([0.0, 1.0])
>>> # z[i, j] corresponds to point (x[j], y[i])
>>> z = np.array([[0.0, 1.0, 2.0],
... [1.0, 2.0, 3.0]])
>>>
>>> interp = scirs2.Interp2d(x, y, z, kind="linear")
>>>
>>> # Evaluate at a single point
>>> value = interp(0.5, 0.5)
>>>
>>> # Evaluate at multiple points
>>> x_new = np.array([0.5, 1.0, 1.5])
>>> y_new = np.array([0.5, 0.5, 0.5])
>>> values = interp.eval_array(x_new, y_new)
>>>
>>> # Evaluate on a regular grid
>>> x_grid = np.array([0.0, 0.5, 1.0])
>>> y_grid = np.array([0.0, 0.5, 1.0])
>>> z_grid = interp.eval_grid(x_grid, y_grid) # Shape: (3, 3)
"""
"""
Create a 2D interpolator on a regular grid.
Parameters:
x: x coordinates (1D array, must be sorted), length n_x
y: y coordinates (1D array, must be sorted), length n_y
z: z values on the grid (2D array with shape (n_y, n_x))
Note: z[i, j] corresponds to point (x[j], y[i])
kind: Interpolation method - 'linear', 'cubic', or 'quintic'
'linear': Bilinear interpolation (fast, C0 continuous)
'cubic': Bicubic interpolation (smooth, C1 continuous)
'quintic': Biquintic interpolation (very smooth, requires >= 6 points)
Raises:
ValueError: If z.shape != (len(y), len(x)) or if x/y are not sorted
Notes:
The z array indexing follows the convention: z[row, col] = z[y_index, x_index]
This matches NumPy's meshgrid convention with indexing='ij'.
"""
...
"""
Evaluate the interpolator at a single point.
Parameters:
x: x coordinate
y: y coordinate
Returns:
Interpolated value at (x, y)
"""
...
"""
Evaluate at multiple scattered points.
Parameters:
x_new: x coordinates (must have same length as y_new)
y_new: y coordinates (must have same length as x_new)
Returns:
1D array of interpolated values, same length as x_new/y_new
Examples:
>>> x_points = np.array([0.5, 1.0, 1.5])
>>> y_points = np.array([0.5, 0.7, 0.3])
>>> values = interp.eval_array(x_points, y_points)
"""
...
"""
Evaluate on a regular grid (Cartesian product of x_new and y_new).
Parameters:
x_new: x coordinates for output grid (1D array)
y_new: y coordinates for output grid (1D array)
Returns:
2D array with shape (len(y_new), len(x_new))
Result[i, j] corresponds to point (x_new[j], y_new[i])
Examples:
>>> x_grid = np.linspace(0, 2, 5)
>>> y_grid = np.linspace(0, 1, 3)
>>> z_grid = interp.eval_grid(x_grid, y_grid)
>>> # z_grid.shape = (3, 5)
"""
...
# =============================================================================
# Signal Processing Module
# =============================================================================
"""
Convolve two 1-D arrays.
Parameters:
a: First input array
v: Second input array
mode: 'full', 'same', or 'valid'
"""
...
"""
Cross-correlation of two 1-D arrays.
Parameters:
a: First input array
v: Second input array
mode: 'full', 'same', or 'valid'
"""
...
"""
Compute analytic signal using Hilbert transform.
Returns:
Dict with 'real' and 'imag' arrays
"""
...
# Window functions
"""Generate Hann window of length n."""
...
"""Generate Hamming window of length n."""
...
"""Generate Blackman window of length n."""
...
"""Generate Bartlett (triangular) window of length n."""
...
"""
Generate Kaiser window.
Parameters:
n: Window length
beta: Shape parameter (0=rectangular, 5=Hamming-like, 6=Hann-like)
"""
...
"""
Find peaks in a 1-D array.
Parameters:
x: Input array
height: Minimum peak height
distance: Minimum distance between peaks
Returns:
Array of peak indices
"""
...
# Filter design functions
"""
Design a Butterworth digital filter.
Parameters:
order: Filter order
cutoff: Cutoff frequency (normalized 0-1, where 1 is Nyquist)
filter_type: 'lowpass', 'highpass', 'bandpass', or 'bandstop'
Returns:
Dict with 'b' (numerator) and 'a' (denominator) coefficients
"""
...
"""
Design a Chebyshev Type I digital filter.
Parameters:
order: Filter order
ripple: Passband ripple in dB
cutoff: Cutoff frequency (normalized 0-1, where 1 is Nyquist)
filter_type: 'lowpass' or 'highpass'
Returns:
Dict with 'b' (numerator) and 'a' (denominator) coefficients
"""
...
"""
Design a FIR filter using window method.
Parameters:
numtaps: Number of filter taps (filter order + 1)
cutoff: Cutoff frequency (normalized 0-1, where 1 is Nyquist)
window: Window function ('hamming', 'hann', 'blackman', 'kaiser')
pass_zero: If True, lowpass; if False, highpass
Returns:
Filter coefficients as numpy array
"""
...
# =============================================================================
# Spatial Module
# =============================================================================
# Distance functions
"""Euclidean distance between two points."""
...
"""Manhattan (city block) distance between two points."""
...
"""Chebyshev distance between two points."""
...
"""
Minkowski distance between two points.
Parameters:
u, v: Input arrays
p: Order of the norm (p=1 is cityblock, p=2 is euclidean)
"""
...
"""Cosine distance between two points (1 - cosine similarity)."""
...
"""
Compute pairwise distances between observations.
Parameters:
x: Input array of shape (n, m)
metric: 'euclidean', 'cityblock', 'manhattan', or 'chebyshev'
Returns:
Condensed distance matrix (n*(n-1)/2,)
"""
...
"""
Compute distances between each pair from two sets of observations.
Parameters:
xa: Input array of shape (na, m)
xb: Input array of shape (nb, m)
metric: 'euclidean', 'cityblock', 'manhattan', or 'chebyshev'
Returns:
Distance matrix of shape (na, nb)
"""
...
"""
Convert condensed distance matrix to square form.
Parameters:
x: Condensed distance matrix from pdist
Returns:
Square distance matrix
"""
...
# Convex Hull
"""
Compute the convex hull of a set of points.
Parameters:
points: Array of shape (n, k) containing n points in k dimensions
Returns:
Dict with 'vertices' (indices), 'simplices', 'volume', and 'area'
"""
...
"""ConvexHull class for working with convex hulls."""
"""
Create a ConvexHull from points.
Parameters:
points: Array of shape (n, k) containing n points in k dimensions
"""
...
"""Get the indices of vertices that form the convex hull."""
...
"""Get the simplices (facets) of the convex hull."""
...
"""Calculate the volume of the convex hull."""
...
"""Calculate the surface area of the convex hull."""
...
"""Check if a point is inside the convex hull."""
...
# KD-Tree spatial data structure
"""KD-Tree for efficient nearest neighbor searches."""
"""
Construct a KD-Tree from points.
Parameters:
data: Array of shape (n, k) containing n points in k dimensions
"""
...
"""
Query the tree for k nearest neighbors.
Parameters:
point: Query point
k: Number of nearest neighbors to find
Returns:
Dict with 'indices' and 'distances' arrays
"""
...
"""
Query the tree for all points within radius r.
Parameters:
point: Query point
r: Search radius
Returns:
Dict with 'indices' and 'distances' arrays
"""
...
# =============================================================================
# Sparse Matrix Module
# =============================================================================
"""
Create a CSR (Compressed Sparse Row) sparse array from triplets.
Parameters
----------
rows : list of int
Row indices of non-zero elements
cols : list of int
Column indices of non-zero elements
data : list of float
Non-zero values
shape : tuple of (int, int)
Shape of the resulting matrix (nrows, ncols)
sum_duplicates : bool, optional
If True, sum values at duplicate (row, col) positions (default: False)
Returns
-------
dict
Dictionary with keys: 'format', 'shape', 'nnz', 'indptr', 'indices', 'data'
"""
...
"""
Create a COO (Coordinate) sparse array from triplets.
Parameters
----------
rows : list of int
Row indices of non-zero elements
cols : list of int
Column indices of non-zero elements
data : list of float
Non-zero values
shape : tuple of (int, int)
Shape of the resulting matrix (nrows, ncols)
sum_duplicates : bool, optional
If True, sum values at duplicate (row, col) positions (default: False)
Returns
-------
dict
Dictionary with keys: 'format', 'shape', 'nnz', 'row', 'col', 'data'
"""
...
"""
Create a CSC (Compressed Sparse Column) sparse array from triplets.
Parameters
----------
rows : list of int
Row indices of non-zero elements
cols : list of int
Column indices of non-zero elements
data : list of float
Non-zero values
shape : tuple of (int, int)
Shape of the resulting matrix (nrows, ncols)
sum_duplicates : bool, optional
If True, sum values at duplicate (row, col) positions (default: False)
Returns
-------
dict
Dictionary with keys: 'format', 'shape', 'nnz', 'indptr', 'indices', 'data'
"""
...
"""
Create a sparse identity matrix of size n x n.
Parameters
----------
n : int
Size of the square identity matrix
Returns
-------
dict
CSR sparse matrix representation of the identity matrix
"""
...
"""
Create a sparse diagonal matrix from a 1-D array.
Parameters
----------
diag : ndarray of shape (n,)
Diagonal elements
Returns
-------
dict
CSR sparse matrix with the given diagonal
"""
...
"""
Convert a sparse matrix (dict representation) to a dense numpy array.
Parameters
----------
sparse_dict : dict
Sparse matrix dict as returned by csr_array_from_triplets or similar
Returns
-------
ndarray
Dense 2-D array
"""
...
"""
Multiply a sparse matrix by a dense vector: y = A @ x.
Parameters
----------
sparse_dict : dict
Sparse matrix dict (CSR format)
x : ndarray of shape (n,)
Dense vector
Returns
-------
ndarray of shape (m,)
Result of matrix-vector multiplication
"""
...
"""
Multiply two sparse matrices: C = A @ B.
Parameters
----------
a_dict : dict
Left sparse matrix (CSR format)
b_dict : dict
Right sparse matrix (CSR format)
Returns
-------
dict
Resulting sparse matrix (CSR format)
"""
...
"""
Transpose a sparse matrix.
Parameters
----------
sparse_dict : dict
Sparse matrix dict
Returns
-------
dict
Transposed sparse matrix
"""
...
# =============================================================================
# N-Dimensional Image Processing Module (ndimage)
# =============================================================================
"""
Apply Gaussian filter to an image.
Parameters
----------
image : ndarray
Input image array (2-D or N-D)
sigma : float
Standard deviation of the Gaussian kernel
Returns
-------
ndarray
Filtered image
"""
...
"""
Apply median filter to an image.
Parameters
----------
image : ndarray
Input image array (2-D or N-D)
size : int
Size of the median filter kernel
Returns
-------
ndarray
Filtered image
"""
...
"""
Apply uniform (box) filter to an image.
Parameters
----------
image : ndarray
Input image array
size : int
Size of the filter kernel
Returns
-------
ndarray
Filtered image
"""
...
"""
Apply Sobel edge-detection filter along a given axis.
Parameters
----------
image : ndarray
Input image array
axis : int
Axis along which to apply the Sobel filter (0 for vertical, 1 for horizontal)
Returns
-------
ndarray
Edge-filtered image
"""
...
"""
Apply Laplace filter for edge detection.
Parameters
----------
image : ndarray
Input image array
Returns
-------
ndarray
Edge-filtered image using the Laplacian operator
"""
...
"""
Apply bilateral filter for edge-preserving smoothing.
Parameters
----------
image : ndarray
Input image array
sigma_spatial : float
Standard deviation in the spatial domain
sigma_intensity : float
Standard deviation in the intensity domain
Returns
-------
ndarray
Filtered image
"""
...
"""
Apply maximum filter to an image.
Parameters
----------
image : ndarray
Input image array
size : int
Size of the filter kernel
Returns
-------
ndarray
Image with maximum filter applied
"""
...
"""
Apply minimum filter to an image.
Parameters
----------
image : ndarray
Input image array
size : int
Size of the filter kernel
Returns
-------
ndarray
Image with minimum filter applied
"""
...
"""
Apply binary erosion morphological operation.
Parameters
----------
image : ndarray
Binary input image (values 0 or 1)
iterations : int
Number of times to apply the erosion
Returns
-------
ndarray
Eroded binary image
"""
...
"""
Apply binary dilation morphological operation.
Parameters
----------
image : ndarray
Binary input image (values 0 or 1)
iterations : int
Number of times to apply the dilation
Returns
-------
ndarray
Dilated binary image
"""
...
"""
Apply binary opening morphological operation (erosion then dilation).
Parameters
----------
image : ndarray
Binary input image (values 0 or 1)
iterations : int
Number of times to apply the operation
Returns
-------
ndarray
Opened binary image
"""
...
"""
Apply binary closing morphological operation (dilation then erosion).
Parameters
----------
image : ndarray
Binary input image (values 0 or 1)
iterations : int
Number of times to apply the operation
Returns
-------
ndarray
Closed binary image
"""
...
"""
Apply grey-scale erosion morphological operation.
Parameters
----------
image : ndarray
Greyscale input image
size : int
Size of the structuring element
Returns
-------
ndarray
Eroded image
"""
...
"""
Apply grey-scale dilation morphological operation.
Parameters
----------
image : ndarray
Greyscale input image
size : int
Size of the structuring element
Returns
-------
ndarray
Dilated image
"""
...
"""
Label connected components in an image.
Parameters
----------
image : ndarray
Binary input image
Returns
-------
tuple of (ndarray, int)
Labeled image array and number of labels found
"""
...
"""
Compute exact Euclidean distance transform.
Parameters
----------
image : ndarray
Binary input image (0 = object, 1 = background)
Returns
-------
ndarray
Distance transform image where each pixel holds the distance to
the nearest non-zero pixel
"""
...
"""
Rotate an image by a given angle.
Parameters
----------
image : ndarray
Input image array
angle : float
Rotation angle in degrees (counter-clockwise)
reshape : bool, optional
If True, resize output to contain entire rotated image (default: True)
Returns
-------
ndarray
Rotated image
"""
...
"""
Zoom an image by a given factor.
Parameters
----------
image : ndarray
Input image array
zoom : float
Zoom factor (> 1 = zoom in, < 1 = zoom out)
Returns
-------
ndarray
Zoomed image
"""
...
"""
Shift an image by given offsets.
Parameters
----------
image : ndarray
Input image array
shift : list of float
Shift in pixels for each dimension
Returns
-------
ndarray
Shifted image
"""
...
"""
Compute the center of mass of an image.
Parameters
----------
image : ndarray
Input image (treated as a mass distribution)
Returns
-------
list of float
Coordinates of the center of mass for each dimension
"""
...
"""
Compute image moments up to a given order.
Parameters
----------
image : ndarray of shape (H, W)
Input 2-D image
order : int
Maximum moment order to compute
Returns
-------
ndarray
Moment values
"""
...
"""
Apply watershed segmentation algorithm.
Parameters
----------
image : ndarray
Greyscale image to segment
markers : ndarray of int
Marker array indicating seed regions (positive integers)
Returns
-------
ndarray of int
Labeled image with watershed segments
"""
...
"""
Compute Otsu's optimal threshold for image binarization.
Parameters
----------
image : ndarray
Greyscale image
Returns
-------
float
Optimal threshold value that minimizes intra-class variance
"""
...
"""
Apply a binary threshold to an image.
Parameters
----------
image : ndarray
Input greyscale image
threshold : float
Threshold value; pixels above become 1.0, below become 0.0
Returns
-------
ndarray
Binary image
"""
...
"""
Apply Canny edge detection.
Parameters
----------
image : ndarray
Input greyscale image
low_threshold : float
Lower hysteresis threshold
high_threshold : float
Upper hysteresis threshold
Returns
-------
ndarray
Binary edge image
"""
...
"""
Detect Harris corners in an image.
Parameters
----------
image : ndarray
Input greyscale image
k : float
Harris detector free parameter (typically 0.04-0.06)
Returns
-------
ndarray
Corner response map
"""
...
"""
Compute Peak Signal-to-Noise Ratio (PSNR).
Parameters
----------
original : ndarray
Original reference image
compressed : ndarray
Compared/compressed image
Returns
-------
float
PSNR in dB (higher is better)
"""
...
"""
Compute Structural Similarity Index Measure (SSIM).
Parameters
----------
img1 : ndarray
First image
img2 : ndarray
Second image
Returns
-------
float
SSIM value in [-1, 1] (1.0 = identical images)
"""
...
"""
Compute the entropy of an image (measure of information content).
Parameters
----------
image : ndarray
Input image
Returns
-------
float
Shannon entropy of the image's pixel intensity histogram
"""
...
# =============================================================================
# Graph Algorithms Module
# =============================================================================
"""
Create an undirected graph from edge list.
Parameters
----------
edges : list of (int, int)
Edge list as pairs of node indices
weights : list of float, optional
Edge weights; if None, all weights default to 1.0
Returns
-------
Graph object (opaque PyAny)
"""
...
"""
Create a directed graph from edge list.
Parameters
----------
edges : list of (int, int)
Edge list as pairs of (from, to) node indices
weights : list of float, optional
Edge weights; if None, all weights default to 1.0
Returns
-------
DiGraph object (opaque PyAny)
"""
...
"""
Generate an Erdos-Renyi random graph G(n, p).
Parameters
----------
n : int
Number of nodes
p : float
Probability of edge between any pair of nodes
Returns
-------
Graph object
"""
...
"""
Generate a Barabasi-Albert scale-free random graph.
Parameters
----------
n : int
Number of nodes
m : int
Number of edges to attach from a new node to existing nodes
Returns
-------
Graph object
"""
...
"""
Generate a Watts-Strogatz small-world random graph.
Parameters
----------
n : int
Number of nodes
k : int
Each node is joined with k nearest neighbors in ring topology
p : float
Probability of rewiring each edge
Returns
-------
Graph object
"""
...
"""
Generate a complete graph with n nodes (every node connected to every other).
Parameters
----------
n : int
Number of nodes
Returns
-------
Graph object
"""
...
"""
Generate a path graph with n nodes.
Parameters
----------
n : int
Number of nodes in the path
Returns
-------
Graph object
"""
...
"""
Generate a cycle graph with n nodes.
Parameters
----------
n : int
Number of nodes in the cycle
Returns
-------
Graph object
"""
...
"""
Generate a star graph with n leaf nodes (n+1 nodes total).
Parameters
----------
n : int
Number of leaf nodes (center node is added automatically)
Returns
-------
Graph object
"""
...
"""
Breadth-first search traversal order.
Parameters
----------
graph : Graph object
Graph to traverse
start : int
Starting node index
Returns
-------
list of int
Nodes visited in BFS order
"""
...
"""
Depth-first search traversal order.
Parameters
----------
graph : Graph object
Graph to traverse
start : int
Starting node index
Returns
-------
list of int
Nodes visited in DFS order
"""
...
"""
Dijkstra's shortest path algorithm.
Parameters
----------
graph : Graph object
Weighted graph
start : int
Source node index
Returns
-------
dict
Dictionary with 'distances' and 'predecessors' for each node
"""
...
"""
Floyd-Warshall all-pairs shortest paths algorithm.
Parameters
----------
graph : Graph object
Weighted graph
Returns
-------
ndarray of shape (n, n)
Distance matrix where entry [i, j] is the shortest path from i to j.
Infinity indicates no path.
"""
...
"""
Find all connected components in an undirected graph.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
list of list of int
Each inner list is a set of node indices forming one connected component
"""
...
"""
Find strongly connected components in a directed graph (Tarjan's algorithm).
Parameters
----------
graph : DiGraph object
Directed graph
Returns
-------
list of list of int
Each inner list is a strongly connected component
"""
...
"""
Find articulation points (cut vertices) in an undirected graph.
Articulation points are nodes whose removal increases the number of
connected components.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
list of int
Node indices that are articulation points
"""
...
"""
Find bridges (cut edges) in an undirected graph.
Bridges are edges whose removal increases the number of connected components.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
list of (int, int)
Edge pairs that are bridges
"""
...
"""
Check if a graph is bipartite.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
bool
True if the graph is bipartite, False otherwise
"""
...
"""
Compute betweenness centrality for all nodes.
Betweenness centrality quantifies the number of times a node acts as a
bridge along the shortest path between two other nodes.
Parameters
----------
graph : Graph object
Graph (directed or undirected)
Returns
-------
dict mapping int to float
Betweenness centrality score for each node
"""
...
"""
Compute closeness centrality for all nodes.
Closeness centrality measures how close a node is to all other nodes.
Parameters
----------
graph : Graph object
Graph
Returns
-------
dict mapping int to float
Closeness centrality score for each node
"""
...
"""
Compute PageRank centrality for all nodes.
Parameters
----------
graph : Graph object
Directed graph
damping : float, optional
Damping factor (default: 0.85)
max_iter : int, optional
Maximum number of iterations (default: 100)
tol : float, optional
Convergence tolerance (default: 1e-6)
Returns
-------
dict mapping int to float
PageRank score for each node
"""
...
"""
Detect communities using the Louvain algorithm.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
list of list of int
Each inner list is a community (set of node indices)
"""
...
"""
Detect communities using label propagation algorithm.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
list of list of int
Each inner list is a community
"""
...
"""
Compute the modularity of a community partition.
Modularity measures the quality of a community partition; higher values
indicate stronger community structure.
Parameters
----------
graph : Graph object
Undirected graph
communities : list of list of int
Community partition
Returns
-------
float
Modularity score in [-1, 1]
"""
...
"""
Compute the diameter of a graph (longest shortest path).
Parameters
----------
graph : Graph object
Connected graph
Returns
-------
float or None
Diameter of the graph; None if the graph is not connected
"""
...
"""
Compute the clustering coefficient for all nodes and the global average.
The clustering coefficient of a node measures how close its neighbors
are to being a complete graph.
Parameters
----------
graph : Graph object
Undirected graph
Returns
-------
dict
Dictionary with 'global' (average) and 'local' (per-node dict) coefficients
"""
...
"""
Compute the density of a graph.
Density = actual edges / maximum possible edges.
Parameters
----------
graph : Graph object
Returns
-------
float
Density in [0, 1]
"""
...
"""
Compute the minimum spanning tree (Kruskal's algorithm).
Parameters
----------
graph : Graph object
Weighted undirected graph
Returns
-------
Graph object
Minimum spanning tree
"""
...
# =============================================================================
# Machine Learning Metrics Module
# =============================================================================
"""
Compute classification accuracy.
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
Returns
-------
float
Fraction of correctly classified samples in [0, 1]
"""
...
"""
Compute precision score.
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
average : str, optional
Averaging strategy: 'macro', 'micro', 'weighted' (default: 'macro')
Returns
-------
float
Precision score
"""
...
"""
Compute recall (sensitivity) score.
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
average : str, optional
Averaging strategy: 'macro', 'micro', 'weighted' (default: 'macro')
Returns
-------
float
Recall score
"""
...
"""
Compute F1 score (harmonic mean of precision and recall).
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
average : str, optional
Averaging strategy: 'macro', 'micro', 'weighted' (default: 'macro')
Returns
-------
float
F1 score
"""
...
"""
Compute F-beta score (generalized F-measure).
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
beta : float
Weight of recall relative to precision; beta=1 gives F1
average : str, optional
Averaging strategy: 'macro', 'micro', 'weighted' (default: 'macro')
Returns
-------
float
F-beta score
"""
...
"""
Compute the confusion matrix.
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
Returns
-------
ndarray of shape (n_classes, n_classes)
Confusion matrix where entry [i, j] is the number of samples
with true class i predicted as class j
"""
...
"""
Compute Receiver Operating Characteristic (ROC) curve.
Parameters
----------
y_true : ndarray of int
True binary labels (0 or 1)
y_score : ndarray of float
Predicted probability scores for the positive class
Returns
-------
dict
Dictionary with 'fpr', 'tpr', and 'thresholds' arrays
"""
...
"""
Compute Area Under the ROC Curve (AUC-ROC).
Parameters
----------
y_true : ndarray of int
True binary labels (0 or 1)
y_score : ndarray of float
Predicted probability scores for the positive class
Returns
-------
float
AUC-ROC score in [0, 1]
"""
...
"""
Compute log loss (cross-entropy loss) for classification.
Parameters
----------
y_true : ndarray of int
True binary labels (0 or 1)
y_pred : ndarray of float
Predicted probabilities for the positive class
Returns
-------
float
Log loss (lower is better)
"""
...
"""
Compute Matthews Correlation Coefficient (MCC).
Parameters
----------
y_true : ndarray of int
True binary labels
y_pred : ndarray of int
Predicted binary labels
Returns
-------
float
MCC in [-1, 1]
"""
...
"""
Compute balanced accuracy (average recall per class).
Parameters
----------
y_true : ndarray of int
True class labels
y_pred : ndarray of int
Predicted class labels
Returns
-------
float
Balanced accuracy in [0, 1]
"""
...
"""
Compute Cohen's kappa score (inter-rater agreement).
Parameters
----------
y_true : ndarray of int
First set of ratings
y_pred : ndarray of int
Second set of ratings
Returns
-------
float
Kappa score
"""
...
"""
Compute Mean Squared Error (MSE) for regression.
Parameters
----------
y_true : ndarray of float
True values
y_pred : ndarray of float
Predicted values
Returns
-------
float
MSE (lower is better)
"""
...
"""
Compute Mean Absolute Error (MAE) for regression.
Parameters
----------
y_true : ndarray of float
True values
y_pred : ndarray of float
Predicted values
Returns
-------
float
MAE (lower is better)
"""
...
"""
Compute R^2 (coefficient of determination) for regression.
Parameters
----------
y_true : ndarray of float
True values
y_pred : ndarray of float
Predicted values
Returns
-------
float
R^2 score; 1.0 = perfect fit, 0.0 = constant baseline
"""
...
"""
Compute Mean Absolute Percentage Error (MAPE).
Parameters
----------
y_true : ndarray of float
True values (must not contain zeros)
y_pred : ndarray of float
Predicted values
Returns
-------
float
MAPE as a percentage (lower is better)
"""
...
"""
Compute explained variance regression score.
Parameters
----------
y_true : ndarray of float
True values
y_pred : ndarray of float
Predicted values
Returns
-------
float
Explained variance score in [0, 1]
"""
...
"""
Compute Adjusted Rand Index (ARI) for clustering evaluation.
Parameters
----------
y_true : ndarray of int
True cluster labels
y_pred : ndarray of int
Predicted cluster labels
Returns
-------
float
ARI in [-1, 1]
"""
...
"""
Compute Normalized Mutual Information (NMI) for clustering evaluation.
Parameters
----------
y_true : ndarray of int
True cluster labels
y_pred : ndarray of int
Predicted cluster labels
Returns
-------
float
NMI in [0, 1]
"""
...
"""
Compute Normalized Discounted Cumulative Gain (NDCG) for ranking evaluation.
Parameters
----------
y_true : ndarray of float
True relevance scores
y_score : ndarray of float
Predicted scores (higher = more relevant)
k : int, optional
Only consider top-k elements. If None, use all elements.
Returns
-------
float
NDCG score in [0, 1]
"""
...
"""
Compute Mean Reciprocal Rank (MRR) for ranking/retrieval evaluation.
Parameters
----------
y_true : ndarray of int
Binary relevance labels (1 = relevant, 0 = not relevant)
y_score : ndarray of float
Predicted scores
Returns
-------
float
MRR score in (0, 1]
"""
...
# =============================================================================
# File I/O Module
# =============================================================================
"""
Read a CSV file into a numpy array.
Parameters
----------
path : str
Path to the CSV file
delimiter : str, optional
Field delimiter (default: ',')
has_header : bool, optional
If True, skip the first line as header (default: True)
Returns
-------
ndarray of float
Data matrix read from the CSV file
"""
...
"""
Write a numpy array to a CSV file.
Parameters
----------
path : str
Output file path
data : ndarray
2-D array to write
delimiter : str, optional
Field delimiter (default: ',')
header : str, optional
Header line to write as the first row
"""
...
"""
Read a sparse matrix in Matrix Market (.mtx) format.
Parameters
----------
path : str
Path to the .mtx file
Returns
-------
dict
Sparse matrix in COO dict representation
"""
...
"""
Write a sparse matrix to Matrix Market (.mtx) format.
Parameters
----------
path : str
Output file path
sparse_dict : dict
Sparse matrix dict
"""
...
"""
Read a dense matrix from a Matrix Market file.
Parameters
----------
path : str
Path to the .mtx file (dense format)
Returns
-------
ndarray of float64
Dense matrix
"""
...
"""
Write a dense matrix to Matrix Market format.
Parameters
----------
path : str
Output file path
data : ndarray
2-D array to write
"""
...
"""
Save a numpy array to a file.
Parameters
----------
path : str
Output file path
data : ndarray
Array to save
format : str, optional
File format: 'npy', 'csv', or 'txt' (default: 'npy')
"""
...
"""
Load a numpy array from a file.
Parameters
----------
path : str
Input file path
format : str, optional
File format: 'npy', 'csv', or 'txt' (default: 'npy')
Returns
-------
ndarray of float64
Loaded array
"""
...
"""
Read a WAV audio file.
Parameters
----------
path : str
Path to the .wav file
Returns
-------
dict
Dictionary with 'samplerate' (int) and 'data' (ndarray) keys
"""
...
"""
Write audio data to a WAV file.
Parameters
----------
path : str
Output file path
samplerate : int
Sample rate in Hz
data : ndarray of float64
Audio samples (1-D array)
"""
...
# =============================================================================
# Datasets Module
# =============================================================================
"""
Load the Iris dataset.
Returns
-------
dict
Dictionary with 'data', 'target', 'feature_names', 'target_names'
"""
...
"""
Load the Boston Housing dataset.
Returns
-------
dict
Dictionary with 'data', 'target', and 'feature_names' keys
"""
...
"""
Load the Diabetes dataset.
Returns
-------
dict
Dictionary with 'data', 'target', and 'feature_names' keys
"""
...
"""
Load the Breast Cancer Wisconsin dataset.
Returns
-------
dict
Dictionary with 'data', 'target', 'feature_names', and 'target_names'
"""
...
"""
Load the Digits handwritten digit dataset.
Returns
-------
dict
Dictionary with 'data', 'target', and 'images' keys
"""
...
"""
Generate a random n-class classification dataset.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
n_features : int, optional
Total number of features (default: 20)
n_informative : int, optional
Number of informative features (default: 2)
n_classes : int, optional
Number of classes (default: 2)
random_state : int, optional
Random seed for reproducibility
Returns
-------
dict
Dictionary with 'X' (feature matrix) and 'y' (class labels)
"""
...
"""
Generate a random regression dataset.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
n_features : int, optional
Number of features (default: 100)
n_informative : int, optional
Number of informative features (default: 10)
noise : float, optional
Gaussian noise standard deviation (default: 0.0)
random_state : int, optional
Random seed for reproducibility
Returns
-------
dict
Dictionary with 'X' (feature matrix) and 'y' (target values)
"""
...
"""
Generate isotropic Gaussian blobs for clustering.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
n_features : int, optional
Number of features (default: 2)
centers : int, optional
Number of cluster centers (default: 3)
cluster_std : float, optional
Standard deviation of each cluster (default: 1.0)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X' (feature matrix) and 'y' (cluster labels)
"""
...
"""
Generate two interleaving half circles (moon shapes).
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
noise : float, optional
Gaussian noise standard deviation (default: 0.1)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X' (n x 2 feature matrix) and 'y' (binary labels)
"""
...
"""
Generate a large circle containing a smaller circle.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
noise : float, optional
Gaussian noise standard deviation (default: 0.1)
factor : float, optional
Scale factor between inner and outer circle (default: 0.8)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X' (n x 2 feature matrix) and 'y' (binary labels)
"""
...
"""
Generate spiral-shaped clusters.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
noise : float, optional
Gaussian noise standard deviation (default: 0.1)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X' (n x 2 feature matrix) and 'y' (binary labels)
"""
...
"""
Generate a Swiss roll dataset.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
noise : float, optional
Gaussian noise standard deviation (default: 0.0)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X' (n x 3 feature matrix) and 't' (1D manifold position)
"""
...
"""
Generate an S-curve dataset.
Parameters
----------
n_samples : int, optional
Number of samples (default: 100)
noise : float, optional
Gaussian noise standard deviation (default: 0.0)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X' (n x 3 feature matrix) and 't' (1D manifold position)
"""
...
"""
Split arrays or matrices into random train and test subsets.
Parameters
----------
X : ndarray
Feature matrix of shape (n_samples, n_features)
y : ndarray
Target array of shape (n_samples,)
test_size : float, optional
Proportion of dataset to include in the test split (default: 0.2)
random_state : int, optional
Random seed
Returns
-------
dict
Dictionary with 'X_train', 'X_test', 'y_train', 'y_test' arrays
"""
...
"""
Generate k-fold cross-validation indices.
Parameters
----------
n_samples : int
Total number of samples
n_splits : int, optional
Number of folds (default: 5)
shuffle : bool, optional
Whether to shuffle before splitting (default: False)
random_state : int, optional
Random seed
Returns
-------
list of (list of int, list of int)
Each element is a (train_indices, test_indices) tuple
"""
...
"""
Scale features to a given range using min-max normalization.
Parameters
----------
data : ndarray
Input data to scale
feature_range : tuple of (float, float), optional
Target range (default: (0.0, 1.0))
Returns
-------
ndarray
Scaled data
"""
...
# =============================================================================
# Data Transformation Module
# =============================================================================
"""
Normalize an array (rows) using the specified norm.
Parameters
----------
data : ndarray of shape (n, m)
Input data matrix
norm : str, optional
Normalization type: 'l1', 'l2', or 'max' (default: 'l2')
Returns
-------
ndarray
Normalized data where each row has unit norm
"""
...
"""
Normalize a 1-D vector using the specified norm.
Parameters
----------
v : ndarray of shape (n,)
Input vector
norm : str, optional
Normalization type: 'l1', 'l2', or 'max' (default: 'l2')
Returns
-------
ndarray
Normalized vector
"""
...
"""
Binarize data according to a threshold.
Parameters
----------
data : ndarray
Input data
threshold : float, optional
Values above this become 1.0, at or below become 0.0 (default: 0.0)
Returns
-------
ndarray
Binary array with the same shape as data
"""
...
"""
Discretize continuous data into equal-width bins.
Parameters
----------
data : ndarray
Input 1-D continuous data
n_bins : int
Number of bins
Returns
-------
ndarray of int
Bin indices for each data point (0-based)
"""
...
"""
Discretize continuous data into equal-frequency (quantile) bins.
Parameters
----------
data : ndarray
Input 1-D continuous data
n_bins : int
Number of bins (approximately equal number of samples per bin)
Returns
-------
ndarray of int
Bin indices for each data point (0-based)
"""
...
"""
Apply log transformation: log(data + shift).
Parameters
----------
data : ndarray
Input data (must be positive after adding shift)
shift : float, optional
Value to add before taking log (default: 0.0)
Returns
-------
ndarray
Log-transformed data
"""
...
"""
Apply power transformation: data^power.
Parameters
----------
data : ndarray
Input data
power : float
Exponent to apply
Returns
-------
ndarray
Power-transformed data
"""
...
# =============================================================================
# Text Processing Module
# =============================================================================
"""
Compute Levenshtein edit distance between two strings.
Parameters
----------
s1 : str
First string
s2 : str
Second string
Returns
-------
int
Edit distance (0 = identical strings)
"""
...
"""
Compute cosine similarity between two vectors.
Parameters
----------
v1 : list of float
First vector
v2 : list of float
Second vector (must have same length as v1)
Returns
-------
float
Cosine similarity in [-1, 1]
"""
...
"""
Compute Jaccard similarity between two strings based on character sets.
Parameters
----------
s1 : str
First string
s2 : str
Second string
Returns
-------
float
Jaccard similarity in [0, 1]
"""
...
"""
Remove HTML tags from a string.
Parameters
----------
text : str
Input string potentially containing HTML tags
Returns
-------
str
String with all HTML tags removed
"""
...
"""
Replace URL patterns in text with a placeholder string.
Parameters
----------
text : str
Input text
replacement : str, optional
String to replace URLs with (default: '<URL>')
Returns
-------
str
Text with URLs replaced
"""
...
"""
Replace email address patterns in text with a placeholder string.
Parameters
----------
text : str
Input text
replacement : str, optional
Replacement string (default: '<EMAIL>')
Returns
-------
str
Text with email addresses replaced
"""
...
"""
Expand common English contractions in text.
Parameters
----------
text : str
Input text with contractions (e.g., "don't", "can't", "it's")
Returns
-------
str
Text with contractions expanded
"""
...
"""
Normalize Unicode characters in text to NFC form.
Parameters
----------
text : str
Input text
Returns
-------
str
Unicode-normalized text
"""
...
"""
Normalize whitespace in text: collapse multiple spaces to one.
Parameters
----------
text : str
Input text
Returns
-------
str
Text with normalized whitespace
"""
...
"""
Remove accent characters (diacritics) from text.
Parameters
----------
text : str
Input text with accented characters
Returns
-------
str
Text with accents removed (e.g., 'e with accent' becomes 'e')
"""
...
# =============================================================================
# Computer Vision Module
# =============================================================================
"""
Convert an RGB image to grayscale.
Parameters
----------
image : ndarray of uint8 and shape (H, W, 3)
Input RGB image
Returns
-------
ndarray of uint8 and shape (H, W)
Grayscale image
"""
...
"""
Convert an RGB image to HSV (Hue, Saturation, Value) color space.
Parameters
----------
image : ndarray of uint8 and shape (H, W, 3)
Input RGB image
Returns
-------
ndarray of float64 and shape (H, W, 3)
HSV image with H in [0, 360], S and V in [0, 1]
"""
...
"""
Detect edges using the Sobel operator.
Parameters
----------
image : ndarray of uint8
Input grayscale image
Returns
-------
ndarray of float64
Edge magnitude image
"""
...
"""
Detect edges using the Canny edge detector.
Parameters
----------
image : ndarray of uint8
Input grayscale image
low_threshold : float
Lower hysteresis threshold
high_threshold : float
Upper hysteresis threshold
Returns
-------
ndarray of uint8
Binary edge image (255 = edge, 0 = background)
"""
...
"""
Detect edges using the Prewitt operator.
Parameters
----------
image : ndarray of uint8
Input grayscale image
Returns
-------
ndarray of float64
Edge magnitude image
"""
...
"""
Detect edges using the Laplacian operator.
Parameters
----------
image : ndarray of uint8
Input grayscale image
Returns
-------
ndarray of float64
Edge response image
"""
...
"""
Apply global histogram equalization to a grayscale image.
Parameters
----------
image : ndarray of uint8
Input grayscale image of shape (H, W)
Returns
-------
ndarray of uint8
Histogram-equalized image
"""
...
"""
Apply Contrast Limited Adaptive Histogram Equalization (CLAHE).
Parameters
----------
image : ndarray of uint8
Input grayscale image
clip_limit : float
Threshold for contrast limiting
tile_grid_size : tuple of (int, int)
Size of grid for histogram equalization tiles
Returns
-------
ndarray of uint8
Contrast-enhanced image
"""
...
"""
Normalize the brightness of an image to a target mean value.
Parameters
----------
image : ndarray of uint8
Input image
target_mean : float
Target mean pixel intensity
Returns
-------
ndarray of uint8
Brightness-normalized image
"""
...
"""
Sharpen an image using the unsharp masking technique.
Parameters
----------
image : ndarray of uint8
Input image
sigma : float
Gaussian blur sigma for creating the mask
strength : float
Sharpening strength factor
Returns
-------
ndarray of uint8
Sharpened image
"""
...
"""
Apply Gaussian blur to a vision image.
Parameters
----------
image : ndarray of uint8
Input image
sigma : float
Standard deviation of the Gaussian kernel
kernel_size : int, optional
Size of the kernel; if None, derived from sigma
Returns
-------
ndarray of uint8
Blurred image
"""
...
"""
Detect SIFT keypoints and compute descriptors.
Parameters
----------
image : ndarray of uint8
Input grayscale image
Returns
-------
dict
Dictionary with 'keypoints' (list of (x, y, size, angle)) and
'descriptors' (ndarray of shape (n_kp, 128))
"""
...
"""
Convert a labeled segmentation map to a color image.
Parameters
----------
labels : ndarray of int32
Labeled image where each unique value is a segment
Returns
-------
ndarray of uint8 and shape (H, W, 3)
RGB color image with each label assigned a distinct color
"""
...
"""
Find a homography matrix mapping source points to destination points.
Parameters
----------
src_points : ndarray of shape (n, 2)
Source image points (at least 4 non-collinear points required)
dst_points : ndarray of shape (n, 2)
Destination image points
Returns
-------
ndarray of shape (3, 3)
Homography matrix H
"""
...
# =============================================================================
# Async Operations Module
# =============================================================================
"""
Asynchronous FFT operation for large arrays (must be awaited).
Parameters
----------
data : ndarray of float64
Real-valued input data
Returns
-------
coroutine
Awaitable returning a complex-valued result dict
"""
...
"""
Asynchronous SVD decomposition for large matrices (must be awaited).
Parameters
----------
matrix : ndarray of shape (m, n)
Input matrix
full_matrices : bool, optional
If True, compute full U and Vt matrices (default: True)
Returns
-------
coroutine
Awaitable returning a dict with 'U', 'S', 'Vt' arrays
"""
...
"""
Asynchronous QR decomposition for large matrices (must be awaited).
Parameters
----------
matrix : ndarray of shape (m, n)
Input matrix
Returns
-------
coroutine
Awaitable returning a dict with 'Q' and 'R' arrays
"""
...
"""
Asynchronous numerical integration (must be awaited).
Parameters
----------
func : callable
Python callable f(x) -> float
a : float
Lower integration limit
b : float
Upper integration limit
epsabs : float, optional
Absolute error tolerance (default: 1e-8)
epsrel : float, optional
Relative error tolerance (default: 1e-8)
Returns
-------
coroutine
Awaitable returning a dict with 'value' and 'error' keys
"""
...
"""
Asynchronous optimization for expensive objective functions (must be awaited).
Parameters
----------
func : callable
Objective function f(x) -> float
x0 : ndarray
Initial guess
method : str, optional
Optimization method (e.g., 'nelder-mead', 'bfgs')
maxiter : int, optional
Maximum number of iterations
Returns
-------
coroutine
Awaitable returning an optimization result dict
"""
...
# =============================================================================
# Batch Statistics Module
# =============================================================================
"""
Compute a quick summary of basic statistics.
Parameters
----------
data : list of float
Input data values
Returns
-------
tuple of (float, float, float)
Tuple of (mean, variance, std)
"""
...
"""
Compute descriptive statistics for multiple arrays in parallel.
Parameters
----------
arrays : list of list of float
List of data arrays
Returns
-------
list of dict
One dict per input array with keys: 'mean', 'variance', 'std',
'min', 'max', 'median', 'count'
"""
...
"""
Compute pairwise Pearson correlation matrix for multiple arrays.
Parameters
----------
arrays : list of list of float
List of data arrays (must all have the same length)
Returns
-------
list of list of float
Correlation matrix as nested list
"""
...
"""
Evaluate a probability density function at multiple points.
Parameters
----------
distribution : str
Name of the distribution (e.g., 'norm', 'gamma', 'beta')
params : list of float
Distribution parameters (vary by distribution)
x_values : list of float
Points at which to evaluate the PDF
Returns
-------
list of float
PDF values at each point
"""
...
# =============================================================================
# Batch Linear Algebra Module
# =============================================================================
"""
Compute batch matrix multiplication: result[i] = a_list[i] @ b_list[i].
Processes pairs of matrices in parallel using Rayon.
Parameters
----------
a_list : list of 2-D matrix (as list of list of float)
List of left-hand matrices
b_list : list of 2-D matrix (as list of list of float)
List of right-hand matrices (must have same length as a_list)
Returns
-------
list of 2-D matrix (as list of list of float)
List of result matrices
"""
...
"""
Compute SVD for a batch of matrices in parallel.
Parameters
----------
matrices : list of 2-D matrix (as list of list of float)
List of matrices to decompose
Returns
-------
list of dict
Each dict has 'u', 's', 'vt' keys with the SVD components
"""
...
"""
Solve a batch of linear systems Ax = b in parallel.
Parameters
----------
a_list : list of 2-D matrix (as list of list of float)
List of coefficient matrices (each must be square)
b_list : list of list of float
List of right-hand side vectors
Returns
-------
list of list of float
List of solution vectors
"""
...
"""
Compute matrix norms for a batch of matrices in parallel.
Parameters
----------
matrices : list of 2-D matrix (as list of list of float)
List of input matrices
ord : str, optional
Norm type: 'fro' (Frobenius), '1', 'inf', '2' (default: 'fro')
Returns
-------
list of float
Norm value for each input matrix
"""
...
# =============================================================================
# Polynomial Fitting (Statistics Extension)
# =============================================================================
"""
Fit a polynomial of the specified degree to data points.
Uses least-squares to find coefficients of a polynomial p(x) = c_0 + c_1*x
+ ... + c_d*x^d that minimizes the sum of squared residuals.
Parameters
----------
x : ndarray of float64
Independent variable (x-coordinates)
y : ndarray of float64
Dependent variable (y-coordinates; must have same length as x)
degree : int
Degree of the polynomial to fit (must be >= 1)
Returns
-------
dict
Dictionary with:
- 'coefficients': ndarray of shape (degree+1,) in ascending order
- 'residuals': float, sum of squared residuals
- 'rank': int, rank of the Vandermonde matrix
Examples
--------
>>> x = np.array([0.0, 1.0, 2.0, 3.0, 4.0])
>>> y = np.array([1.0, 3.0, 7.0, 13.0, 21.0]) # y = x^2 + x + 1
>>> result = scirs2.polyfit_py(x, y, degree=2)
"""
...