Exemple #1
0
def pearsonr(x, y, axis=None):
    '''
    Calculates a Pearson correlation coefficient and the p-value for testing non-correlation.

    The Pearson correlation coefficient measures the linear relationship between two datasets. 
    Strictly speaking, Pearson’s correlation requires that each dataset be normally distributed, 
    and not necessarily zero-mean. Like other correlation coefficients, this one varies between 
    -1 and +1 with 0 implying no correlation. Correlations of -1 or +1 imply an exact linear 
    relationship. Positive correlations imply that as x increases, so does y. Negative 
    correlations imply that as x increases, y decreases.

    The p-value roughly indicates the probability of an uncorrelated system producing datasets 
    that have a Pearson correlation at least as extreme as the one computed from these datasets. 
    The p-values are not entirely reliable but are probably reasonable for datasets larger than 
    500 or so.
    
    :param x: (*array_like*) x data array.
    :param y: (*array_like*) y data array.
    :param axis: (*int*) By default, the index is into the flattened array, otherwise 
        along the specified axis.
    
    :returns: Pearson’s correlation coefficient and 2-tailed p-value.
    '''
    if isinstance(x, list):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, list):
        y = MIArray(ArrayUtil.array(y))
    if axis is None:
        r = StatsUtil.pearsonr(x.asarray(), y.asarray())
        return r[0], r[1]
    else:
        r = StatsUtil.pearsonr(x.array, y.array, axis)
        return MIArray(r[0]), MIArray(r[1])
Exemple #2
0
def pearsonr(x, y, axis=None):
    '''
    Calculates a Pearson correlation coefficient and the p-value for testing non-correlation.

    The Pearson correlation coefficient measures the linear relationship between two datasets. 
    Strictly speaking, Pearson’s correlation requires that each dataset be normally distributed, 
    and not necessarily zero-mean. Like other correlation coefficients, this one varies between 
    -1 and +1 with 0 implying no correlation. Correlations of -1 or +1 imply an exact linear 
    relationship. Positive correlations imply that as x increases, so does y. Negative 
    correlations imply that as x increases, y decreases.

    The p-value roughly indicates the probability of an uncorrelated system producing datasets 
    that have a Pearson correlation at least as extreme as the one computed from these datasets. 
    The p-values are not entirely reliable but are probably reasonable for datasets larger than 
    500 or so.
    
    :param x: (*array_like*) x data array.
    :param y: (*array_like*) y data array.
    :param axis: (*int*) By default, the index is into the flattened array, otherwise 
        along the specified axis.
    
    :returns: Pearson’s correlation coefficient and 2-tailed p-value.
    '''
    if isinstance(x, list):
        x = np.array(x)
    if isinstance(y, list):
        y = np.array(y)
    if axis is None:
        r = StatsUtil.pearsonr(x.asarray(), y.asarray())
        return r[0], r[1]
    else:
        r = StatsUtil.pearsonr(x.array, y.array, axis)
        return np.array(r[0]), np.array(r[1])
Exemple #3
0
def cov(m, y=None, rowvar=True, bias=False):
    '''
    Estimate a covariance matrix.
    
    :param m: (*array_like*) A 1-D or 2-D array containing multiple variables and observations.
    :param y: (*array_like*) Optional. An additional set of variables and observations. y has the same form as 
        that of m.
    :param rowvar: (*boolean*) If ``rowvar`` is True (default), then each row represents a variable, with 
        observations in the columns. Otherwise, the relationship is transposed: each column represents a 
        variable, while the rows contain observations.
    :param bias: (*boolean*) Default normalization (False) is by (N - 1), where N is the number of observations 
        given (unbiased estimate). If bias is True, then normalization is by N.
    
    :returns: Covariance.
    '''
    if isinstance(m, list):
        m = MIArray(ArrayUtil.array(m))
    if rowvar == True and m.ndim == 2:
        m = m.T
    if y is None:        
        r = StatsUtil.cov(m.asarray(), not bias)
        if isinstance(r, Array):
            return MIArray(r)
        else:
            return r
    else:
        if isinstance(y, list):
            y = MIArray(ArrayUtil.array(y))
        if rowvar == True and y.ndim == 2:
            y = y.T
        r = StatsUtil.cov(m.asarray(), y.asarray(), not bias)
        return MIArray(r)
Exemple #4
0
def cov(m, y=None, rowvar=True, bias=False):
    '''
    Estimate a covariance matrix.
    
    :param m: (*array_like*) A 1-D or 2-D array containing multiple variables and observations.
    :param y: (*array_like*) Optional. An additional set of variables and observations. y has the same form as 
        that of m.
    :param rowvar: (*boolean*) If ``rowvar`` is True (default), then each row represents a variable, with 
        observations in the columns. Otherwise, the relationship is transposed: each column represents a 
        variable, while the rows contain observations.
    :param bias: (*boolean*) Default normalization (False) is by (N - 1), where N is the number of observations 
        given (unbiased estimate). If bias is True, then normalization is by N.
    
    :returns: Covariance.
    '''
    if isinstance(m, list):
        m = MIArray(ArrayUtil.array(m))
    if rowvar == True and m.ndim == 2:
        m = m.T
    if y is None:
        r = StatsUtil.cov(m.asarray(), not bias)
        if isinstance(r, Array):
            return MIArray(r)
        else:
            return r
    else:
        if isinstance(y, list):
            y = MIArray(ArrayUtil.array(y))
        if rowvar == True and y.ndim == 2:
            y = y.T
        r = StatsUtil.cov(m.asarray(), y.asarray(), not bias)
        return MIArray(r)
Exemple #5
0
def percentile(a, q, axis=None):
    '''
    Compute the qth percentile of the data along the specified axis.
    
    :param a: (*array_like*) Input array.
    :param q: (*float*) float in range of [0,100].
        Percentile to compute, which must be between 0 and 100 inclusive.
    :param axis: (*int*) Axis or axes along which the percentiles are computed. The default is 
        to compute the percentile along a flattened version of the array.
    
    :returns: (*float*) qth percentile value.
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(x))
    if axis is None:
        r = StatsUtil.percentile(a.asarray(), q)
    else:
        r = StatsUtil.percentile(a.asarray(), q, axis)
        r = MIArray(r)
    return r
Exemple #6
0
def percentile(a, q, axis=None):
    '''
    Compute the qth percentile of the data along the specified axis.
    
    :param a: (*array_like*) Input array.
    :param q: (*float*) float in range of [0,100].
        Percentile to compute, which must be between 0 and 100 inclusive.
    :param axis: (*int*) Axis or axes along which the percentiles are computed. The default is 
        to compute the percentile along a flattened version of the array.
    
    :returns: (*float*) qth percentile value.
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(x))
    if axis is None:
        r = StatsUtil.percentile(a.asarray(), q)
    else:
        r = StatsUtil.percentile(a.asarray(), q, axis)
        r = MIArray(r)
    return r
Exemple #7
0
def spearmanr(m, y=None, axis=0):
    '''
    Calculates a Spearman rank-order correlation coefficient.
    
    The Spearman correlation is a nonparametric measure of the monotonicity of the relationship 
    between two datasets. Unlike the Pearson correlation, the Spearman correlation does not 
    assume that both datasets are normally distributed. Like other correlation coefficients, 
    this one varies between -1 and +1 with 0 implying no correlation. Correlations of -1 or +1 
    imply an exact monotonic relationship. Positive correlations imply that as x increases, so 
    does y. Negative correlations imply that as x increases, y decreases.
    
    :param m: (*array_like*) A 1-D or 2-D array containing multiple variables and observations.
    :param y: (*array_like*) Optional. An additional set of variables and observations. y has the same form as 
        that of m.
    :param axis: (*int*) If axis=0 (default), then each column represents a variable, with 
        observations in the rows. If axis=1, the relationship is transposed: each row represents 
        a variable, while the columns contain observations..
    
    :returns: Spearman correlation matrix.
    '''
    if isinstance(m, list):
        m = MIArray(ArrayUtil.array(m))
    if axis == 1 and m.ndim == 2:
        m = m.T
    if y is None:
        r = StatsUtil.spearmanr(m.asarray())
        if isinstance(r, Array):
            return MIArray(r)
        else:
            return r
    else:
        if isinstance(y, list):
            y = MIArray(ArrayUtil.array(y))
        if axis == 1 and y.ndim == 2:
            y = y.T
        r = StatsUtil.spearmanr(m.asarray(), y.asarray())
        return MIArray(r)
Exemple #8
0
def spearmanr(m, y=None, axis=0):
    '''
    Calculates a Spearman rank-order correlation coefficient.
    
    The Spearman correlation is a nonparametric measure of the monotonicity of the relationship 
    between two datasets. Unlike the Pearson correlation, the Spearman correlation does not 
    assume that both datasets are normally distributed. Like other correlation coefficients, 
    this one varies between -1 and +1 with 0 implying no correlation. Correlations of -1 or +1 
    imply an exact monotonic relationship. Positive correlations imply that as x increases, so 
    does y. Negative correlations imply that as x increases, y decreases.
    
    :param m: (*array_like*) A 1-D or 2-D array containing multiple variables and observations.
    :param y: (*array_like*) Optional. An additional set of variables and observations. y has the same form as 
        that of m.
    :param axis: (*int*) If axis=0 (default), then each column represents a variable, with 
        observations in the rows. If axis=1, the relationship is transposed: each row represents 
        a variable, while the columns contain observations..
    
    :returns: Spearman correlation matrix.
    '''
    if isinstance(m, list):
        m = MIArray(ArrayUtil.array(m))
    if axis == 1 and m.ndim == 2:
        m = m.T
    if y is None:        
        r = StatsUtil.spearmanr(m.asarray())
        if isinstance(r, Array):
            return MIArray(r)
        else:
            return r
    else:
        if isinstance(y, list):
            y = MIArray(ArrayUtil.array(y))
        if axis == 1 and y.ndim == 2:
            y = y.T
        r = StatsUtil.spearmanr(m.asarray(), y.asarray())
        return MIArray(r)
Exemple #9
0
def mlinregress(y, x):
    '''
    Implements ordinary least squares (OLS) to estimate the parameters of a multiple linear 
    regression model.
    
    :param y: (*array_like*) Y sample data - one dimension array.
    :param x: (*array_like*) X sample data - two dimension array.
    
    :returns: Estimated regression parameters and residuals.
    '''
    if isinstance(x, list):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, list):
        y = MIArray(ArrayUtil.array(y))
    r = StatsUtil.multipleLineRegress_OLS(y.asarray(), x.asarray())
    return MIArray(r[0]), MIArray(r[1])
Exemple #10
0
def ttest_1samp(a, popmean):
    '''
    Calculate the T-test for the mean of ONE group of scores.

    This is a two-sided test for the null hypothesis that the expected value (mean) of 
    a sample of independent observations a is equal to the given population mean, popmean.
    
    :param a: (*array_like*) Sample observation.
    :param popmean: (*float*) Expected value in null hypothesis.
    
    :returns: t-statistic and p-value
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(x))
    r = StatsUtil.tTest(a.asarray(), popmean)
    return r[0], r[1]
Exemple #11
0
def ttest_1samp(a, popmean):
    '''
    Calculate the T-test for the mean of ONE group of scores.

    This is a two-sided test for the null hypothesis that the expected value (mean) of 
    a sample of independent observations a is equal to the given population mean, popmean.
    
    :param a: (*array_like*) Sample observation.
    :param popmean: (*float*) Expected value in null hypothesis.
    
    :returns: t-statistic and p-value
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(x))
    r = StatsUtil.tTest(a.asarray(), popmean)
    return r[0], r[1]
Exemple #12
0
def mlinregress(y, x):
    '''
    Implements ordinary least squares (OLS) to estimate the parameters of a multiple linear 
    regression model.
    
    :param y: (*array_like*) Y sample data - one dimension array.
    :param x: (*array_like*) X sample data - two dimension array.
    
    :returns: Estimated regression parameters and residuals.
    '''
    if isinstance(x, list):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, list):
        y = MIArray(ArrayUtil.array(y))
    r = StatsUtil.multipleLineRegress_OLS(y.asarray(), x.asarray())
    return MIArray(r[0]), MIArray(r[1])
Exemple #13
0
def chi2_contingency(observed):
    '''
    Chi-square test of independence of variables in a contingency table.

    This function computes the chi-square statistic and p-value for the hypothesis test of 
    independence of the observed frequencies in the contingency table observed.
    
    :param observed: (*array_like*) The contingency table. The table contains the observed 
        frequencies (i.e. number of occurrences) in each category. In the two-dimensional case, 
        the table is often described as an `R x C table`.
    
    :returns: Chi-square statistic and p-value
    '''
    if isinstance(observed, list):
        observed = MIArray(ArrayUtil.array(observed))
    r = StatsUtil.chiSquareTest(observed.asarray())
    return r[0], r[1]
Exemple #14
0
def chi2_contingency(observed):
    '''
    Chi-square test of independence of variables in a contingency table.

    This function computes the chi-square statistic and p-value for the hypothesis test of 
    independence of the observed frequencies in the contingency table observed.
    
    :param observed: (*array_like*) The contingency table. The table contains the observed 
        frequencies (i.e. number of occurrences) in each category. In the two-dimensional case, 
        the table is often described as an `R x C table`.
    
    :returns: Chi-square statistic and p-value
    '''
    if isinstance(observed, list):
        observed = MIArray(ArrayUtil.array(observed))
    r = StatsUtil.chiSquareTest(observed.asarray())
    return r[0], r[1]
Exemple #15
0
def ttest_rel(a, b):
    '''
    Calculates the T-test on TWO RELATED samples of scores, a and b.

    This is a two-sided test for the null hypothesis that 2 related or repeated samples 
    have identical average (expected) values.
    
    :param a: (*array_like*) Sample data a.
    :param b: (*array_like*) Sample data b.
    
    :returns: t-statistic and p-value
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(a))
    if isinstance(b, list):
        b = MIArray(ArrayUtil.array(b))
    r = StatsUtil.pairedTTest(a.asarray(), b.asarray())
    return r[0], r[1]
Exemple #16
0
def ttest_rel(a, b):
    '''
    Calculates the T-test on TWO RELATED samples of scores, a and b.

    This is a two-sided test for the null hypothesis that 2 related or repeated samples 
    have identical average (expected) values.
    
    :param a: (*array_like*) Sample data a.
    :param b: (*array_like*) Sample data b.
    
    :returns: t-statistic and p-value
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(a))
    if isinstance(b, list):
        b = MIArray(ArrayUtil.array(b))
    r = StatsUtil.pairedTTest(a.asarray(), b.asarray())
    return r[0], r[1]
Exemple #17
0
def covariance(x, y, bias=False):
    '''
    Calculate covariance of two array.
    
    :param x: (*array_like*) A 1-D array containing multiple variables and observations.
    :param y: (*array_like*) An additional set of variables and observations. y has the same form as 
        that of x.
    :param bias: (*boolean*) Default normalization (False) is by (N - 1), where N is the number of observations 
        given (unbiased estimate). If bias is True, then normalization is by N.
        
    returns: Covariance
    '''
    if isinstance(x, (list, tuple)):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, (list, tuple)):
        y = MIArray(ArrayUtil.array(y))
    r = StatsUtil.covariance(x.asarray(), y.asarray(), bias)
    return r
Exemple #18
0
def covariance(x, y, bias=False):
    '''
    Calculate covariance of two array.
    
    :param x: (*array_like*) A 1-D array containing multiple variables and observations.
    :param y: (*array_like*) An additional set of variables and observations. y has the same form as 
        that of x.
    :param bias: (*boolean*) Default normalization (False) is by (N - 1), where N is the number of observations 
        given (unbiased estimate). If bias is True, then normalization is by N.
        
    returns: Covariance
    '''
    if isinstance(x, (list, tuple)):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, (list, tuple)):
        y = MIArray(ArrayUtil.array(y))
    r = StatsUtil.covariance(x.asarray(), y.asarray(), bias)
    return r
Exemple #19
0
def ttest_ind(a, b):
    '''
    Calculates the T-test for the means of TWO INDEPENDENT samples of scores.

    This is a two-sided test for the null hypothesis that 2 independent samples have 
    identical average (expected) values. This test assumes that the populations have 
    identical variances.
    
    :param a: (*array_like*) Sample data a.
    :param b: (*array_like*) Sample data b.
    
    :returns: t-statistic and p-value
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(a))
    if isinstance(b, list):
        b = MIArray(ArrayUtil.array(b))
    r = StatsUtil.tTest(a.asarray(), b.asarray())
    return r[0], r[1]
Exemple #20
0
def ttest_ind(a, b):
    '''
    Calculates the T-test for the means of TWO INDEPENDENT samples of scores.

    This is a two-sided test for the null hypothesis that 2 independent samples have 
    identical average (expected) values. This test assumes that the populations have 
    identical variances.
    
    :param a: (*array_like*) Sample data a.
    :param b: (*array_like*) Sample data b.
    
    :returns: t-statistic and p-value
    '''
    if isinstance(a, list):
        a = MIArray(ArrayUtil.array(a))
    if isinstance(b, list):
        b = MIArray(ArrayUtil.array(b))
    r = StatsUtil.tTest(a.asarray(), b.asarray())
    return r[0], r[1]
Exemple #21
0
def kendalltau(x, y):
    '''
    Calculates Kendall's tau, a correlation measure for ordinal data.
    
    Kendall's tau is a measure of the correspondence between two rankings.
    Values close to 1 indicate strong agreement, values close to -1 indicate
    strong disagreement.  This is the 1945 "tau-b" version of Kendall's
    tau [2]_, which can account for ties and which reduces to the 1938 "tau-a"
    version [1]_ in absence of ties.
    
    :param x: (*array_like*) x data array.
    :param y: (*array_like*) y data array.
    
    :returns: Correlation.
    
    Notes
    -----
    The definition of Kendall's tau that is used is [2]_::
      tau = (P - Q) / sqrt((P + Q + T) * (P + Q + U))
    where P is the number of concordant pairs, Q the number of discordant
    pairs, T the number of ties only in `x`, and U the number of ties only in
    `y`.  If a tie occurs for the same pair in both `x` and `y`, it is not
    added to either T or U.
    References
    ----------
    .. [1] Maurice G. Kendall, "A New Measure of Rank Correlation", Biometrika
           Vol. 30, No. 1/2, pp. 81-93, 1938.
    .. [2] Maurice G. Kendall, "The treatment of ties in ranking problems",
           Biometrika Vol. 33, No. 3, pp. 239-251. 1945.
    .. [3] Gottfried E. Noether, "Elements of Nonparametric Statistics", John
           Wiley & Sons, 1967.
    .. [4] Peter M. Fenwick, "A new data structure for cumulative frequency
           tables", Software: Practice and Experience, Vol. 24, No. 3,
           pp. 327-336, 1994.
    '''
    if isinstance(x, list):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, list):
        y = MIArray(ArrayUtil.array(y))
    r = StatsUtil.kendalltau(x.asarray(), y.asarray())
    return r
Exemple #22
0
def kendalltau(x, y):
    '''
    Calculates Kendall's tau, a correlation measure for ordinal data.
    
    Kendall's tau is a measure of the correspondence between two rankings.
    Values close to 1 indicate strong agreement, values close to -1 indicate
    strong disagreement.  This is the 1945 "tau-b" version of Kendall's
    tau [2]_, which can account for ties and which reduces to the 1938 "tau-a"
    version [1]_ in absence of ties.
    
    :param x: (*array_like*) x data array.
    :param y: (*array_like*) y data array.
    
    :returns: Correlation.
    
    Notes
    -----
    The definition of Kendall's tau that is used is [2]_::
      tau = (P - Q) / sqrt((P + Q + T) * (P + Q + U))
    where P is the number of concordant pairs, Q the number of discordant
    pairs, T the number of ties only in `x`, and U the number of ties only in
    `y`.  If a tie occurs for the same pair in both `x` and `y`, it is not
    added to either T or U.
    References
    ----------
    .. [1] Maurice G. Kendall, "A New Measure of Rank Correlation", Biometrika
           Vol. 30, No. 1/2, pp. 81-93, 1938.
    .. [2] Maurice G. Kendall, "The treatment of ties in ranking problems",
           Biometrika Vol. 33, No. 3, pp. 239-251. 1945.
    .. [3] Gottfried E. Noether, "Elements of Nonparametric Statistics", John
           Wiley & Sons, 1967.
    .. [4] Peter M. Fenwick, "A new data structure for cumulative frequency
           tables", Software: Practice and Experience, Vol. 24, No. 3,
           pp. 327-336, 1994.
    '''
    if isinstance(x, list):
        x = MIArray(ArrayUtil.array(x))
    if isinstance(y, list):
        y = MIArray(ArrayUtil.array(y))
    r = StatsUtil.kendalltau(x.asarray(), y.asarray())
    return r
Exemple #23
0
def chisquare(f_obs, f_exp=None):
    '''
    Calculates a one-way chi square test.

    The chi square test tests the null hypothesis that the categorical data has the 
    given frequencies.
    
    :param f_obs: (*array_like*) Observed frequencies in each category.
    :param f_exp: (*array_like*) Expected frequencies in each category. By default the categories 
        are assumed to be equally likely.
    
    :returns: Chi-square statistic and p-value
    '''
    if isinstance(f_obs, list):
        f_obs = MIArray(ArrayUtil.array(f_obs))
    if f_exp is None:
        n = len(f_obs)
        f_exp = minum.ones(n) / n * f_obs.sum()
    elif isinstance(f_exp, list):
        f_exp = MIArray(ArrayUtil.array(f_exp))
    r = StatsUtil.chiSquareTest(f_exp.asarray(), f_obs.asarray())
    return r[0], r[1]
Exemple #24
0
def chisquare(f_obs, f_exp=None):
    '''
    Calculates a one-way chi square test.

    The chi square test tests the null hypothesis that the categorical data has the 
    given frequencies.
    
    :param f_obs: (*array_like*) Observed frequencies in each category.
    :param f_exp: (*array_like*) Expected frequencies in each category. By default the categories 
        are assumed to be equally likely.
    
    :returns: Chi-square statistic and p-value
    '''
    if isinstance(f_obs, list):
        f_obs = MIArray(ArrayUtil.array(f_obs))
    if f_exp is None:
        n = len(f_obs)
        f_exp = minum.ones(n) / n * f_obs.sum()
    elif isinstance(f_exp, list):
        f_exp = MIArray(ArrayUtil.array(f_exp))
    r = StatsUtil.chiSquareTest(f_exp.asarray(), f_obs.asarray())
    return r[0], r[1]
Exemple #25
0
def lstsq(a, b):
    '''
    Compute least-squares solution to equation Ax = b.

    Compute a vector x such that the 2-norm |b - A x| is minimized.
    
    Parameters
    ----------
    a : (M, N) array
        Left hand side matrix (2-D array).
    b : (M,) array
        Right hand side vector.
        
    Returns
    -------
    x : (N,) array
        Least-squares solution. Return shape matches shape of b.
    residues : (0,) or () or (K,) ndarray
        Sums of residues, squared 2-norm for each column in b - a x.
    '''
    r = StatsUtil.multipleLineRegress_OLS(b.asarray(), a.asarray(), True)
    return NDArray(r[0]), NDArray(r[1])
Exemple #26
0
def lstsq(a, b):
    '''
    Compute least-squares solution to equation Ax = b.

    Compute a vector x such that the 2-norm |b - A x| is minimized.
    
    Parameters
    ----------
    a : (M, N) array
        Left hand side matrix (2-D array).
    b : (M,) array
        Right hand side vector.
        
    Returns
    -------
    x : (N,) array
        Least-squares solution. Return shape matches shape of b.
    residues : (0,) or () or (K,) ndarray
        Sums of residues, squared 2-norm for each column in b - a x.
    '''
    r = StatsUtil.multipleLineRegress_OLS(b.asarray(), a.asarray(), True)
    return MIArray(r[0]), MIArray(r[1])