How to use the pingouin.nonparametric.harrelldavis function in pingouin

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github raphaelvallat / pingouin / pingouin / plotting.py View on Github external
assert ny >= 10, 'y must have at least 10 samples.'
    assert 0 < ci < 1, 'ci must be between 0 and 1.'
    if paired:
        assert nx == ny, 'x and y must have the same size when paired=True.'

    # Robust percentile
    x_per = hd(x, percentiles)
    y_per = hd(y, percentiles)
    delta = y_per - x_per

    # Compute bootstrap distribution of differences
    rng = np.random.RandomState(seed)
    if paired:
        bootsam = rng.choice(np.arange(nx), size=(nx, n_boot), replace=True)
        bootstat = (hd(y[bootsam], percentiles, axis=0) -
                    hd(x[bootsam], percentiles, axis=0))
    else:
        x_list = rng.choice(x, size=(nx, n_boot), replace=True)
        y_list = rng.choice(y, size=(ny, n_boot), replace=True)
        bootstat = (hd(y_list, percentiles, axis=0) -
                    hd(x_list, percentiles, axis=0))

    # Find upper and lower confidence interval for each quantiles
    # Bias-corrected confidence interval
    lower, median_per, upper = [], [], []
    for i, d in enumerate(delta):
        ci = _bca(bootstat[i, :], d, n_boot)
        median_per.append(_bca(bootstat[i, :], d, n_boot, alpha=1)[0])
        lower.append(ci[0])
        upper.append(ci[1])

    lower = np.asarray(lower)
github raphaelvallat / pingouin / pingouin / plotting.py View on Github external
# Robust percentile
    x_per = hd(x, percentiles)
    y_per = hd(y, percentiles)
    delta = y_per - x_per

    # Compute bootstrap distribution of differences
    rng = np.random.RandomState(seed)
    if paired:
        bootsam = rng.choice(np.arange(nx), size=(nx, n_boot), replace=True)
        bootstat = (hd(y[bootsam], percentiles, axis=0) -
                    hd(x[bootsam], percentiles, axis=0))
    else:
        x_list = rng.choice(x, size=(nx, n_boot), replace=True)
        y_list = rng.choice(y, size=(ny, n_boot), replace=True)
        bootstat = (hd(y_list, percentiles, axis=0) -
                    hd(x_list, percentiles, axis=0))

    # Find upper and lower confidence interval for each quantiles
    # Bias-corrected confidence interval
    lower, median_per, upper = [], [], []
    for i, d in enumerate(delta):
        ci = _bca(bootstat[i, :], d, n_boot)
        median_per.append(_bca(bootstat[i, :], d, n_boot, alpha=1)[0])
        lower.append(ci[0])
        upper.append(ci[1])

    lower = np.asarray(lower)
    median_per = np.asarray(median_per)
    upper = np.asarray(upper)

    # Create long-format dataFrame for use with Seaborn
github raphaelvallat / pingouin / pingouin / plotting.py View on Github external
# Robust percentile
    x_per = hd(x, percentiles)
    y_per = hd(y, percentiles)
    delta = y_per - x_per

    # Compute bootstrap distribution of differences
    rng = np.random.RandomState(seed)
    if paired:
        bootsam = rng.choice(np.arange(nx), size=(nx, n_boot), replace=True)
        bootstat = (hd(y[bootsam], percentiles, axis=0) -
                    hd(x[bootsam], percentiles, axis=0))
    else:
        x_list = rng.choice(x, size=(nx, n_boot), replace=True)
        y_list = rng.choice(y, size=(ny, n_boot), replace=True)
        bootstat = (hd(y_list, percentiles, axis=0) -
                    hd(x_list, percentiles, axis=0))

    # Find upper and lower confidence interval for each quantiles
    # Bias-corrected confidence interval
    lower, median_per, upper = [], [], []
    for i, d in enumerate(delta):
        ci = _bca(bootstat[i, :], d, n_boot)
        median_per.append(_bca(bootstat[i, :], d, n_boot, alpha=1)[0])
        lower.append(ci[0])
        upper.append(ci[1])

    lower = np.asarray(lower)
    median_per = np.asarray(median_per)
    upper = np.asarray(upper)

    # Create long-format dataFrame for use with Seaborn
    data = pd.DataFrame({'value': np.concatenate([x, y]),
github raphaelvallat / pingouin / pingouin / plotting.py View on Github external
x = np.asarray(x)
    y = np.asarray(y)
    percentiles = np.asarray(percentiles) / 100  # Convert to 0 - 1 range
    assert x.ndim == 1, 'x must be 1D.'
    assert y.ndim == 1, 'y must be 1D.'
    nx, ny = x.size, y.size
    assert not np.isnan(x).any(), 'Missing values are not allowed.'
    assert not np.isnan(y).any(), 'Missing values are not allowed.'
    assert nx >= 10, 'x must have at least 10 samples.'
    assert ny >= 10, 'y must have at least 10 samples.'
    assert 0 < ci < 1, 'ci must be between 0 and 1.'
    if paired:
        assert nx == ny, 'x and y must have the same size when paired=True.'

    # Robust percentile
    x_per = hd(x, percentiles)
    y_per = hd(y, percentiles)
    delta = y_per - x_per

    # Compute bootstrap distribution of differences
    rng = np.random.RandomState(seed)
    if paired:
        bootsam = rng.choice(np.arange(nx), size=(nx, n_boot), replace=True)
        bootstat = (hd(y[bootsam], percentiles, axis=0) -
                    hd(x[bootsam], percentiles, axis=0))
    else:
        x_list = rng.choice(x, size=(nx, n_boot), replace=True)
        y_list = rng.choice(y, size=(ny, n_boot), replace=True)
        bootstat = (hd(y_list, percentiles, axis=0) -
                    hd(x_list, percentiles, axis=0))

    # Find upper and lower confidence interval for each quantiles
github raphaelvallat / pingouin / pingouin / plotting.py View on Github external
y = np.asarray(y)
    percentiles = np.asarray(percentiles) / 100  # Convert to 0 - 1 range
    assert x.ndim == 1, 'x must be 1D.'
    assert y.ndim == 1, 'y must be 1D.'
    nx, ny = x.size, y.size
    assert not np.isnan(x).any(), 'Missing values are not allowed.'
    assert not np.isnan(y).any(), 'Missing values are not allowed.'
    assert nx >= 10, 'x must have at least 10 samples.'
    assert ny >= 10, 'y must have at least 10 samples.'
    assert 0 < ci < 1, 'ci must be between 0 and 1.'
    if paired:
        assert nx == ny, 'x and y must have the same size when paired=True.'

    # Robust percentile
    x_per = hd(x, percentiles)
    y_per = hd(y, percentiles)
    delta = y_per - x_per

    # Compute bootstrap distribution of differences
    rng = np.random.RandomState(seed)
    if paired:
        bootsam = rng.choice(np.arange(nx), size=(nx, n_boot), replace=True)
        bootstat = (hd(y[bootsam], percentiles, axis=0) -
                    hd(x[bootsam], percentiles, axis=0))
    else:
        x_list = rng.choice(x, size=(nx, n_boot), replace=True)
        y_list = rng.choice(y, size=(ny, n_boot), replace=True)
        bootstat = (hd(y_list, percentiles, axis=0) -
                    hd(x_list, percentiles, axis=0))

    # Find upper and lower confidence interval for each quantiles
    # Bias-corrected confidence interval