.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/stats/plot_oneWay_Manova.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_stats_plot_oneWay_Manova.py: ==================================================================== One Way manova ==================================================================== One way manova to compare Left vs Right. .. GENERATED FROM PYTHON SOURCE LINES 8-26 .. code-block:: Python from time import time from matplotlib import pyplot as plt import seaborn as sns from mne import Epochs, pick_types, events_from_annotations from mne.io import concatenate_raws from mne.io.edf import read_raw_edf from mne.datasets import eegbci from sklearn.pipeline import make_pipeline from sklearn.linear_model import LogisticRegression from pyriemann.stats import PermutationDistance, PermutationModel from pyriemann.estimation import Covariances from pyriemann.spatialfilters import CSP sns.set_style('whitegrid') .. GENERATED FROM PYTHON SOURCE LINES 27-29 Set parameters and read data ---------------------------- .. GENERATED FROM PYTHON SOURCE LINES 29-74 .. code-block:: Python # avoid classification of evoked responses by using epochs that start 1s after # cue onset. tmin, tmax = 1., 3. event_id = dict(hands=2, feet=3) subject = 1 runs = [6, 10, 14] # motor imagery: hands vs feet raw_files = [ read_raw_edf(f, preload=True, verbose=False) for f in eegbci.load_data(subject, runs) ] raw = concatenate_raws(raw_files) # Apply band-pass filter raw.filter(7., 35., method='iir') events, _ = events_from_annotations(raw, event_id=dict(T1=2, T2=3)) picks = pick_types( raw.info, meg=False, eeg=True, stim=False, eog=False, exclude='bads') picks = picks[::4] # Read epochs (train will be done only between 1 and 2s) # Testing will be done with a running classifier epochs = Epochs( raw, events, event_id, tmin, tmax, proj=True, picks=picks, baseline=None, preload=True, verbose=False) labels = epochs.events[:, -1] - 2 # get epochs epochs_data = epochs.get_data(copy=False) # compute covariance matrices covmats = Covariances().fit_transform(epochs_data) n_perms = 500 .. rst-class:: sphx-glr-script-out .. code-block:: none Filtering raw data in 3 contiguous segments Setting up band-pass filter from 7 - 35 Hz IIR filter parameters --------------------- Butterworth bandpass zero-phase (two-pass forward and reverse) non-causal filter: - Filter order 16 (effective, after forward-backward) - Cutoffs at 7.00, 35.00 Hz: -6.02, -6.02 dB Used Annotations descriptions: ['T1', 'T2'] .. GENERATED FROM PYTHON SOURCE LINES 75-77 Pairwise distance based permutation test ---------------------------------------- .. GENERATED FROM PYTHON SOURCE LINES 77-91 .. code-block:: Python t_init = time() p_test = PermutationDistance(n_perms, metric='riemann', mode='pairwise') p, F = p_test.test(covmats, labels) duration = time() - t_init fig, axes = plt.subplots(1, 1, figsize=[6, 3], sharey=True) p_test.plot(nbins=10, axes=axes) plt.title('Pairwise distance - %.2f sec.' % duration) print('p-value: %.3f' % p) sns.despine() plt.tight_layout() plt.show() .. image-sg:: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_001.png :alt: Pairwise distance - 0.13 sec. :srcset: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Performing permutations : [0.2%] Performing permutations : [0.4%] Performing permutations : [0.6%] Performing permutations : [0.8%] Performing permutations : [1.0%] Performing permutations : [1.2%] Performing permutations : [1.4%] Performing permutations : [1.6%] Performing permutations : 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GENERATED FROM PYTHON SOURCE LINES 92-94 t-test distance based permutation test -------------------------------------- .. GENERATED FROM PYTHON SOURCE LINES 94-108 .. code-block:: Python t_init = time() p_test = PermutationDistance(n_perms, metric='riemann', mode='ttest') p, F = p_test.test(covmats, labels) duration = time() - t_init fig, axes = plt.subplots(1, 1, figsize=[6, 3], sharey=True) p_test.plot(nbins=10, axes=axes) plt.title('t-test distance - %.2f sec.' % duration) print('p-value: %.3f' % p) sns.despine() plt.tight_layout() plt.show() .. image-sg:: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_002.png :alt: t-test distance - 39.43 sec. :srcset: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Performing permutations : [0.2%] Performing permutations : [0.4%] Performing permutations : [0.6%] Performing permutations : [0.8%] Performing permutations : [1.0%] Performing permutations : [1.2%] Performing permutations : [1.4%] Performing permutations : [1.6%] Performing permutations : [1.8%] 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Performing permutations : [31.6%] Performing permutations : [31.8%] Performing permutations : [32.0%] Performing permutations : [32.2%] Performing permutations : [32.4%] Performing permutations : [32.6%] Performing permutations : [32.8%] Performing permutations : [33.0%] Performing permutations : [33.2%] Performing permutations : [33.4%] Performing permutations : [33.6%] Performing permutations : [33.8%] Performing permutations : [34.0%] Performing permutations : [34.2%] Performing permutations : [34.4%] Performing permutations : [34.6%] Performing permutations : [34.8%] Performing permutations : [35.0%] Performing permutations : [35.2%] Performing permutations : [35.4%] Performing permutations : [35.6%] Performing permutations : [35.8%] Performing permutations : [36.0%] Performing permutations : [36.2%] Performing permutations : [36.4%] Performing permutations : [36.6%] Performing permutations : [36.8%] Performing permutations : [37.0%] Performing permutations : [37.2%] Performing 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Performing permutations : [49.2%] Performing permutations : [49.4%] Performing permutations : [49.6%] Performing permutations : [49.8%] Performing permutations : [50.0%] Performing permutations : [50.2%] Performing permutations : [50.4%] Performing permutations : [50.6%] Performing permutations : [50.8%] Performing permutations : [51.0%] Performing permutations : [51.2%] Performing permutations : [51.4%] Performing permutations : [51.6%] Performing permutations : [51.8%] Performing permutations : [52.0%] Performing permutations : [52.2%] Performing permutations : [52.4%] Performing permutations : [52.6%] Performing permutations : [52.8%] Performing permutations : [53.0%] Performing permutations : [53.2%] Performing permutations : [53.4%] Performing permutations : [53.6%] Performing permutations : [53.8%] Performing permutations : [54.0%] Performing permutations : [54.2%] Performing permutations : [54.4%] Performing permutations : [54.6%] Performing permutations : [54.8%] Performing 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Performing permutations : [66.8%] Performing permutations : [67.0%] Performing permutations : [67.2%] Performing permutations : [67.4%] Performing permutations : [67.6%] Performing permutations : [67.8%] Performing permutations : [68.0%] Performing permutations : [68.2%] Performing permutations : [68.4%] Performing permutations : [68.6%] Performing permutations : [68.8%] Performing permutations : [69.0%] Performing permutations : [69.2%] Performing permutations : [69.4%] Performing permutations : [69.6%] Performing permutations : [69.8%] Performing permutations : [70.0%] Performing permutations : [70.2%] Performing permutations : [70.4%] Performing permutations : [70.6%] Performing permutations : [70.8%] Performing permutations : [71.0%] Performing permutations : [71.2%] Performing permutations : [71.4%] Performing permutations : [71.6%] Performing permutations : [71.8%] Performing permutations : [72.0%] Performing permutations : [72.2%] Performing permutations : [72.4%] Performing 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Performing permutations : [84.4%] Performing permutations : [84.6%] Performing permutations : [84.8%] Performing permutations : [85.0%] Performing permutations : [85.2%] Performing permutations : [85.4%] Performing permutations : [85.6%] Performing permutations : [85.8%] Performing permutations : [86.0%] Performing permutations : [86.2%] Performing permutations : [86.4%] Performing permutations : [86.6%] Performing permutations : [86.8%] Performing permutations : [87.0%] Performing permutations : [87.2%] Performing permutations : [87.4%] Performing permutations : [87.6%] Performing permutations : [87.8%] Performing permutations : [88.0%] Performing permutations : [88.2%] Performing permutations : [88.4%] Performing permutations : [88.6%] Performing permutations : [88.8%] Performing permutations : [89.0%] Performing permutations : [89.2%] Performing permutations : [89.4%] Performing permutations : [89.6%] Performing permutations : [89.8%] Performing permutations : [90.0%] Performing permutations : [90.2%] Performing permutations : [90.4%] Performing permutations : [90.6%] Performing permutations : [90.8%] Performing permutations : [91.0%] Performing permutations : [91.2%] Performing permutations : [91.4%] Performing permutations : [91.6%] Performing permutations : [91.8%] Performing permutations : [92.0%] Performing permutations : [92.2%] Performing permutations : [92.4%] Performing permutations : [92.6%] Performing permutations : [92.8%] Performing permutations : [93.0%] Performing permutations : [93.2%] Performing permutations : [93.4%] Performing permutations : [93.6%] Performing permutations : [93.8%] Performing permutations : [94.0%] Performing permutations : [94.2%] Performing permutations : [94.4%] Performing permutations : [94.6%] Performing permutations : [94.8%] Performing permutations : [95.0%] Performing permutations : [95.2%] Performing permutations : [95.4%] Performing permutations : [95.6%] Performing permutations : [95.8%] Performing permutations : [96.0%] Performing permutations : [96.2%] Performing permutations : [96.4%] Performing permutations : [96.6%] Performing permutations : [96.8%] Performing permutations : [97.0%] Performing permutations : [97.2%] Performing permutations : [97.4%] Performing permutations : [97.6%] Performing permutations : [97.8%] Performing permutations : [98.0%] Performing permutations : [98.2%] Performing permutations : [98.4%] Performing permutations : [98.6%] Performing permutations : [98.8%] Performing permutations : [99.0%] Performing permutations : [99.2%] Performing permutations : [99.4%] Performing permutations : [99.6%] Performing permutations : [99.8%] p-value: 0.002 .. GENERATED FROM PYTHON SOURCE LINES 109-111 F-test distance based permutation test -------------------------------------- .. GENERATED FROM PYTHON SOURCE LINES 111-125 .. code-block:: Python t_init = time() p_test = PermutationDistance(n_perms, metric='riemann', mode='ftest') p, F = p_test.test(covmats, labels) duration = time() - t_init fig, axes = plt.subplots(1, 1, figsize=[6, 3], sharey=True) p_test.plot(nbins=10, axes=axes) plt.title('F-test distance - %.2f sec.' % duration) print('p-value: %.3f' % p) sns.despine() plt.tight_layout() plt.show() .. image-sg:: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_003.png :alt: F-test distance - 40.15 sec. :srcset: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Performing permutations : [0.2%] Performing permutations : [0.4%] Performing permutations : [0.6%] Performing permutations : [0.8%] Performing permutations : [1.0%] Performing permutations : [1.2%] Performing permutations : [1.4%] Performing permutations : [1.6%] Performing permutations : [1.8%] Performing permutations : [2.0%] Performing permutations : [2.2%] Performing permutations : [2.4%] Performing permutations : [2.6%] Performing permutations : [2.8%] Performing permutations : [3.0%] Performing permutations : [3.2%] Performing permutations : [3.4%] Performing permutations : [3.6%] Performing permutations : [3.8%] Performing permutations : [4.0%] Performing permutations : [4.2%] Performing permutations : [4.4%] Performing permutations : [4.6%] Performing permutations : [4.8%] Performing permutations : [5.0%] Performing permutations : [5.2%] Performing permutations : [5.4%] Performing permutations : [5.6%] Performing permutations : [5.8%] Performing permutations : [6.0%] Performing permutations : [6.2%] Performing permutations : [6.4%] Performing permutations : [6.6%] Performing permutations : [6.8%] Performing permutations : [7.0%] Performing permutations : [7.2%] Performing permutations : [7.4%] Performing permutations : [7.6%] Performing permutations : [7.8%] Performing 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Performing permutations : [31.6%] Performing permutations : [31.8%] Performing permutations : [32.0%] Performing permutations : [32.2%] Performing permutations : [32.4%] Performing permutations : [32.6%] Performing permutations : [32.8%] Performing permutations : [33.0%] Performing permutations : [33.2%] Performing permutations : [33.4%] Performing permutations : [33.6%] Performing permutations : [33.8%] Performing permutations : [34.0%] Performing permutations : [34.2%] Performing permutations : [34.4%] Performing permutations : [34.6%] Performing permutations : [34.8%] Performing permutations : [35.0%] Performing permutations : [35.2%] Performing permutations : [35.4%] Performing permutations : [35.6%] Performing permutations : [35.8%] Performing permutations : [36.0%] Performing permutations : [36.2%] Performing permutations : [36.4%] Performing permutations : [36.6%] Performing permutations : [36.8%] Performing permutations : [37.0%] Performing permutations : [37.2%] Performing 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Performing permutations : [49.2%] Performing permutations : [49.4%] Performing permutations : [49.6%] Performing permutations : [49.8%] Performing permutations : [50.0%] Performing permutations : [50.2%] Performing permutations : [50.4%] Performing permutations : [50.6%] Performing permutations : [50.8%] Performing permutations : [51.0%] Performing permutations : [51.2%] Performing permutations : [51.4%] Performing permutations : [51.6%] Performing permutations : [51.8%] Performing permutations : [52.0%] Performing permutations : [52.2%] Performing permutations : [52.4%] Performing permutations : [52.6%] Performing permutations : [52.8%] Performing permutations : [53.0%] Performing permutations : [53.2%] Performing permutations : [53.4%] Performing permutations : [53.6%] Performing permutations : [53.8%] Performing permutations : [54.0%] Performing permutations : [54.2%] Performing permutations : [54.4%] Performing permutations : [54.6%] Performing permutations : [54.8%] Performing permutations : [55.0%] Performing permutations : [55.2%] Performing permutations : [55.4%] Performing permutations : [55.6%] Performing permutations : [55.8%] Performing permutations : [56.0%] Performing permutations : [56.2%] Performing permutations : [56.4%] Performing permutations : [56.6%] Performing permutations : [56.8%] Performing permutations : [57.0%] Performing permutations : [57.2%] Performing permutations : [57.4%] Performing permutations : [57.6%] Performing permutations : [57.8%] Performing permutations : [58.0%] Performing permutations : [58.2%] Performing permutations : [58.4%] Performing permutations : [58.6%] Performing permutations : [58.8%] Performing permutations : [59.0%] Performing permutations : [59.2%] Performing permutations : [59.4%] Performing permutations : [59.6%] Performing permutations : [59.8%] Performing permutations : [60.0%] Performing permutations : [60.2%] Performing permutations : [60.4%] Performing permutations : [60.6%] Performing permutations : [60.8%] Performing permutations : [61.0%] Performing permutations : [61.2%] Performing permutations : [61.4%] Performing permutations : [61.6%] Performing permutations : [61.8%] Performing permutations : [62.0%] Performing permutations : [62.2%] Performing permutations : [62.4%] Performing permutations : [62.6%] Performing permutations : [62.8%] Performing permutations : [63.0%] Performing permutations : [63.2%] Performing permutations : [63.4%] Performing permutations : [63.6%] Performing permutations : [63.8%] Performing permutations : [64.0%] Performing permutations : [64.2%] Performing permutations : [64.4%] Performing permutations : [64.6%] Performing permutations : [64.8%] Performing permutations : [65.0%] Performing permutations : [65.2%] Performing permutations : [65.4%] Performing permutations : [65.6%] Performing permutations : [65.8%] Performing permutations : [66.0%] Performing permutations : [66.2%] Performing permutations : [66.4%] Performing permutations : [66.6%] Performing permutations : [66.8%] Performing permutations : [67.0%] Performing permutations : [67.2%] Performing permutations : [67.4%] Performing permutations : [67.6%] Performing permutations : [67.8%] Performing permutations : [68.0%] Performing permutations : [68.2%] Performing permutations : [68.4%] Performing permutations : [68.6%] Performing permutations : [68.8%] Performing permutations : [69.0%] Performing permutations : [69.2%] Performing permutations : [69.4%] Performing permutations : [69.6%] Performing permutations : [69.8%] Performing permutations : [70.0%] Performing permutations : [70.2%] Performing permutations : [70.4%] Performing permutations : [70.6%] Performing permutations : [70.8%] Performing permutations : [71.0%] Performing permutations : [71.2%] Performing permutations : [71.4%] Performing permutations : [71.6%] Performing permutations : [71.8%] Performing permutations : [72.0%] Performing permutations : [72.2%] Performing permutations : [72.4%] Performing 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permutations : [90.2%] Performing permutations : [90.4%] Performing permutations : [90.6%] Performing permutations : [90.8%] Performing permutations : [91.0%] Performing permutations : [91.2%] Performing permutations : [91.4%] Performing permutations : [91.6%] Performing permutations : [91.8%] Performing permutations : [92.0%] Performing permutations : [92.2%] Performing permutations : [92.4%] Performing permutations : [92.6%] Performing permutations : [92.8%] Performing permutations : [93.0%] Performing permutations : [93.2%] Performing permutations : [93.4%] Performing permutations : [93.6%] Performing permutations : [93.8%] Performing permutations : [94.0%] Performing permutations : [94.2%] Performing permutations : [94.4%] Performing permutations : [94.6%] Performing permutations : [94.8%] Performing permutations : [95.0%] Performing permutations : [95.2%] Performing permutations : [95.4%] Performing permutations : [95.6%] Performing permutations : [95.8%] Performing permutations : [96.0%] Performing permutations : [96.2%] Performing permutations : [96.4%] Performing permutations : [96.6%] Performing permutations : [96.8%] Performing permutations : [97.0%] Performing permutations : [97.2%] Performing permutations : [97.4%] Performing permutations : [97.6%] Performing permutations : [97.8%] Performing permutations : [98.0%] Performing permutations : [98.2%] Performing permutations : [98.4%] Performing permutations : [98.6%] Performing permutations : [98.8%] Performing permutations : [99.0%] Performing permutations : [99.2%] Performing permutations : [99.4%] Performing permutations : [99.6%] Performing permutations : [99.8%] p-value: 0.002 .. GENERATED FROM PYTHON SOURCE LINES 126-128 Classification based permutation test ------------------------------------- .. GENERATED FROM PYTHON SOURCE LINES 128-143 .. code-block:: Python clf = make_pipeline(CSP(4), LogisticRegression()) t_init = time() p_test = PermutationModel(n_perms, model=clf, cv=3, scoring='roc_auc') p, F = p_test.test(covmats, labels) duration = time() - t_init fig, axes = plt.subplots(1, 1, figsize=[6, 3], sharey=True) p_test.plot(nbins=10, axes=axes) plt.title('Classification - %.2f sec.' % duration) print('p-value: %.3f' % p) sns.despine() plt.tight_layout() plt.show() .. image-sg:: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_004.png :alt: Classification - 14.47 sec. :srcset: /auto_examples/stats/images/sphx_glr_plot_oneWay_Manova_004.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Performing permutations : [0.2%] Performing permutations : [0.4%] Performing permutations : [0.6%] Performing permutations : [0.8%] Performing permutations : [1.0%] Performing permutations : [1.2%] Performing permutations : [1.4%] Performing 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Performing permutations : [48.8%] Performing permutations : [49.0%] Performing permutations : [49.2%] Performing permutations : [49.4%] Performing permutations : [49.6%] Performing permutations : [49.8%] Performing permutations : [50.0%] Performing permutations : [50.2%] Performing permutations : [50.4%] Performing permutations : [50.6%] Performing permutations : [50.8%] Performing permutations : [51.0%] Performing permutations : [51.2%] Performing permutations : [51.4%] Performing permutations : [51.6%] Performing permutations : [51.8%] Performing permutations : [52.0%] Performing permutations : [52.2%] Performing permutations : [52.4%] Performing permutations : [52.6%] Performing permutations : [52.8%] Performing permutations : [53.0%] Performing permutations : [53.2%] Performing permutations : [53.4%] Performing permutations : [53.6%] Performing permutations : [53.8%] Performing permutations : [54.0%] Performing permutations : [54.2%] Performing permutations : [54.4%] Performing 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Performing permutations : [66.4%] Performing permutations : [66.6%] Performing permutations : [66.8%] Performing permutations : [67.0%] Performing permutations : [67.2%] Performing permutations : [67.4%] Performing permutations : [67.6%] Performing permutations : [67.8%] Performing permutations : [68.0%] Performing permutations : [68.2%] Performing permutations : [68.4%] Performing permutations : [68.6%] Performing permutations : [68.8%] Performing permutations : [69.0%] Performing permutations : [69.2%] Performing permutations : [69.4%] Performing permutations : [69.6%] Performing permutations : [69.8%] Performing permutations : [70.0%] Performing permutations : [70.2%] Performing permutations : [70.4%] Performing permutations : [70.6%] Performing permutations : [70.8%] Performing permutations : [71.0%] Performing permutations : [71.2%] Performing permutations : [71.4%] Performing permutations : [71.6%] Performing permutations : [71.8%] Performing permutations : [72.0%] Performing 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permutations : [89.8%] Performing permutations : [90.0%] Performing permutations : [90.2%] Performing permutations : [90.4%] Performing permutations : [90.6%] Performing permutations : [90.8%] Performing permutations : [91.0%] Performing permutations : [91.2%] Performing permutations : [91.4%] Performing permutations : [91.6%] Performing permutations : [91.8%] Performing permutations : [92.0%] Performing permutations : [92.2%] Performing permutations : [92.4%] Performing permutations : [92.6%] Performing permutations : [92.8%] Performing permutations : [93.0%] Performing permutations : [93.2%] Performing permutations : [93.4%] Performing permutations : [93.6%] Performing permutations : [93.8%] Performing permutations : [94.0%] Performing permutations : [94.2%] Performing permutations : [94.4%] Performing permutations : [94.6%] Performing permutations : [94.8%] Performing permutations : [95.0%] Performing permutations : [95.2%] Performing permutations : [95.4%] Performing permutations : [95.6%] Performing permutations : [95.8%] Performing permutations : [96.0%] Performing permutations : [96.2%] Performing permutations : [96.4%] Performing permutations : [96.6%] Performing permutations : [96.8%] Performing permutations : [97.0%] Performing permutations : [97.2%] Performing permutations : [97.4%] Performing permutations : [97.6%] Performing permutations : [97.8%] Performing permutations : [98.0%] Performing permutations : [98.2%] Performing permutations : [98.4%] Performing permutations : [98.6%] Performing permutations : [98.8%] Performing permutations : [99.0%] Performing permutations : [99.2%] Performing permutations : [99.4%] Performing permutations : [99.6%] Performing permutations : [99.8%] p-value: 0.002 .. rst-class:: sphx-glr-timing **Total running time of the script:** (1 minutes 35.933 seconds) .. _sphx_glr_download_auto_examples_stats_plot_oneWay_Manova.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_oneWay_Manova.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_oneWay_Manova.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_