EVOLUTION-MANAGER

Edit File: test_contingency.py

from __future__ import division, print_function, absolute_import

import numpy as np
from numpy.testing import (assert_equal, assert_array_equal,
         assert_array_almost_equal, assert_approx_equal, assert_allclose)
from pytest import raises as assert_raises

from scipy.special import xlogy
from scipy.stats.contingency import margins, expected_freq, chi2_contingency

def test_margins():
    a = np.array([1])
    m = margins(a)
    assert_equal(len(m), 1)
    m0 = m[0]
    assert_array_equal(m0, np.array([1]))

a = np.array([[1]])
    m0, m1 = margins(a)
    expected0 = np.array([[1]])
    expected1 = np.array([[1]])
    assert_array_equal(m0, expected0)
    assert_array_equal(m1, expected1)

a = np.arange(12).reshape(2, 6)
    m0, m1 = margins(a)
    expected0 = np.array([[15], [51]])
    expected1 = np.array([[6, 8, 10, 12, 14, 16]])
    assert_array_equal(m0, expected0)
    assert_array_equal(m1, expected1)

a = np.arange(24).reshape(2, 3, 4)
    m0, m1, m2 = margins(a)
    expected0 = np.array([[[66]], [[210]]])
    expected1 = np.array([[[60], [92], [124]]])
    expected2 = np.array([[[60, 66, 72, 78]]])
    assert_array_equal(m0, expected0)
    assert_array_equal(m1, expected1)
    assert_array_equal(m2, expected2)

def test_expected_freq():
    assert_array_equal(expected_freq([1]), np.array([1.0]))

observed = np.array([[[2, 0], [0, 2]], [[0, 2], [2, 0]], [[1, 1], [1, 1]]])
    e = expected_freq(observed)
    assert_array_equal(e, np.ones_like(observed))

observed = np.array([[10, 10, 20], [20, 20, 20]])
    e = expected_freq(observed)
    correct = np.array([[12., 12., 16.], [18., 18., 24.]])
    assert_array_almost_equal(e, correct)

def test_chi2_contingency_trivial():
    # Some very simple tests for chi2_contingency.

# A trivial case
    obs = np.array([[1, 2], [1, 2]])
    chi2, p, dof, expected = chi2_contingency(obs, correction=False)
    assert_equal(chi2, 0.0)
    assert_equal(p, 1.0)
    assert_equal(dof, 1)
    assert_array_equal(obs, expected)

# A *really* trivial case: 1-D data.
    obs = np.array([1, 2, 3])
    chi2, p, dof, expected = chi2_contingency(obs, correction=False)
    assert_equal(chi2, 0.0)
    assert_equal(p, 1.0)
    assert_equal(dof, 0)
    assert_array_equal(obs, expected)

def test_chi2_contingency_R():
    # Some test cases that were computed independently, using R.

Rcode = \
    """
    # Data vector.
    data <- c(
      12, 34, 23,     4,  47,  11,
      35, 31, 11,    34,  10,  18,
      12, 32,  9,    18,  13,  19,
      12, 12, 14,     9,  33,  25
      )

# Create factor tags:r=rows, c=columns, t=tiers
    r <- factor(gl(4, 2*3, 2*3*4, labels=c("r1", "r2", "r3", "r4")))
    c <- factor(gl(3, 1,   2*3*4, labels=c("c1", "c2", "c3")))
    t <- factor(gl(2, 3,   2*3*4, labels=c("t1", "t2")))

# 3-way Chi squared test of independence
    s = summary(xtabs(data~r+c+t))
    print(s)
    """
    Routput = \
    """
    Call: xtabs(formula = data ~ r + c + t)
    Number of cases in table: 478
    Number of factors: 3
    Test for independence of all factors:
            Chisq = 102.17, df = 17, p-value = 3.514e-14
    """
    obs = np.array(
        [[[12, 34, 23],
          [35, 31, 11],
          [12, 32, 9],
          [12, 12, 14]],
         [[4, 47, 11],
          [34, 10, 18],
          [18, 13, 19],
          [9, 33, 25]]])
    chi2, p, dof, expected = chi2_contingency(obs)
    assert_approx_equal(chi2, 102.17, significant=5)
    assert_approx_equal(p, 3.514e-14, significant=4)
    assert_equal(dof, 17)

Rcode = \
    """
    # Data vector.
    data <- c(
        #
        12, 17,
        11, 16,
        #
        11, 12,
        15, 16,
        #
        23, 15,
        30, 22,
        #
        14, 17,
        15, 16
        )

# Create factor tags:r=rows, c=columns, d=depths(?), t=tiers
    r <- factor(gl(2, 2,  2*2*2*2, labels=c("r1", "r2")))
    c <- factor(gl(2, 1,  2*2*2*2, labels=c("c1", "c2")))
    d <- factor(gl(2, 4,  2*2*2*2, labels=c("d1", "d2")))
    t <- factor(gl(2, 8,  2*2*2*2, labels=c("t1", "t2")))

# 4-way Chi squared test of independence
    s = summary(xtabs(data~r+c+d+t))
    print(s)
    """
    Routput = \
    """
    Call: xtabs(formula = data ~ r + c + d + t)
    Number of cases in table: 262
    Number of factors: 4
    Test for independence of all factors:
            Chisq = 8.758, df = 11, p-value = 0.6442
    """
    obs = np.array(
        [[[[12, 17],
           [11, 16]],
          [[11, 12],
           [15, 16]]],
         [[[23, 15],
           [30, 22]],
          [[14, 17],
           [15, 16]]]])
    chi2, p, dof, expected = chi2_contingency(obs)
    assert_approx_equal(chi2, 8.758, significant=4)
    assert_approx_equal(p, 0.6442, significant=4)
    assert_equal(dof, 11)

def test_chi2_contingency_g():
    c = np.array([[15, 60], [15, 90]])
    g, p, dof, e = chi2_contingency(c, lambda_='log-likelihood', correction=False)
    assert_allclose(g, 2*xlogy(c, c/e).sum())

g, p, dof, e = chi2_contingency(c, lambda_='log-likelihood', correction=True)
    c_corr = c + np.array([[-0.5, 0.5], [0.5, -0.5]])
    assert_allclose(g, 2*xlogy(c_corr, c_corr/e).sum())

c = np.array([[10, 12, 10], [12, 10, 10]])
    g, p, dof, e = chi2_contingency(c, lambda_='log-likelihood')
    assert_allclose(g, 2*xlogy(c, c/e).sum())

def test_chi2_contingency_bad_args():
    # Test that "bad" inputs raise a ValueError.

# Negative value in the array of observed frequencies.
    obs = np.array([[-1, 10], [1, 2]])
    assert_raises(ValueError, chi2_contingency, obs)

# The zeros in this will result in zeros in the array
    # of expected frequencies.
    obs = np.array([[0, 1], [0, 1]])
    assert_raises(ValueError, chi2_contingency, obs)

# A degenerate case: `observed` has size 0.
    obs = np.empty((0, 8))
    assert_raises(ValueError, chi2_contingency, obs)