from io import StringIO

import numpy as np

from statsmodels.stats.anova import anova_lm
from statsmodels.formula.api import ols
from pandas import read_csv

kidney_table = StringIO("""Days      Duration Weight ID
    0.0      1      1      1
    2.0      1      1      2
    1.0      1      1      3
    3.0      1      1      4
    0.0      1      1      5
    2.0      1      1      6
    0.0      1      1      7
    5.0      1      1      8
    6.0      1      1      9
    8.0      1      1     10
    2.0      1      2      1
    4.0      1      2      2
    7.0      1      2      3
   12.0      1      2      4
   15.0      1      2      5
    4.0      1      2      6
    3.0      1      2      7
    1.0      1      2      8
    5.0      1      2      9
   20.0      1      2     10
   15.0      1      3      1
   10.0      1      3      2
    8.0      1      3      3
    5.0      1      3      4
   25.0      1      3      5
   16.0      1      3      6
    7.0      1      3      7
   30.0      1      3      8
    3.0      1      3      9
   27.0      1      3     10
    0.0      2      1      1
    1.0      2      1      2
    1.0      2      1      3
    0.0      2      1      4
    4.0      2      1      5
    2.0      2      1      6
    7.0      2      1      7
    4.0      2      1      8
    0.0      2      1      9
    3.0      2      1     10
    5.0      2      2      1
    3.0      2      2      2
    2.0      2      2      3
    0.0      2      2      4
    1.0      2      2      5
    1.0      2      2      6
    3.0      2      2      7
    6.0      2      2      8
    7.0      2      2      9
    9.0      2      2     10
   10.0      2      3      1
    8.0      2      3      2
   12.0      2      3      3
    3.0      2      3      4
    7.0      2      3      5
   15.0      2      3      6
    4.0      2      3      7
    9.0      2      3      8
    6.0      2      3      9
    1.0      2      3     10
""")

kidney_table.seek(0)
kidney_table = read_csv(kidney_table, sep=r"\s+", engine='python').astype(int)

class TestAnovaLM:
    @classmethod
    def setup_class(cls):
        # kidney data taken from JT's course
        # do not know the license
        cls.data = kidney_table
        cls.kidney_lm = ols('np.log(Days+1) ~ C(Duration) * C(Weight)',
                        data=cls.data).fit()

    def test_results(self):
        Df = np.array([1, 2, 2, 54])
        sum_sq = np.array([2.339693, 16.97129, 0.6356584, 28.9892])
        mean_sq = np.array([2.339693, 8.485645, 0.3178292, 0.536837])
        f_value = np.array([4.358293, 15.80674, 0.5920404, np.nan])
        pr_f = np.array([0.0415617, 3.944502e-06, 0.5567479, np.nan])

        results = anova_lm(self.kidney_lm)
        np.testing.assert_equal(results['df'].values, Df)
        np.testing.assert_almost_equal(results['sum_sq'].values, sum_sq, 4)
        np.testing.assert_almost_equal(results['F'].values, f_value, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, pr_f)


class TestAnovaLMNoconstant:
    @classmethod
    def setup_class(cls):
        # kidney data taken from JT's course
        # do not know the license
        cls.data = kidney_table
        cls.kidney_lm = ols('np.log(Days+1) ~ C(Duration) * C(Weight) - 1',
                        data=cls.data).fit()

    def test_results(self):
        Df = np.array([2, 2, 2, 54])
        sum_sq = np.array([158.6415227, 16.97129, 0.6356584, 28.9892])
        mean_sq = np.array([79.3207613, 8.485645, 0.3178292, 0.536837])
        f_value = np.array([147.7557648, 15.80674, 0.5920404, np.nan])
        pr_f = np.array([1.262324e-22, 3.944502e-06, 0.5567479, np.nan])

        results = anova_lm(self.kidney_lm)
        np.testing.assert_equal(results['df'].values, Df)
        np.testing.assert_almost_equal(results['sum_sq'].values, sum_sq, 4)
        np.testing.assert_almost_equal(results['F'].values, f_value, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, pr_f)

        # > sum2.lm = lm(logDays ~ Duration * Weight - 1, contrasts=list(Duration=contr.sum, Weight=contr.sum))
        # > anova.lm.sum2 <- anova(sum2.lm)
        # > anova.lm.sum2
        # Analysis of Variance Table
        #
        # Response: logDays
        #                 Df  Sum Sq Mean Sq F value    Pr(>F)
        # Duration         2 158.642  79.321 147.756 < 2.2e-16 ***
        # Weight           2  16.971   8.486  15.807 3.945e-06 ***
        # Duration:Weight  2   0.636   0.318   0.592    0.5567
        # Residuals       54  28.989   0.537
        # ---
        # Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1



class TestAnovaLMCompare(TestAnovaLM):
    def test_results(self):
        new_model = ols("np.log(Days+1) ~ C(Duration) + C(Weight)",
                        self.data).fit()
        results = anova_lm(new_model, self.kidney_lm)

        Res_Df = np.array([
             56, 54
            ])
        RSS = np.array([
             29.62486, 28.9892
            ])
        Df = np.array([
             0, 2
            ])
        Sum_of_Sq = np.array([
             np.nan, 0.6356584
            ])
        F = np.array([
             np.nan, 0.5920404
            ])
        PrF = np.array([
             np.nan, 0.5567479
            ])

        np.testing.assert_equal(results["df_resid"].values, Res_Df)
        np.testing.assert_almost_equal(results["ssr"].values, RSS, 4)
        np.testing.assert_almost_equal(results["df_diff"].values, Df)
        np.testing.assert_almost_equal(results["ss_diff"].values, Sum_of_Sq)
        np.testing.assert_almost_equal(results["F"].values, F)
        np.testing.assert_almost_equal(results["Pr(>F)"].values, PrF)


class TestAnovaLMCompareNoconstant(TestAnovaLM):
    def test_results(self):
        new_model = ols("np.log(Days+1) ~ C(Duration) + C(Weight) - 1",
                        self.data).fit()
        results = anova_lm(new_model, self.kidney_lm)

        Res_Df = np.array([
             56, 54
            ])
        RSS = np.array([
             29.62486, 28.9892
            ])
        Df = np.array([
             0, 2
            ])
        Sum_of_Sq = np.array([
             np.nan, 0.6356584
            ])
        F = np.array([
             np.nan, 0.5920404
            ])
        PrF = np.array([
             np.nan, 0.5567479
            ])

        np.testing.assert_equal(results["df_resid"].values, Res_Df)
        np.testing.assert_almost_equal(results["ssr"].values, RSS, 4)
        np.testing.assert_almost_equal(results["df_diff"].values, Df)
        np.testing.assert_almost_equal(results["ss_diff"].values, Sum_of_Sq)
        np.testing.assert_almost_equal(results["F"].values, F)
        np.testing.assert_almost_equal(results["Pr(>F)"].values, PrF)


class TestAnova2(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_ii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             3.067066, 13.27205, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 2, 2, 51
            ])
        F_value = np.array([
             5.667033, 12.26141, 0.1760025, np.nan
            ])
        PrF = np.array([
             0.02106078, 4.487909e-05, 0.8391231, np.nan
            ])

        results = anova_lm(anova_ii, typ="II")
        np.testing.assert_equal(results['df'].values, Df)
        np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F_value, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)


class TestAnova2Noconstant(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_ii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum) - 1",
                                data).fit()

        Sum_Sq = np.array([
             154.7131692, 13.27205, 0.1905093, 27.60181
            ])
        Df = np.array([
             2, 2, 2, 51
            ])
        F_value = np.array([
             142.9321191, 12.26141, 0.1760025, np.nan
            ])
        PrF = np.array([
             1.238624e-21, 4.487909e-05, 0.8391231, np.nan
            ])

        results = anova_lm(anova_ii, typ="II")
        np.testing.assert_equal(results['df'].values, Df)
        np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F_value, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

        # > sum2.lm.dropped <- lm(logDays ~ Duration * Weight - 1,  dta.dropped,
        #                 contrasts=list(Duration=contr.sum, Weight=contr.sum))
        # > anova.ii.dropped2 <- Anova(sum2.lm.dropped, type='II')
        # > anova.ii.dropped2
        # Anova Table (Type II tests)
        #
        # Response: logDays
        #                  Sum Sq Df F value    Pr(>F)
        # Duration        154.713  2 142.932 < 2.2e-16 ***
        # Weight           13.272  2  12.261 4.488e-05 ***
        # Duration:Weight   0.191  2   0.176    0.8391
        # Residuals        27.602 51


class TestAnova2HC0(TestAnovaLM):
    #NOTE: R does not return SSq with robust covariance. Why?
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_ii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 2, 2, 51
            ])
        F = np.array([
             6.972744, 13.7804, 0.1709936, np.nan
            ])
        PrF = np.array([
             0.01095599, 1.641682e-05, 0.8433081, np.nan
            ])

        results = anova_lm(anova_ii, typ="II", robust="hc0")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova2HC1(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_ii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 2, 2, 51
            ])
        F = np.array([
             6.238771, 12.32983, 0.1529943, np.nan
            ])
        PrF = np.array([
             0.01576555, 4.285456e-05, 0.858527, np.nan
            ])

        results = anova_lm(anova_ii, typ="II", robust="hc1")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova2HC2(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_ii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 2, 2, 51
            ])
        F = np.array([
             6.267499, 12.25354, 0.1501224, np.nan
            ])
        PrF = np.array([
             0.01554009, 4.511826e-05, 0.8609815, np.nan
            ])


        results = anova_lm(anova_ii, typ="II", robust="hc2")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova2HC3(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_ii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 2, 2, 51
            ])
        F = np.array([
             5.633786, 10.89842, 0.1317223, np.nan
            ])
        PrF = np.array([
             0.02142223, 0.0001145965, 0.8768817, np.nan
            ])

        results = anova_lm(anova_ii, typ="II", robust="hc3")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova3(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_iii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 1, 2, 2, 51
            ])
        F_value = np.array([
             279.7545, 5.367071, 12.43245, 0.1760025, np.nan
            ])
        PrF = np.array([
             2.379855e-22, 0.02457384, 3.999431e-05, 0.8391231, np.nan
            ])

        results = anova_lm(anova_iii, typ="III")
        np.testing.assert_equal(results['df'].values, Df)
        np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F_value, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova3HC0(TestAnovaLM):
    #NOTE: R does not return SSq with robust covariance. Why?
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_iii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 1, 2, 2, 51
            ])
        F = np.array([
             298.3404, 5.723638, 13.76069, 0.1709936, np.nan
            ])
        PrF = np.array([
             5.876255e-23, 0.02046031, 1.662826e-05, 0.8433081, np.nan
            ])

        results = anova_lm(anova_iii, typ="III", robust="hc0")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova3HC1(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_iii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 1, 2, 2, 51
            ])
        F = np.array([
             266.9361, 5.12115, 12.3122, 0.1529943, np.nan
            ])
        PrF = np.array([
             6.54355e-22, 0.02792296, 4.336712e-05, 0.858527, np.nan
            ])

        results = anova_lm(anova_iii, typ="III", robust="hc1")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova3HC2(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_iii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 1, 2, 2, 51
            ])
        F = np.array([
             264.5137, 5.074677, 12.19158, 0.1501224, np.nan
            ])
        PrF = np.array([
             7.958286e-22, 0.02860926, 4.704831e-05, 0.8609815, np.nan
            ])

        results = anova_lm(anova_iii, typ="III", robust="hc2")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)

class TestAnova3HC3(TestAnovaLM):
    # drop some observations to make an unbalanced, disproportionate panel
    # to make sure things are okay
    def test_results(self):
        data = self.data.drop([0,1,2])
        anova_iii = ols("np.log(Days+1) ~ C(Duration, Sum)*C(Weight, Sum)",
                                data).fit()

        Sum_Sq = np.array([
             151.4065, 2.904723, 13.45718, 0.1905093, 27.60181
            ])
        Df = np.array([
             1, 1, 2, 2, 51
            ])
        F = np.array([
             234.4026, 4.496996, 10.79903, 0.1317223, np.nan
            ])
        PrF = np.array([
             1.037224e-20, 0.03883841, 0.0001228716, 0.8768817, np.nan
            ])

        results = anova_lm(anova_iii, typ="III", robust="hc3")
        np.testing.assert_equal(results['df'].values, Df)
        #np.testing.assert_almost_equal(results['sum_sq'].values, Sum_Sq, 4)
        np.testing.assert_almost_equal(results['F'].values, F, 4)
        np.testing.assert_almost_equal(results['PR(>F)'].values, PrF)