test_integration.py

import pandas as pd

import tea
import os

base_url = 'https://homes.cs.washington.edu/~emjun/tea-lang/datasets/'
file_names = ['UScrime.csv', 'statex77.csv', 'catsData.csv', 'cholesterol.csv', 'soya.csv', 'co2.csv', 'exam.csv', 'liar.csv',
              'pbcorr.csv', 'spiderLong_within.csv', 'drug.csv', 'alcohol.csv', 'ecstasy.csv', 'gogglesData.csv', 'gogglesData_dummy.csv']
data_paths = [None] * len(file_names)


def load_data():
    global base_url, data_paths, file_names
    global drug_path

    for i in range(len(data_paths)):
        csv_name = file_names[i]

        csv_url = os.path.join(base_url, csv_name)
        data_paths[i] = tea.download_data(csv_url, csv_name)


def get_data_path(filename):
    load_data()
    try:
        data_idx = file_names.index(filename)
    except:
        raise ValueError(f"File is not found!:{filename}")
    data_path = data_paths[data_idx]

    return data_path

# Example from Kabacoff
# Expected outcome: Pearson correlation
def test_pearson_corr():
    data_path = get_data_path('statex77.csv')
    # data_path2 = get_data_path('statex87.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Illiteracy',
            'data type': 'interval',
            'categories': [0, 100]
        },
        {
            'name': 'Life Exp',
            'data type': 'ratio',
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': ['Illiteracy', 'Life Exp'],
        'outcome variables': ''
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
        'normal distribution': ['Illiteracy']
    }

    tea.data(data_path)
    # tea.data(data_path2)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions, 'strict')

    results = tea.hypothesize(['Illiteracy', 'Life Exp'], [
                              'Illiteracy ~ Life Exp'])
    # print("\nfrom Kabacoff")
    # print("Expected outcome: Pearson")
    print('++++++++++++')


def test_pearson_corr_2():
    data_path = get_data_path('exam.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Exam',
            'data type': 'ratio',
            'range': [0, 100]
        },
        {
            'name': 'Anxiety',
            'data type': 'interval',
            'range': [0, 100]
        },
        {
            'name': 'Gender',
            'data type': 'nominal',
            'categories': ['Male', 'Female']
        },
        {
            'name': 'Revise',
            'data type': 'ratio'
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': ['Anxiety', 'Gender', 'Revise'],
        'outcome variables': 'Exam'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    results = tea.hypothesize(['Anxiety', 'Exam'])
    results = tea.hypothesize(['Revise', 'Exam'])
    results = tea.hypothesize(['Anxiety', 'Revise'])
    # print("\nfrom Field et al.")
    # print("Expected outcome: Pearson")
    print('++++++++++++')


def test_spearman_corr():
    data_path = get_data_path('liar.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Creativity',
            'data type': 'interval'
        },
        {
            'name': 'Position',
            'data type': 'ordinal',
            'categories': [6, 5, 4, 3, 2, 1]  # ordered from lowest to highest
        },
        {
            'name': 'Novice',
            'data type': 'nominal',
            'categories': [0, 1]
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': ['Novice', 'Creativity'],
        'outcome variables': 'Position'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    # TODO: allow for partial orders?
    results = tea.hypothesize(['Position', 'Creativity'], ['Position:1 > 6'])
    # print("\nfrom Field et al.")
    # print("Expected outcome: Spearman")
    print('++++++++++++')

# Same as test for Spearman rho


def test_kendall_tau_corr():
    data_path = get_data_path('liar.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Creativity',
            'data type': 'interval'
        },
        {
            'name': 'Position',
            'data type': 'ordinal',
            'categories': [6, 5, 4, 3, 2, 1]  # ordered from lowest to highest
        },
        {
            'name': 'Novice',
            'data type': 'nominal',
            'categories': [0, 1]
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': ['Novice', 'Creativity'],
        'outcome variables': 'Position'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    results = tea.hypothesize(['Position', 'Creativity'], [
                              'Position:1 > 6', 'Position:1 > 2'])  # I think this works!?
    # print("\nfrom Field et al.")
    # print("Expected outcome: Kendall Tau")
    print('++++++++++++')


def test_pointbiserial_corr():
    data_path = get_data_path('pbcorr.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'time',
            'data type': 'ratio'
        },
        {
            'name': 'gender',
            'data type': 'nominal',
            'categories': [0, 1]  # ordered from lowest to highest
        },
        {
            'name': 'recode',
            'data type': 'nominal',
            'categories': [0, 1]
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': ['gender', 'recode'],
        'outcome variables': 'time'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    # I think this works!?
    tea.hypothesize(['time', 'gender'], ['gender:1 > 0'])
    # print("\nfrom Field et al.")
    # print("Expected outcome: Pointbiserial")
    print('++++++++++++')


def test_indep_t_test():
    data_path = get_data_path('UScrime.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'So',
            'data type': 'nominal',
            'categories': [0, 1]
        },
        {
            'name': 'Prob',
            'data type': 'ratio',
            'range': [0, 1]
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': 'So',
        'outcome variables': 'Prob',
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
        'groups normally distributed': [['Prob', 'So']]
    }

    transformations = {
        'log': ['Prob']
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['So', 'Prob'], ['So:1 > 0'])  # Southern is greater
    # print("\nfrom Kabacoff")
    # print("Expected outcome: Student's t-test")
    print('++++++++++++')


def test_paired_t_test():
    data_path = get_data_path('spiderLong_within.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Group',
            'data type': 'nominal',
            'categories': ['Picture', 'Real Spider']
        },
        {
            'name': 'Anxiety',
            'data type': 'ratio'
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': 'Group',
        'dependent variables': 'Anxiety',
        'within subjects': 'Group'

    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05
    }

    tea.data(data_path, key="id")
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['Group', 'Anxiety'], ['Group:Real Spider > Picture'])

    # print("\nfrom Field et al.")
    # print("Expected outcome: Paired/Dependent t-test")
    print('++++++++++++')


def test_wilcoxon_signed_rank():
    data_path = get_data_path('alcohol.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'drug',
            'data type': 'nominal',
            'categories': ['Alcohol']
        },
        {
            'name': 'day',
            'data type': 'nominal',
            'categories': ['sundayBDI', 'wedsBDI']
        },
        {
            'name': 'value',
            'data type': 'ratio'
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': 'day',
        'dependent variables': 'value',
        'within subjects': 'day'

    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['day', 'value'], ['day:sundayBDI != wedsBDI'])
    
    # print("\nfrom Field et al.")
    # print("Expected outcome: Wilcoxon signed rank test")
    print('++++++++++++')


def test_f_test():
    data_path = get_data_path('cholesterol.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'trt',
            'data type': 'nominal',
            'categories': ['1time', '2times', '4times', 'drugD', 'drugE']
        },
        {
            'name': 'response',
            'data type': 'ratio'
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': 'trt',
        'dependent variables': 'response',
        'between subjects': 'trt'

    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['trt', 'response'])
    # print("\nFrom Field et al.")
    # print("Expected outcome: Oneway ANOVA (F) test")
    print('++++++++++++')


def test_kruskall_wallis():
    data_path = get_data_path('soya.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Sperm',
            'data type': 'interval'
        },
        {
            'name': 'Soya',
            'data type': 'ordinal',
            'categories': ['No Soya', '1 Soya Meal', '4 Soya Meals', '7 Soya Meals']
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': 'Soya',
        'dependent variables': 'Sperm',
        'between subjects': 'Soya'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['Soya', 'Sperm'])

    # print("\nFrom Field et al.")
    # print("Expected outcome: Kruskall Wallis")
    print('++++++++++++')


def test_rm_one_way_anova():
    data_path = get_data_path('co2.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'uptake',
            'data type': 'interval'
        },
        {
            'name': 'Type',
            'data type': 'nominal',
            'categories': ['Quebec', 'Mississippi']
        },
        {
            'name': 'conc',
            'data type': 'ordinal',
            'categories': [95, 175, 250, 350, 500, 675, 1000]
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': ['Type', 'conc'],
        'dependent variables': 'uptake',
        'within subjects': 'conc',
        'between subjects': 'Type'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path, key="Plant")
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['uptake', 'conc'])

    # print("\nFrom Field et al.")
    # print("Expected outcome: Repeated Measures One Way ANOVA")
    print('++++++++++++')


def test_factorial_anova():
    data_path = get_data_path('gogglesData.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'gender',
            'data type': 'nominal',
            'categories': ['Female', 'Male']
        },
        {
            'name': 'alcohol',
            'data type': 'nominal',
            'categories': ['None', '2 Pints', '4 Pints']
        },
        {
            'name': 'attractiveness',
            'data type': 'interval'
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': ['gender', 'alcohol'],
        'dependent variables': 'attractiveness',
        'between subjects': ['gender', 'alcohol']
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['attractiveness', 'gender', 'alcohol'])
    # alcohol main effect?
    # print("\nFrom Field et al.")
    # print("Expected outcome: Factorial ANOVA")
    print('++++++++++++')


def test_two_way_anova():
    data_path = get_data_path('co2.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'uptake',
            'data type': 'interval'
        },
        {
            'name': 'Type',
            'data type': 'nominal',
            'categories': ['Quebec', 'Mississippi']
        },
        {
            'name': 'conc',
            'data type': 'ordinal',
            'categories': [95, 175, 250, 350, 500, 675, 1000]
        }
    ]
    experimental_design = {
        'study type': 'experiment',
        'independent variables': ['Type', 'conc'],
        'dependent variables': 'uptake',
        'within subjects': 'conc',
        'between subjects': 'Type'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
        'groups normally distributed': [['Type', 'uptake'], ['Type', 'conc']],
        'equal variance': [['Type', 'uptake'], ['conc', 'uptake']]
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions, mode='relaxed')

    # Fails: not all groups are normal
    tea.hypothesize(['uptake', 'conc', 'Type'])
    # Type main effect?
    # print('Supposed to be 2 way ANOVA')
    print('++++++++++++')


def test_chi_square():
    data_path = get_data_path('catsData.csv')

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Training',
            'data type': 'nominal',
            'categories': ['Food as Reward', 'Affection as Reward']
        },
        {
            'name': 'Dance',
            'data type': 'nominal',
            'categories': ['Yes', 'No']
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': 'Training',
        'outcome variables': 'Dance'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_path)
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['Training', 'Dance'])
    # print('Chi square')
    print('++++++++++++')


def test_chi_square_with_dataframe():
    data_path = get_data_path('catsData.csv')

    data_frame = pd.read_csv(data_path)

    # Declare and annotate the variables of interest
    variables = [
        {
            'name': 'Training',
            'data type': 'nominal',
            'categories': ['Food as Reward', 'Affection as Reward']
        },
        {
            'name': 'Dance',
            'data type': 'nominal',
            'categories': ['Yes', 'No']
        }
    ]
    experimental_design = {
        'study type': 'observational study',
        'contributor variables': 'Training',
        'outcome variables': 'Dance'
    }
    assumptions = {
        'Type I (False Positive) Error Rate': 0.05,
    }

    tea.data(data_frame)  # Passes data_frame instead of data_path
    tea.define_variables(variables)
    # Allows for using multiple study designs for the same dataset (could lead to phishing but also practical for saving analyses and reusing as many parts of analyses as possible)
    tea.define_study_design(experimental_design)
    tea.assume(assumptions)

    tea.hypothesize(['Training', 'Dance'])
    # print('Chi square')
    print('++++++++++++')