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Use scipy.stats.chisquare to compare observed category counts with specified expected frequencies; use scipy.stats.chi2_contingency to test whether categorical variables are independent in a contingency table. Both return a statistic and p-value. The second also returns degrees of freedom and expected cell counts.

Choose the function that matches your question

Question SciPy function Input Expected counts
Do counts for one categorical variable differ from stated proportions? scipy.stats.chisquare Observed frequencies and, usually, expected frequencies in matching categories You provide them; if omitted, SciPy assumes equal category probabilities.
Are two or more categorical variables independent? scipy.stats.chi2_contingency A table of observed frequencies SciPy calculates them from the table margins under the independence assumption.

These are distinct tests, even though both use the chi-square distribution for their usual asymptotic p-values. The SciPy chisquare reference describes a goodness-of-fit test; the chi2_contingency reference describes the contingency-table test.

Run a goodness-of-fit test with chisquare

Use this test when you have one categorical variable and a specified distribution to compare against. Supply counts—not raw continuous measurements—and align observed and expected values category by category.

import numpy as np
from scipy.stats import chisquare

observed = np.array([16, 18, 16, 14, 12, 12])
expected = np.array([16, 16, 16, 16, 16, 8])

result = chisquare(f_obs=observed, f_exp=expected)
print(result.statistic, result.pvalue)

Here, f_obs contains the observed frequencies, and f_exp contains the expected frequencies for those same categories. If you omit f_exp, SciPy treats the categories as equally likely. For expected proportions, convert them to expected counts using the sample total. For example, if the expected proportions are 0.5 and 0.5 and you observed 100 cases, the expected counts are 50 and 50.

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Check totals and degrees of freedom

For the ordinary Pearson goodness-of-fit test, observed and expected frequencies should have matching totals. SciPy’s sum_check checks this by default; do not bypass that check unless the statistical model and the reason for doing so are clear.

The usual degrees of freedom are the number of categories minus one. If you estimated parameters from the data, the degrees of freedom may need to be reduced. SciPy documents k - 1 - p for the efficient maximum-likelihood case, where k is the number of categories and p is the number of estimated parameters. The function’s ddof argument adjusts the degrees of freedom used for the p-value. Parameter estimation can also mean that the asymptotic distribution is not chi-square, so a degrees-of-freedom adjustment is not automatically sufficient.

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Test independence with chi2_contingency

Use this function for a cross-tabulation: rows and columns represent category values of different variables, and each cell holds the observed count. SciPy derives the counts expected under independence from the row and column totals.

import numpy as np
from scipy.stats import chi2_contingency

observed_table = np.array([
    [10, 10, 20],
    [20, 20, 20]
])

result = chi2_contingency(observed_table)
print("Statistic:", result.statistic)
print("p-value:", result.pvalue)
print("Degrees of freedom:", result.dof)
print("Expected frequencies:")
print(result.expected_freq)

The result includes the test statistic, p-value, degrees of freedom, and expected-frequency table. Inspect the expected table before interpreting the asymptotic p-value, especially when some categories are uncommon.

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Correction, statistic, and resampling options

  • Continuity correction: correction=True is the default. When the degrees of freedom equal one, SciPy applies Yates’ correction by moving each observed count 0.5 toward its expected count. Set correction=False if you intentionally want the uncorrected statistic.
  • Alternative statistics: The default lambda_=None selects Pearson’s chi-square statistic. Setting lambda_ selects another statistic from the Cressie–Read power-divergence family.
  • Resampling p-values: In the SciPy 1.18.0 documentation, the method option supports permutation or Monte Carlo p-values only for a two-way table, with correction=False and the default lambda. The documented Monte Carlo setup uses scipy.stats.random_table. These constraints are version-sensitive; check the reference for the SciPy version you have installed.

Check whether the chi-square approximation is suitable

Both functions are intended for frequency counts in categorical data. A common diagnostic guideline is that observed and expected cell frequencies should be at least 5, but this is not a universal guarantee. SciPy warns that small observed or expected counts can make the approximation unreliable. Review the expected frequencies and the study design rather than treating one cutoff as proof that the test is valid.

If the counts are too sparse for a reliable approximation, choose an alternative that fits the design and table. SciPy’s related references include Fisher’s exact test for 2-by-2 tables and exact alternatives such as Barnard’s test; they are not interchangeable in every setting.

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Interpret the statistic and p-value correctly

The p-value measures how incompatible the observed counts are with the test’s null hypothesis, assuming the test’s conditions hold. A small p-value is evidence against that null; it does not give the probability that the null is true.

For an independence test, a small p-value does not identify which cells drive the result, show the direction of a relationship, or measure its practical strength. The test is two-sided. Consider examining the observed and expected table and reporting an association measure such as Cramer’s V when a measure of strength is useful. See SciPy’s chi-square hypothesis-testing tutorial and association measure reference.

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Report enough detail for someone to understand the test

  • Name the test and the variables or categories being analyzed.
  • Show the observed counts or provide a clearly identified contingency table.
  • Report the statistic, degrees of freedom, and p-value.
  • For goodness-of-fit, state the expected proportions or counts and whether model parameters were estimated.
  • For independence, include or summarize the expected-count check.
  • State whether you used Yates’ correction, a non-default statistic, or resampling.
  • Add an effect-size measure when useful; do not present the p-value as a measure of effect size or direction.

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