Solving the ValueError in Python When Comparing Sampling Distributions with the ks_2samp Function

Discover how to fix the "ValueError: operands could not be broadcast together" issue in Python when comparing distributions using the `ks_2samp` function.
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Understanding and Resolving the ValueError in Python's KS Test

In the world of statistical analysis and methods in Python, encountering errors is not an unusual occurrence, especially when working with libraries like NumPy and SciPy. One common error that many users face is the ValueError: operands could not be broadcast together with shapes (2, 1000) (2,). This can be particularly frustrating when you've done everything according to your understanding of the function you are using. In this post, we will dive into this specific error that occurs in the context of comparing two sampling distributions using the KS test, and how to effectively resolve it.

The Problem

You've achieved the admirable task of creating a function that defines a test statistic based on the mode of resampled data matrices. The function works with two matrices, matrix2 and matrix3, to generate a sampling distribution of modes and then compare these distributions using the KS test. However, despite your best efforts, you're encountering a ValueError during execution. The error message reads as follows:

[[See Video to Reveal this Text or Code Snippet]]

This indicates that there is a mismatch between the shapes of the arrays you are trying to compare or operate on. The error arises specifically when you attempt to work with the results of the ks_2samp function.

Understanding the KS Test Return Type

The ks_2samp function from SciPy is used to compare two samples for equality. It returns more than just the p-value; it returns an object containing both the test statistic and the p-value. The key to resolving the error lies in understanding what this return type includes and how to use it correctly.

Return Structure of ks_2samp

The output of ks_2samp is actually a KstestResult object that contains two main attributes of interest:

statistic — the KS statistic computed from the two samples.

pvalue — the p-value for the hypothesis test.

When you call the function like this:

[[See Video to Reveal this Text or Code Snippet]]

what you receive is an object rather than simply a numeric return which could cause shape conflicts when used improperly.

The Solution

To fix the ValueError that arises at the point of executing your permutation test, you need to access the statistic attribute from the ks_2samp result when defining your function. Here’s how to do that correctly.

Steps to Resolve

Modify your newTestStat function to extract only the KS statistic from the ks_2samp return value.

Update this line:

[[See Video to Reveal this Text or Code Snippet]]

to:

[[See Video to Reveal this Text or Code Snippet]]

Continue with the rest of your code as it was intended, since this change will ensure only the numeric value of the KS statistic is returned, eliminating any shape conflicts during further calculations.

Conclusion

Errors like the ValueError discussed can be quite challenging, but understanding the return types of functions in libraries can lead you toward a solution. The key takeaway here is to always check the structure and types of return values, especially when you're manipulating the results of statistical methods.

By implementing the necessary changes to your code, you should now be able to successfully run the permutation test without the broadcasting error. Happy coding, and may your data analysis endeavors be fruitful!