parameter_estimators_test.py

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High-level description

This file contains unit tests for the parameter_estimators.py module in Cassiopeia. The tests cover functions that estimate parameters related to mutation rates and missing data in lineage tracing data.

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Code Structure

The TestCassiopeiaTree class contains multiple test methods, each testing different aspects of the parameter estimation functions. The tests are structured around two example trees: self.discrete_tree and self.continuous_tree, representing discrete and continuous character data respectively.

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Symbols

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TestCassiopeiaTree

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Description

A class containing unit tests for parameter estimation functions.

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Inputs

None

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Outputs

None

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Internal Logic

The class uses the unittest framework to define and run tests. It sets up two example trees (self.discrete_tree and self.continuous_tree) in the setUp method, which are then used by the individual test methods.

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test_proportions

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Description

Tests the get_proportion_of_mutation and get_proportion_of_missing_data functions.

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Inputs

Uses self.discrete_tree and self.continuous_tree

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Outputs

None

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Internal Logic

• Calculates the proportion of mutations and missing data for both trees using the functions being tested.
• Asserts that the calculated proportions match the expected values.

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test_estimate_mutation_rate

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Description

Tests the estimate_mutation_rate function.

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Inputs

Uses self.discrete_tree and self.continuous_tree

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Outputs

None

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Internal Logic

• Estimates the mutation rate for both trees using the function being tested, with different combinations of the continuous and assume_root_implicit_branch parameters.
• Asserts that the estimated mutation rates are close to the expected values.

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test_estimate_missing_data_bad_cases

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Description

Tests the error handling of the estimate_missing_data_rates function.

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Inputs

Uses self.discrete_tree and self.continuous_tree

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Outputs

None

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Internal Logic

• Defines several scenarios where the estimate_missing_data_rates function should raise either a ParameterEstimateError or a ParameterEstimateWarning.
• Uses assertRaises to verify that the expected exceptions are raised in each scenario.

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test_estimate_stochastic_missing_data_probability

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Description

Tests the estimate_missing_data_rates function for estimating the stochastic missing data probability.

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Inputs

Uses self.discrete_tree and self.continuous_tree

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Outputs

None

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Internal Logic

• Estimates the stochastic missing data probability for both trees using the function being tested, with different combinations of the continuous, assume_root_implicit_branch, and heritable_missing_rate parameters.
• Asserts that the estimated probabilities are close to the expected values.

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test_estimate_heritable_missing_data_rate

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Description

Tests the estimate_missing_data_rates function for estimating the heritable missing data rate.

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Inputs

Uses self.discrete_tree and self.continuous_tree

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Outputs

None

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Internal Logic

• Estimates the heritable missing data rate for both trees using the function being tested, with different combinations of the continuous, assume_root_implicit_branch, and stochastic_missing_probability parameters.
• Asserts that the estimated rates are close to the expected values.

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Dependencies

• unittest
• networkx
• numpy
• pandas
• cassiopeia
• cassiopeia.tools.parameter_estimators
• cassiopeia.mixins

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Error Handling

The tests in this file primarily focus on verifying the correct error handling of the parameter estimation functions. They check for scenarios where ParameterEstimateError and ParameterEstimateWarning exceptions should be raised due to invalid input parameters or estimated values.