Resampling Statistics

The module provides tools for resampling (e.g., statistical bootstrapping) in the context of pandas DataFrames in general and specifically OpenPathSampling. This provides tools for estimating statistical error on multiple quantities simultaneously.

Purpose of Module

Providing an estimate of uncertainty is essential when presenting scientific results. This module provides the ability to perform statistical analysis of a large simulation from OpenPathSampling by using the sampled trajectories to create subsamples, which are then assumed to be independent. The subsamples are analyzed separately, and this module makes it easy to obtain mean, standard deviation, or percentile values. In particular, this module provides the tools to do such an analysis on functions that return a table of data using a pandas.DataFrame object, as the OpenPathSampling rate matrix calculation does.

Most of the code is generic, and could be used for any function that produces a pandas.DataFrame as its output. Therefore this module may be useful for many projects other than OpenPathSampling. Within OpenPathSampling, this can be used to obtain statistics on rates, fluxes, and other such quantities.

These tools are implemented in two main classes. The first is BlockResampling, which organizes the input (MC steps in OPS) into blocks to be passed to a function that does the analysis. This allows us to obtain several results for the analysis. The second is ResamplingStatistics, which takes those blocks and a function (that returns a pandas.DataFrame) as input. It then applies that function to each of those blocks, and then makes it easy to access properties such as the mean, standard deviation, or percentile values for each frame element.

While BlockResampling is the only resampling method implemented in the module (as it is the one needed for TIS rate calculations), it would be straightforward to extend this framework with other resampling methods, such as variants of bootstrapping.

Background Information

This module builds on OpenPathSampling, a Python package for path sampling simulations. To learn more about OpenPathSampling, you might be interested in reading:


Tests in OpenPathSampling use the nose package.

This module has been included in the OpenPathSampling core. Its tests can be run by setting up a developer install of OpenPathSampling and running the command nosetests from the root directory of the repository.

Source Code

This module has been merged into OpenPathSampling. It is composed of the following pull requests: