statistics-resampling

A statistics toolbox with a variety of bootstrap and other resampling tools. (This is most recent and developmental version of the toolbox).

Read me

Package maintainer

Andrew Penn ([e-mail])

Package contributors

Andrew Penn
(More contributors are welcome!)

Citations

If you use this package, please include the following citation(s):

• Penn, Andrew Charles. (2020). Resampling methods for small samples or samples with complex dependence structures. Zenodo. https://doi.org/10.5281/zenodo.3992392

(Note that package versions 5.4.3 and below were named the 'statistics-bootstrap' package. The 'statistics-resampling' package is a more developed version of the older 'iboot' package).

Description

The statistics-resampling package is an Octave package and Matlab toolbox that can be used to perform a wide variety of statistics tasks using non-parametric resampling methods. In particular, the functions included can be used to estimate bias, uncertainty (standard errors and confidence intervals), prediction error, and calculate p-values for null hypothesis significance tests. Variations of the resampling methods are included that improve the accuracy of the statistics for small samples and samples with complex dependence structures.

Using the statistics-resampling package online

Try out the statistics-resampling package in your browser at statistics-resampling-online : a ready-to-go implementation of statistics-resampling in a JupyterLab Notebook with an Octave kernel. Note that the first time (since the last repository commit) that you use statistics-resampling online with Binder you can expect it to take a while to build a docker image, but subsequent access to statistics-resampling-online will take less than a minute or so.

Collaborative student projects in GNU Octave can use the statistics-resampling package at Octave-Online. Doing so requires users to download the latest release of the Source code (tar.gz) from here and follow steps 2-5 of these instructions.

Users who prefer Jupyter and have a workflow that is collaborative and/or crosses over multiple programming languages may find it more convenient to install and use the statistics-resampling package at COCALC. The approach described above (for Octave-Online) also applies to installing the statistics-resampling package via a Jupyter Notebook with an Octave kernel at COCALC.

Alternatively, if you have an account with MATLAB you can try out the statistics-resampling package at Matlab-Online by either following the local installation instructions below, or by adding the toolbox (not collection) version of the package via Apps >> Get More Apps.

Follow the links in the 'Quick start' section below to obtain some examples of data and code to try out with the package.

Requirements and dependencies

Users with greater computational demands may want to consider installing and running the statistics-resampling package offline. Installation of the statistics-resampling package has some software requirements. The core functions in this package require, and are known to be compatible with, GNU Octave (version >= 4.4.0) and Matlab (version >= R2007a 7.4.0). Some optional features of this package have further dependencies:

• All parallel computing options require either the parallel package (in Octave) or the Parallel Computing Matlab Toolbox (in Matlab). Note that the Parallel package in Octave also requires the struct package.
• The optional jackknife functionality in boot1way requires the statistics package (in Octave) or the Statistics and Machine Learning Toolbox (in Matlab).

Installation

To install (or test) the statistics-resampling package in your computer at a location of your choice, for either Matlab or Octave, follow these steps:

• Download the latest package release from here. Extract (not just browse) the contents of the compressed file (.zip or .tar.gz), and move the package directory to the desired location.
• Open Octave or Matlab (command prompt).
• Change directory (cd) into the package folder. (The directory contains a file called 'make.m' and 'install.m', among others)
• Type make to compile the MEX files from source (or use the precompiled binaries if available. If suitable precompiled binaries are not available for your platform, then Matlab/Octave will need access to a C++11 compiler. Note that if you skip the make step, then the package functions will still work, but some will run slower. This step is interactive so check the command window.)
• Type install. The package will load now (and automatically in the future) when you start Octave/Matlab.

If you want or need to uninstall the package, change directory (cd) into the package folder and type uninstall.

Alternatively, Octave users can install the latest release of the package just like any other Octave package by typing:

pkg install -forge statistics-resampling

Or for the most recent developmental version of the package:

pkg install "https://github.com/gnu-octave/statistics-resampling/archive/refs/heads/master.zip"

The package can then be loaded on demand in Octave with the following commmand:

pkg load statistics-resampling

(Note that this isn't necessary if you used the local installation instructions first described in this section)

Alternatively, MATLAB users can conveniently install the package functions as a toolbox by double-clicking the 'statistics-resampling.mltbx' file in the matlab subdirectory. The toolbox installed in this way can be disabled or uninstalled via MATLAB's Add-On manager. MEX files are included with the toolbox installation for Windows (32- or 64-bit), MacOS (Intel or Apple Silicon 64-bit) and Linux (64-bit).

Usage

All help and demos are documented on the 'Function Reference' page in the manual. If you do not see the navigation pane on the manual web pages, please enable javascript in your browser. If you need further help with using any of the functions in this package, please post your questions on the discussions page.

Function help can also be requested directly from the Octave/MATLAB command prompt, by typing help function-name - substituting in the actual function name.

In Octave only, you can get a basic overview of the package and it's functions by typing: pkg describe -verbose statistics-resampling, or request demonstrations of function usage by typing demo function-name. Users can also request help with using functions and programming in Octave at the discourse group.

TIPS: You can now document and publish your statistics-resampling analysis in Jupyter Notebooks (with an Octave kernel) at your GitHub repository using the nbgitpuller link generator and the statistics-resampling-online Binder environment . Alternatively, you could fork the repository or use it as a template for you own GitHub repository. Using Jupyter notebooks, you can also integrate use of the statistics-resampling package into your analysis workflow alongside other programming languages including Python, R and Julia

Quick start

Below are links to demonstrations of how the bootstrap or randomization functions from this package can be used to perform variants of some commonly used statistical tests, but without the Normality assumption:

• t-test to compare two independent samples (assuming equal variances)

• t-test to compare two independent samples (assuming equal variances) (but also robust to outliers)

• t-test to compare two independent samples (but also robust to heteroscedasticity, i.e. unequal variance)

• Nested t-test to compare two independent samples. (See example listed below for nested one-way ANOVA)

• t-test to compare two paired or matching samples

• One-way ANOVA to compare two or more independent samples (but also robust to heteroscedasticity)

• Nested one-way ANOVA to compare two or more independent samples (but also robust to heteroscedasticity and grouping of observations)

• Balanced two-way factorial ANOVA (but also robust to heteroscedasticity)

• Unbalanced two-way factorial ANOVA (but also robust to heteroscedasticity)

• Simple linear regression (but also robust to heteroscedasticity)

• One-way ANCOVA (but also robust to heteroscedasticity)

• One-way repeated measures ANOVA

• Randomization or permutation tests to compare the distributions of two independent or paired/matching samples

• Randomization or permutation tests to compare the distributions of two independent samples with clustered observations

• Statistically evaluate the number of modes (i.e. peaks) in a distribution

• Correcting sample size calculations for a two-sample test with nested design

For examples of how to import data sets from a human-readable text file, like a tab-separated-value (TSV) and comma-separated-value (CSV) file, see the examples in the JupyterLab Notebook at statistics-resampling-online and the last demonstration listed on this page

Issues

If you find bugs or have any suggestions, please raise an issue on GitHub here. If you have any problems specifically with Binder for statistics-resampling online, please raise an issue on GitHub here. Please make sure that, when reporting a bug, you provide as much information as possible for other users to be able to replicate it.

Package: statistics-resampling