A collection of statistical functions

version: 0.4.0

This repository offers a collection of Python-based statistical methods spanning:

• hypothesis testing,
• (confidence) interval estimation,
• bootstrap and jack-knife re-sampling methods,
• Firth's logistic regression for (semi) perfect separation,
• fixed effect and random effects meta-analysis,
• tools for (survival) prediction model evaluation.

Please consult the stats-misc documentation, which includes quick-start notebooks.

Installation

The package is available on PyPI, and conda, with the latest source code available on gitlab.

Installation using PyPI

To install the package from PyPI, run:

pip install stats-misc

This installs the latest stable release along with its dependencies.

Installation using conda

A Conda package is maintained in my personal Conda channel. To install from this channel, run:

conda install afschmidt::stats-misc

Installation using gitlab

If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.

First, clone the repository and move into its root directory:

git clone git@gitlab.com:SchmidtAF/stats-misc.git
cd stat-misc

Install the dependencies:

# From the root of the repository
conda env create --file ./resources/conda/envs/conda_create.yaml

To add to an existing environment use:

# From the root of the repository
conda env update --file ./resources/conda/envs/conda_create.yaml

Next the package can be installed:

make install

Development

For development work, install the package in editable mode with Git commit hooks configured:

make install-dev

This command installs the package in editable mode and configures Git commit hooks, allowing you to run git pull to update the repository or switch branches without reinstalling.

Alternatively, you can install manually:

python -m pip install -e .
python .setup_git_hooks.py

Git Hooks Configuration

When setting up a development environment, the setup-hooks command configures Git hooks to enforce conventional commit message formatting and spell check using codespell.

To view the commit message format requirements, run:

./.githooks/commit-msg -help

For frequent use, add this function to your shell configuration (~/.bashrc or ~/.zshrc):

commit-format-help() {
    local git_root
    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
    
    if [ -z "$git_root" ]; then
        echo "Error: Not inside a git repository"
        return 1
    fi
    
    local hook_path="$git_root/.githooks/commit-msg"
    
    if [ ! -f "$hook_path" ]; then
        echo "Error: commit-msg hook not found"
        return 1
    fi
    
    "$hook_path" --help
}

Validating the package

After installation, you may wish to run the included test suite with pytest to verify that the package is functioning as expected.

# From the root of the repository
pytest tests

Usage

Please have a look at the examples in resources .