tarpan 0.1.9

A collection of tools for analysing cmdspanpy output, written in Python

A Python library for analysing cmdstanpy output

This is a collection of function for analysing output of cmdstanpy library. The main idea is to do a quick data analysis by calling a single function that makes:

• traceplots of samples,

• text and plots of the summaries of model parameters,

• histograms and pair plots of posterior distributions of parameters.

The only known illustration of a tarpan made from life, depicting a five month old colt (Borisov, 1841). Source: Wikimedia Commons.

Setup

First, install cmdstanpy library, and then do:

pip install tarpan

Usage

Do complete analysis: save_analysis

This is the main function of the library that saves summaries and trace/pair/tree plots in model_info directory. See the example code of using save_analysis function and description of its output files.

from tarpan.cmdstanpy.analyse import save_analysis
model = CmdStanModel(stan_file="your_model.stan")
fit = model.sample(data=your_data)
save_analysis(fit, param_names=['mu', 'sigma'])

Make tree plot: save_tree_plot

Function save_tree_plot creates a tree plot in model_info directory. See example code here.

from tarpan.cmdstanpy.tree_plot import save_tree_plot
fit = CmdStanModel(stan_file="your_model.stan")
save_tree_plot([fit], param_names=['mu', 'sigma'])

Comparing multiple models on a tree plot

Supply multiple fits in order to compares parameters from multiple models. See example code here.

from tarpan.cmdstanpy.tree_plot import save_tree_plot
fit1 = CmdStanModel(stan_file="your_model1.stan")
fit2 = CmdStanModel(stan_file="your_model2.stan")

data = { "mu": 2.2, "tau": 1.3 }  # Add extra markers (optional)
save_tree_plot([fit1, fit2], extra_values=data, param_names=['mu', 'sigma'])

Run unit tests

pytest

The unlicense

This work is in public domain.

🐴🐴🐴

This work is dedicated to Tarpan, an extinct subspecies of wild horse.