Executing The Code

This code was written to be executed in a particular file structure, diagrammed as follows:

With a GitHub account you can clone a repository with all data and code in place in the correct directory structure. Please follow the installation instructions on the GitHub repository.

Computational Environment

All analysis and data processing was performed with the following software configurations.

# Python Version
CPython 3.6.7
IPython 7.1.1

# Package Versions

# System Information
compiler   : GCC 4.2.1 Compatible Clng 4.0.1 (tagss/RELEASE_401/final)
system     : Darwin
release    : 18.2.0
machine    : x86_64
processor  : i386
CPU cores  : 4
interpreter: 64bit

The mut Module

This work required a moderate amount of home-grown code. To ensure reproducibility, we have written it as a Python module that can be installed from the master branch of the GitHub repository. Please see the installation instructions for details. This module is required to execute all of the following scripts.

Figure Generation

All Figures in this work (save for Fig. 2) were generated programmatically.

Interactive Figures

The two interactive figures associated with this work (the model explorer and the data collapse figure) were generated using the Bokeh plotting framework using a combination of Python code and Javascript. The Python code (which includes the javascript) can be downloaded below.

Inferential Models

All parameter inference was performed using the Stan probabilistic programming language. The following Stan model files perform the described analysis.

The following scripts were used to execute the inference models.

Supplementary Materials

The following code was used to generate the supplementary figures as well as any data generated via simulation.