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Integrative Meta-Regression Framework for Descriptive Epidemmiology

Project description

Latest Version

Introduction

This project is the descriptive epidemiological meta-regression tool, DisMod-MR, which grew out of the Global Burden of Disease (GBD) Study 2010. DisMod-MR has been developed for the Institute of Health Metrics and Evaluation at the University of Washington from 2008-2013.

Installation

Dismod MR requires PyMC2 which does not play nicely with normal Python installation tools. Fortunately, conda has solved this issue for us. So first you’ll need to setup a conda environment (after installing conda, if necessary) and install pymc. Then you can install dismod_mr using pip.

conda create --name=dismod_mr python=3.6 pymc
conda activate dismod_mr
pip install dismod_mr

If you get an error stating

ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/pip-install-d9fbq7v3/pymc/setup.py", line 8, in <module>
    from numpy.distutils.misc_util import Configuration
ModuleNotFoundError: No module named 'numpy'
----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-d9fbq7v3/pymc/

or something similar, you do not have pymc properly installed.

Installing from source

If you want to install dismod_mr locally in an editable mode, the instructions are very similar. We’ll clone the repository and install it from a local directory instead of using pip to grab it from the Python package index.

conda create --name=dismod_mr python=3.6 pymc
conda activate dismod_mr
git clone git@github.com:ihmeuw/dismod_mr.git
cd dismod_mr
pip install -e .

Coding Practices

  • Write tests before code
  • Write equations before tests
  • Test quantitatively with simulation data
  • Test qualitatively with real data
  • Automate tests
  • Use a package instead of DIY
  • Test the package
  • Optimize code later
  • Optimize code for readability before speed
  • .py files should be short, less than 500 lines
  • Functions should be short, less than 25 lines

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Files for dismod-mr, version 1.1.1
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