dismod-mr 1.1.2.7

Examples

A motivating example: descriptive epidemiological meta-regression of Parkinson’s Disease

All examples

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 version 2.3.8. Then you can install dismod_mr using pip.

conda create --name=dismod_mr python=3.6 pymc==2.3.8
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.

conda create --name=dismod_mr python=3.6 pymc==2.3.8
conda activate dismod_mr
git clone git@github.com:ihmeuw/dismod_mr.git
cd dismod_mr
pip install -e .

pip install pytest
pytest

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