It'd be really good to have a full working example. This means:
input data files, in the right format (validated by #7 ), with some sort of documentation about what the data means
an example of how to run the analysis & generate the outputs (could be example code in a README.md file, or just an example .py file)
some commentary about how to interpret the generated output files
This worked example should be written for a person who understands what this code is trying to do, but hasn't necessarily seen the original MATLAB code. So the instructions can't just explain things in terms of what's different from the original MATLAB code.
So the instructions for the worked example do need to be self-contained, including:
what values the user needs to provide (strata infection rates? ward capacities?)
a short code example of how to install the patientpaths module from PyPI, and call it (including how to provide the necessary inputs)
an explanation of where the results will end up, and what the output numbers represent
For the moment, you can assume (for point 1) that the user is working in an Australian context, i.e. that their jurisdiction is at least "stubbed out" (with NaNs).
It'd be really good to have a full working example. This means:
README.mdfile, or just an example.pyfile)This worked example should be written for a person who understands what this code is trying to do, but hasn't necessarily seen the original MATLAB code. So the instructions can't just explain things in terms of what's different from the original MATLAB code.
So the instructions for the worked example do need to be self-contained, including:
patientpathsmodule fromPyPI, and call it (including how to provide the necessary inputs)For the moment, you can assume (for point 1) that the user is working in an Australian context, i.e. that their jurisdiction is at least "stubbed out" (with
NaNs).