Exercise

Check the source code for the measSIR pomp object, using the spy command. Does the code implement the model described?

  1. Does the code implement the model described?

Let us know if you find a discrepancy. Some bugs can be discovered by reading code, but many slip through this test. We cannot assume that code which looks okay is bug-free.

Papers should be written to be readable, and therefore people rarely choose to clutter papers with numerical details which they hope and believe are scientifically irrelevant.

  1. What problems can arise due to the conflict between readability and reproducibility?

Reproducibility requires that all details are fully described. For most readers, most of the time, presenting all the technical details may serve a negative purpose of obscuring the main points of the paper.

  1. What solutions are available?

Rnw and Rmd file formats (for R) and Jupyter notebooks (for python and R) are popular methods for reproducible computing.


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