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Polish example notebooks#62

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astoeriko merged 4 commits into
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polish-examples
Jul 23, 2026
Merged

Polish example notebooks#62
astoeriko merged 4 commits into
developfrom
polish-examples

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@astoeriko

@astoeriko astoeriko commented Jul 2, 2026

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This PR adds better documentation to two example notebooks:

  • one more complete reactive-transport example that demonstrates pathogen transport
  • one simple transport example that demonstrates integration with PyMC

Addresses #43

TODO: Make sure that units and parameter values are consistent
throughout the notebook.
Parameter values are now roughly oriented at the ones in Schijven et el.
(1999)

Schijven, J. F., Hoogenboezem, W., Hassanizadeh, M., & Peters, J. H. (1999). Modeling removal of bacteriophages MS2 and PRD1 by dune recharge at Castricum, Netherlands. Water Resources Research, 35(4), 1101–1111. https://doi.org/10.1029/1998WR900108
@astoeriko

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This took longer than expected because I needed to resolve some merge conflicts in the notebooks.

The PyMC example can for sure be improved but it is good enough to merge it for now. @edvinskis This is ready to be added to the documentation. I can give it a go and try if I can rebuild the documentation. I will also add the mixed reactor example that I created when splitting the System class.

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@astoeriko

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This took longer than expected because I needed to resolve some merge conflicts in the notebooks.

The PyMC example can for sure be improved but it is good enough to merge it for now. @edvinskis This is ready to be added to the documentation. I can give it a go and try if I can rebuild the documentation. I will also add the mixed reactor example that I created when splitting the System class.

@astoeriko
astoeriko marked this pull request as ready for review July 23, 2026 09:47
@astoeriko
astoeriko merged commit 320b805 into develop Jul 23, 2026
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