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Examples and documentation#128

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JoYvBa wants to merge 21 commits intomainfrom
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Examples and documentation#128
JoYvBa wants to merge 21 commits intomainfrom
examples_documentation

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@JoYvBa JoYvBa commented Jan 15, 2026

Finalizes example notebooks and documentation. Ads field site case study examples.

Fixes #88
Fixes #95
Fixes #118

Furthermore:

  • Included notebooks exploring aspects of the transport equation theory.
  • Test parameters are based on field data, instead of artificial data.
  • Changed formulation of source depletion term in Anatrans
  • Import mibitrans as mbt in examples, instead of each separate class or function separately.
  • Removed most animations from examples, since not robust in notebooks.

@JoYvBa JoYvBa added this to the Version 1.0 milestone Jan 15, 2026
@JoYvBa JoYvBa self-assigned this Jan 15, 2026
@JoYvBa JoYvBa added this to MIBIREM Jan 15, 2026
@JoYvBa JoYvBa added documentation Improvements or additions to documentation priority: 1 Important feature needed for proper functionality, or otherwise of high priority labels Jan 15, 2026
@JoYvBa JoYvBa moved this to In Progress in MIBIREM Jan 15, 2026
JoYvBa added 15 commits January 19, 2026 16:12
Changed %matplotlib notebook to %matplotlib ipympl
Removed conversion from ft to m from notebook. Improved section title formatting.
-k_source - decay_rate should be k_source - decay_rate.
Change increases adaptability of model class
Anatrans now uses the mathematically sound source depletion expression. Bioscreen still uses the expression as used in BIOSCREEN. All test parameters and data have been adapted to represent the Keesler site, in order to test on actual field data instead of dummy data.
Equation formulation example attempted to show two different aspects of the formulation of the equation, and therefore accomplished neither. They have now been split up for the sake of clarity.
Additionally, some elaboration on Keesler example
Notebook compares output from mibitrans models with the models from BIOSCREEN and BIOSCREEN-AT for proof of functionality.
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documentation Improvements or additions to documentation priority: 1 Important feature needed for proper functionality, or otherwise of high priority

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Implement testing for example notebooks Include new examples for different case studies Include code snippet examples in docstrings

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