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Continue investigating environment modifications and related mechanisms

Yunus Sevinchan requested to merge envmod-contd into master

This is the successor of !14 (merged), where environment modifications were first implemented. It continues with the investigation of those, but also adds a number of extensions to the base functionality of the model.

This MR ...

  • ... implements analysis of extinction cascades #13 (closed)
  • ... allows associating costs with lower niche width #27 (closed)
  • ... adds inheritance_strength (#15) based on m/f ratio
  • ... adds functional diversity measures
  • ... adds recycling_factor
  • ... adds extinction cascade statistics
  • ... adds PropertyTracker with aggregated properties of species, written upon their removal:
    • age
    • mean_trophic_level
    • TL_diff
    • extinction_delay
  • ... adds CascadeSizeTracker
  • ... adds flushing of buffered write properties, such that all that data is ensured to be written out
  • ... adds several new configuration sets
  • ... extends and improves plot functions:
    • value_spans now accepts color
    • snsplot improvements
  • ... moves all plot configurations into the base plots and makes more use of plot config inheritance
  • ... adds snapshotting feature for ODESystem, allowing to restore from more states than the final state

Related

Closes #27 (closed), #13 (closed)

Edited by Yunus Sevinchan

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