ImperialCollegeLondon / virtual_ecosystem

This repository is the home for the codebase for the Virtual Ecosystem project.
https://virtual-ecosystem.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Adding non-predation mortality and semelparity to the Animal Module. #422

Closed TaranRallings closed 3 months ago

TaranRallings commented 4 months ago

Description

This adds a new trait to functional groups, reproductive type, which is broken into two variations, iteroparity (reproducing multiple times) and semelparity (reproducing once and then dying). Iteroparous organisms reproduce as before, semelparous organisms also use some of their non-reproductive mass in the reproductive event and then the cohort dies.

This PR also expands non-predation mortality to include a fixed background mortality, senescence mortality, and starvation mortality. There were small errors in the Madingley paper for the latter two mortalities so you may notice an excess of diagnostics in the testing from when I was trying to figure out if I had gone mad. I left them in, in case they might be useful later. Let me know if you think I should remove them.

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codecov-commenter commented 4 months ago

Codecov Report

Attention: Patch coverage is 96.15385% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 94.69%. Comparing base (626476b) to head (f0d1a4a).

Files Patch % Lines
...ual_ecosystem/models/animals/animal_communities.py 88.23% 2 Missing :warning:
virtual_ecosystem/models/animals/animal_cohorts.py 96.55% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #422 +/- ## =========================================== + Coverage 94.62% 94.69% +0.06% =========================================== Files 69 69 Lines 3666 3732 +66 =========================================== + Hits 3469 3534 +65 - Misses 197 198 +1 ```

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