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Add mortality in dynamical equations and change default parameter values. #72

Merged
merged 27 commits into from
Dec 16, 2022
Merged

Add mortality in dynamical equations and change default parameter values. #72

merged 27 commits into from
Dec 16, 2022

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ismael-lajaaiti
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Main features of this PR:

  • add a mortality term (incorporated in ModelParameters and dBdt!)
  • change the default parameters values for the attack rates and handling time to match Miele et al. 2019
  • correct the classic functional response by multiplying the denominator by predator body-mass (again see Miele et al. 2019)

@ismael-lajaaiti
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Just made a new commit to export two functions that I need for the StabilityMetrics package and thought that these functions could be useful for the users.

@iago-lito iago-lito mentioned this pull request Nov 7, 2022
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iago-lito requested changes Nov 7, 2022
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@iago-lito iago-lito left a comment •
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Great :) Again this is good work and I see no problem with the implementation so I can only nitpick here and there. I'm still confused why a new method for the functor is needed (with (B, network) signature), can you explain?

Unrelatedly, you have made use of |> operator which I'm unfamiliar with.. and which I think could improve the package ergonomics a lot from the user POV. Cheers! Stay tuned :D [EDIT] see #73

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src/inputs/functional_response.jl
@@ -492,6 +495,22 @@ function (F::FunctionalResponse)(B)
end
(F::FunctionalResponse)(B, _::EcologicalNetwork) = F(B)

function (F::ClassicResponse)(B, network::FoodWeb)
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I'm sorry I don't understand why this new method is needed?

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Long version in a comment below.
Short version: to compute the classic functional response, I need the species biomasses M which is stored in the network.

@iago-lito iago-lito mentioned this pull request Nov 7, 2022
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@ismael-lajaaiti
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Great :) Again this is good work and I see no problem with the implementation so I can only nitpick here and there. I'm still confused why a new method for the functor is needed (with (B, network) signature), can you explain?

Unrelatedly, you have made use of |> operator which I'm unfamiliar with.. and which I think could improve the package ergonomics a lot from the user POV. Cheers! Stay tuned :D

Thanks for your review, I'm gonna incorporate the changes you suggested. Let you know when it's done.

For the new signature, now I also need to pass the network to the the functional response (specifically to the ClassicResponse) because that response depends on the species body-mass M and M is stored in the network<:EcologicalNetwork object.

For the pipe operator do you think of things like foodweb |> MultiplexNetwork (to convert a foodweb to a MultiplexNetwork). If so, I already had this in mind and I think that in some cases it can be very neat, but most of the time the user would like to also provide keyword arguments, and in this case I'm not sure the pipe syntax can be used (maybe wrong).

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Yes, I would reserve pipe syntax for functions with only 1 argument.. or with very, very, overly-used defaults. See #73 about that ;)

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ismael-lajaaiti commented Nov 16, 2022 •
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Here is the modifications you requested @iago-lito (last commit).
Let me know if it's good for you, and thanks again for your comments! :)

This was referenced Nov 17, 2022
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alaindanet and others added 14 commits December 7, 2022 10:54
@alaindanet @iago-lito
Add contributing guidelines
fe3c814
@ismael-lajaaiti @iago-lito
Ismael's suggestions
87ee104 
Mainly aesthetic stuff.
@iago-lito
Iago's pass over CONTRIBUTING.md.
9154397
@alaindanet @iago-lito
Typo fix
45ebd25
@ismael-lajaaiti @iago-lito
Manage zombies and extinct species
3e92145 
:finger_crossed:
@ismael-lajaaiti @iago-lito
Mandatory update in functioning.jl
47117cd
@ismael-lajaaiti @iago-lito
Remove trailing whitespaces in functioning.jl
676fd82
@ismael-lajaaiti @iago-lito
Rename and export ExtinctionCallback
9e004ea
@ismael-lajaaiti @iago-lito
Add Tom example to test-simulate.jl
4dc8504
@ismael-lajaaiti @iago-lito
abs() trick for is isoutofdomain
2e2fca7
@ismael-lajaaiti @iago-lito
Check that B0 contains positive values
56d263d
@ismael-lajaaiti @iago-lito
Use a Set for extinct species
2439d26
@ismael-lajaaiti @iago-lito
Merging duplicate code for extinction callback
2673b4d
@iago-lito
Integrate zombies fixes into boost options.
998333a 
- Ease/Force systematic testing of the three simulation flavours.
- Use `extinct_species` in `:raw` generated code.
- Use `extinct_species` in `:compact` generated code.
ismael-lajaaiti and others added 11 commits December 15, 2022 10:33
@ismael-lajaaiti @iago-lito
extinct_sp include time of extinction
d7fda7b 
+ some tambouille about sol.k
@iago-lito
Minor fixes to #78, skipping the review process.
8719515 
- Reference #65 to explain why setting `B[i_extinct] = 0` is needed in `dBdt!`.
- Simplify calculation of initial `extinct_sp` values.
- Avoid checking `isa(extinction_threshold, Number)` on every timestep.
@ismael-lajaaiti @iago-lito
Update simulate() docstring
8d280cc
@ismael-lajaaiti @iago-lito
Change default handling times
3e3f1f9
@ismael-lajaaiti @iago-lito
Add death to ModelParemeters
5ffd77f 
Not yet integrated in the ODEs.
@ismael-lajaaiti @iago-lito
Add death to dBdt!
cf4c7d5 
Also added few tests.
Still have to update the doc.
@ismael-lajaaiti @iago-lito
Update paradox of enrichment example
e57a73c
@ismael-lajaaiti @iago-lito
Change default attack rates
b84868b
@ismael-lajaaiti @iago-lito
Divide ClassicResponse by consumer body-mass
afb158a 
Forgot one term in the denominator of the classic functional response.
@ismael-lajaaiti @iago-lito
Export and document preys_of and predators_of
520ed6a
@ismael-lajaaiti @iago-lito
Incorporate Iago's suggestions
db1c874
@iago-lito iago-lito merged commit db1c874 into BecksLab:develop Dec 16, 2022
@ismael-lajaaiti ismael-lajaaiti deleted the miele2019_params branch December 16, 2022 16:03
This was linked to issues Jan 13, 2023
Add mortality term to the ODEs #30
Closed
Default argument values #33
Closed
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Default argument values Add mortality term to the ODEs
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@ismael-lajaaiti @iago-lito @alaindanet