🐦 Modeling the Trophic Network of Europa: Focus on Tropicbirds as Prey

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🌍 Context and Aims

Europa is a small French island with an exceptional diversity of seabird species.
Two species of tropicbirds (white-tailed and red-tailed tropicbird), one of which is an endemic subspecies (the white-tailed), are currently threatened due to predation by:

• 🐀 Black rats
• 🐦 Pied crows
• 🦉 Barn owls

The latter two predators also feed on rats, creating a complex web of trophic interactions.

The aim of this study is to build this trophic network using differential equations, in order to:

• Model the viability of each population
• Simulate the effects of conservation actions on ecosystem stability

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🗂 Project Structure

This project follows a simple structure:

• output/ ➜ Model outputs and generated plots

  ├─ Scenarii_relalistic/ ➜ Output with realistic parameters

  ├─ Sensibility_actions/

    ├─ Raterad_1shotcorvus_reg ➜ *Output for rat eradication and one control action to
    reduce pied crow at 50 pairs and then annual regulation from 0.1 to 0.8*
  
    ├─ Reg_Crow  ➜ *Output for pied crow annual regulation from 0 to 1*
  
    ├─ Reg_Rats ➜ *Output for pied crow annual regulation from 0 to 6*
  
    ├─ Reg_Rats_Crow ➜ *Output for pied crow annual regulation from 0 to 6 and rat eradication or regulation*
  

  ├─ Sensibility_crow/ ➜ Output for several population growth of pied crow (-1 to 1)

  ├─ Sensibility_owl/ ➜ Output for several estimates parameter for barn owl

   ├─ ECH/
   ├─ GCH/
   ├─ PHIACH/
   ├─ PHIJCH/
   ├─ SRCH/
  

  ├─ Sensibility_rats/ ➜ Output for several population growth of rats (-1 to 6) ├─ Pred_crow2/ ➜ For rate predation of pied crow on rats equal to 2 ├─ Pred_crow10/ ➜ For rate predation of pied crow on rats equal to 10

• R/

  ├─ Make.R ➜ Main script to run the full workflow

  ├─ Fct.R ➜ Functions defining the system of differential equations using deSolve package

  ├─ Var.R ➜ Script specifying the initial conditions for each variable

  ├─ Sensitivity_barnowl.R ➜ Script to estimate barn owls lambda sensitivity to the variation of parameters

• README.md

• Scenarii.xlsx ➜ Details of scenarii and setting parameters

🔢 Variable Abbreviations and Meanings

Species Codes

Code	Species
BJ	White-tailed tropicbird ("Bec Jaune" in french)
BR	Red-tailed tropicbird ("Brins Rouges" in french)
R	Rats
Co	Pied crows ("COrbeaux pies" in french)
CH	Barn owls ("CHouettes" in french)

Age-Class Prefix

Prefix	Meaning
A	Adult (sexually mature)
P	Combine egg and chick
Y	Yearling (from egg laying to one year old)
J	Juvenile of age species in suffix (e.g., JBJ1 = one-year-old juvenile white-tailed tropicbird)

⚠️ Note: Different age-classes were not considered for Rats and Pied Crows.

Biological Parameter Prefix

Prefix	Meaning
F	Fecundity
K	Maximum carrying capacity
φ	Survival rate
μ	Mortality rate
prXY	Predation rate of X on Y
Proies_	All the prey ("Proies" in french") consumed by the defined species
r	Intrinsic population growth
ro	Regulation (individual per time step)

Other Parameters

Code	Meaning
E	Number of clutches per dt
a	Birth sex ratio
G	Clutch size
SR	Natural breeding success ("Succès reproducteur" in french)
Au	Other birds (including sooty terns and zosterops, "Autres" in french)
I	Insects
Pl	Plants
Sc	Skinks ("Scinque" in french)
Tor	Baby turtles

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⚡ Notes

• Variable names may combine a biological parameter prefix with an age-class and species code.
• Example: phiJBJ1 → Survival rate (phi) of juvenile of 1years old (J__1) of white-tailed tropicbird (BJ).

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Legend : Brown : Barn owl, Purple : pied crow, Blue : rats, Red : red-tailed tropicbirds, Yellow : white-tailed tropicbird. Black arrow means "eats"