GECOT, the Graph-based Ecological Connectivity Optimization Tool, is an open-source C++ tool designed to tackle systematic conservation (or restoration) planning problems. Given a graph representation of the landscape for each target species, a list of actions for improving the graphs elements and a budget, GECOT allows to select a group of actions whose cost is below the budget and whose impacts on the Landscapes maximizes the ecological connectivity, measured with the Probability of Connectivity indicator (PC).
Installation guidelines for this project
gecot_solve <algorithm_name> <instance_file> <budget_value> [<option>=<value>]
"<algorithm_name>" is the name of the algorithm to use for solving the input problem. The list of available algorithm can be displayed with the command :
gecot_solve --list-algorithms
Typical output :
GECOT — Graph-based Ecological Connectivity Optimization Tool
Version: 1.0 (built on Mar 16 2024)
Available algorithms:
static_incr From the base landscape, add the options with the best
gain/cost ratio.
static_decr From the improved landscape, remove the options with the
worst gain/cost ratio.
greedy_incr From the base landscape, iteratively add the option with the
best gain/cost ratio.
greedy_decr From the improved landscape, iteratively remove the option
with the worst gain/cost ratio (Zonation Algorithm).
mip MIP formulation without preprocessing, from 'Optimizing the
ecological connectivity of landscapes', F. Hamonic,
C. H. Albert, B. Couëtoux, Y. Vaxès
prep_mip MIP formulation with preprocessing, from 'Optimizing the
ecological connectivity of landscapes', F. Hamonic,
C. H. Albert, B. Couëtoux, Y. Vaxès
"<instance_file>" is the path to a json file describing problem to solve.
Some examples of instance are available in the folder test/instances.
Lets take a look the the file test/instances/Aude.json :
{
"options": {
"csv_file": "Aude/dams.csv",
"csv_columns": {
"id": "name",
"cost": "cost"
}
},
"cases": {
"trout": {
"vertices": {
"csv_file": "Aude/stretches.csv",
"csv_columns": {
"id": "id",
"quality": "length"
}
},
"arcs": {
"csv_file": "Aude/arcs.csv",
"csv_columns": {
"id": "arc_id",
"from": "source_id",
"to": "target_id",
"probability": "probability"
}
},
"arcs_improvements": {
"csv_file": "Aude/dams_arcs.csv",
"csv_columns": {
"arc_id": "arc_id",
"option_id": "dam_id",
"improved_probability": "improved_prob"
}
}
}
},
"criterion": "trout"
}This work is part of the PhD thesis of François Hamonic which is funded by Region Sud (https://www.maregionsud.fr/) and Natural Solutions (https://www.natural-solutions.eu/).