ADRIAIndicators.jl

ADRIAIndicators provides a set of standard metrics for summarizing the state of reef ecological model outputs.

Installation

To install ADRIAIndicators.jl, open a Julia REPL and run:

using Pkg
Pkg.add("ADRIAIndicators")

Testing

In the ADRIAIndicators.jl testing environment,

julia> ]test

Usage

Each metric has an option to write the metric into a provided buffer, this version of the function is denoted by a ! at the end of the function name.

using ADRIAIndicators

# Create some dummy data
n_timesteps = 10
n_groups = 6
n_sizes = 6
n_locations = 5

# Raw model coral cover outputs with dimensions [timesteps ⋅ groups ⋅ sizes ⋅ locations]
raw_model_cover = rand(Float64, n_timesteps, n_groups, n_sizes, n_locations);

# Juveniles mask with dimensions [sizes]
is_juvenile = [true, true, false, false, false, false];

# Calculate and allocate new array for metric
rel_juveniles = relative_juveniles(raw_model_cover, is_juvenile);

# Perform the computation and write the metric into a provided buffer.
rel_juveniles_out = zeros(Float64, n_timesteps, n_locations);
relative_juveniles!(raw_model_cover, is_juvenile, rel_juveniles_out);

Available Metrics

• Relative/Absolute/LTMP Cover
• Relative/Absolute Shelter Volume
• Relative/Absolute Juveniles
• Juvenile Indicator
• Coral Diversity
• Coral Evenness
• Reef Condition Index
• Reef Biodiversity Condition Index
• Reef Tourism Index
• Reef Fish Index

Contributing

Contributions are welcome! Please see the contributing guidelines for more information.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Building Documentation

To build documentation locally:

cd docs

julia --project=. make.jl

Then open index.html in the docs/build directory.