Reef Indices

reef_biodiversity_condition_index!(rc::AbstractArray{T,2}, cd::AbstractArray{T,2}, sv::AbstractArray{T,2}, out_rbci::AbstractArray{T,2})::Nothing where {T<:AbstractFloat}

Calculate the Reef Biodiversity Condition Index (RBCI). This is implementation is limited to using outputs that can be provided by coral ecology models.

Arguments

• rc : Relative coral cover.
• cd : Coral diversity.
• sv : Relative shelter volume.
• out_rbci : Output array buffer for the RCI.

reef_biodiversity_condition_index(relative_cover::AbstractArray{T,2}, coral_diversity::AbstractArray{T,2}, shelter_volume::AbstractArray{T,2})::AbstractArray{T,2} where {T<:AbstractFloat}

Calculate the Reef Biodiversity Condition Index (RBCI). The RBCI is simply the average of relative cover (RC), coral diversity (CD), and shelter volume (SV). Given as

\[\begin{align*} \text{RBCI} = \frac{\text{RC} + \text{CD} + \text{SV}}{3}. \end{align*}\]

This is implementation is limited to using outputs that can be provided by coral ecology models.

Arguments

• relative_cover : Relative coral cover.
• coral_diversity : Coral diversity.
• shelter_volume : Relative shelter volume.

Returns

A 2D array of the Reef Condition Index.

reef_condition_index!(ltmp_cover::AbstractArray{T,2}, relative_shelter_volume::AbstractArray{T,2}, juvenile_indicator::AbstractArray{T,2}, rubble::AbstractArray{T,2}, out_rci::AbstractArray{T,2})::Nothing where {T<:AbstractFloat}

Calculate the Reef Condition Index (RCI).

This method uses four inputs: LTMP cover, relative shelter volume, juvenile indicator, and rubble. This is implementation is limited to using outputs that can be provided by ecological models that only model corals.

Arguments

• ltmp_cover : LTMP Coral Cover with dimensions [timesteps ⋅ locations].
• relative_shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• juvenile_indicator: Juvenile Indicator with dimensions [timesteps ⋅ locations].
• rubble : Relative rubble cover with dimensions [timesteps ⋅ locations].
• out_rci : Output RCI buffer with dimensions [timesteps ⋅ locations].

References

1. Ryan F. Heneghan, Gabriela Scheufele, Yves-Marie Bozec et al. A framework to inform economic valuation of non-use benefits from coral-reef intervention efforts, 02 October 2025, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-7644150/v1]

reef_condition_index!(ltmp_cover::AbstractArray{T,2}, relative_shelter_volume::AbstractArray{T,2}, juvenile_indicator::AbstractArray{T,2}, out_rci::AbstractArray{T,2})::Nothing where {T<:AbstractFloat}

Calculate the Reef Condition Index (RCI).

This method uses three inputs: LTMP coral cover, relative shelter volume, and juvenile indicator. This is implementation is limited to using outputs that can be provided by ecological models that only model corals.

Arguments

• ltmp_cover : LTMP Coral Cover with dimensions [timesteps ⋅ locations].
• relative_shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• juvenile_indicator: Juvenile Indicator with dimensions [timesteps ⋅ locations].
• out_rci : Output RCI buffer with dimensions [timesteps ⋅ locations].

References

1. Ryan F. Heneghan, Gabriela Scheufele, Yves-Marie Bozec et al. A framework to inform economic valuation of non-use benefits from coral-reef intervention efforts, 02 October 2025, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-7644150/v1]

reef_condition_index(relative_cover::AbstractArray{T,2}, shelter_volume::AbstractArray{T,2}, relative_juveniles::AbstractArray{T,2}, rubble::AbstractArray{T,2})::AbstractArray{T,2} where {T<:AbstractFloat}

Calculate the Reef Condition Index (RCI).

This method uses four inputs: LTMP cover, relative shelter volume, juvenile indicator, and rubble.

The RCI is a categorical index assessing the overall health and condition of a reef location based on four key ecological metrics. The index assigns a discrete score (0.1, 0.3, 0.5, 0.7, or 0.9) representing categories from "Very Poor" to "Very Good".

For each input there are five levels of condition ranging from very poor to very good. Rubble cover is inverted, where high values indicate worse condition. Then the location is assigned a condition of very poor to very good if that location meets at least 2 of the metrics condition criteria. The condition level is then assigned a numerical value based on its categorisation.

Arguments

• ltmp_cover : Relative Coral Cover with dimensions [timesteps ⋅ locations].
• relative_shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• juvenile_indicator: Relative juvenile cover with dimensions [timesteps ⋅ locations].
• rubble : Relative rubble cover with dimensions [timesteps ⋅ locations].

Returns

Output RCI buffer with dimensions [timesteps ⋅ locations].

References

1. Ryan F. Heneghan, Gabriela Scheufele, Yves-Marie Bozec et al. A framework to inform economic valuation of non-use benefits from coral-reef intervention efforts, 02 October 2025, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-7644150/v1]

reef_condition_index(ltmp_cover::AbstractArray{T,2}, relative_shelter_volume::AbstractArray{T,2}, juvenile_indicator::AbstractArray{T,2})::AbstractArray{T,2} where {T<:AbstractFloat}

Calculate the Reef Condition Index (RCI).

This method uses three inputs: LTMP cover, relative shelter volume, and juvenile indicator.

The RCI is a categorical index assessing the overall health and condition of a reef location based on three key ecological metrics. The index assigns a discrete score (0.1, 0.3, 0.5, 0.7, or 0.9) representing categories from "Very Poor" to "Very Good".

For each input there are five levels of condition ranging from very poor to very good. Then the location is assigned a condition of very poor to very good if that location meets at least two of the metrics condition criteria. The condition level is then assigned a numerical value based on its categorisation.

Arguments

• ltmp_cover : Relative Coral Cover with dimensions [timesteps ⋅ locations].
• relative_shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• juvenile_indicator: Relative juvenile cover with dimensions [timesteps ⋅ locations].

Returns

Output RCI buffer with dimensions [timesteps ⋅ locations].

References

1. Ryan F. Heneghan, Gabriela Scheufele, Yves-Marie Bozec et al. A framework to inform economic valuation of non-use benefits from coral-reef intervention efforts, 02 October 2025, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-7644150/v1]

reef_fish_index!(rc::AbstractArray, out_rfi::AbstractArray)::Nothing

Calculate the Reef Fish Index (RFI) for a single scenario.

Arguments

• rc : Relative coral cover with dimensions [timesteps ⋅ locations].
• out_rfi : Output array buffer for the RFI with dimensions [timesteps ⋅ locations].

reef_fish_index(relative_cover::AbstractArray{T,2},)::AbstractArray{T,2} where {T<:Real}

Calculate the Reef Fish Index (RFI) for a single scenario. The RFI is composed of two linear regressions mapping relative coral cover to structural complexity and finally, structural complexity to fish biomass. The index is based off figure 4a and 6b in Graham et al., 2013 [1]. RFI (kg/km²) as a functional of relative cover ($x$) is given as

\[\begin{align*} \text{SC}(x) &= 1.232 .+ 0.007476 ⋅ x ⋅ 100\\ \text{RFI} &= 0.01 ⋅ (-1623.6 + 1883.3 ⋅ SC), \end{align*}\]

where SC is the structural complexity of the location.

Arguments

• relative_cover : Relative coral cover with dimensions [timesteps ⋅ locations].

Returns

A 2D array of the Reef Fish Index with dimensions [timesteps ⋅ locations].

References

1. Graham, N.A.J., Nash, K.L. The importance of structural complexity in coral reef ecosystems. Coral Reefs 32, 315–326 (2013). https://doi.org/10.1007/s00338-012-0984-y

reef_tourism_index!(relative_cover::AbstractArray{T,2}, shelter_volume::AbstractArray{T,2}, relative_juveniles::AbstractArray{T,2}, rubble::AbstractArray{T,2}, out_rti::AbstractArray{T,2})::Nothing where {T<:AbstractFloat}

Calculate the Reef Tourism Index (RTI) for a single scenario.

This method uses four inputs: relative cover, shelter volume, relative juveniles, and rubble.

Arguments

• relative_cover : Relative coral cover with dimensions [timesteps ⋅ locations].
• shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• relative_juveniles : Relative juvenile cover with dimensions [timesteps ⋅ locations].
• rubble : Rubble as a proportion of location area with dimensions [timesteps ⋅ locations].
• out_rti : Output array buffer for the RTI with dimensions [timesteps ⋅ locations].

reef_tourism_index(relative_cover::AbstractArray{T,2}, shelter_volume::AbstractArray{T,2}, relative_juveniles::AbstractArray{T,2}, rubble::AbstractArray{T,2})::AbstractArray{T,2} where {T<:AbstractFloat}

Calculate the Reef Tourism Index (RTI) for a single scenario. The RTI is the Reef Condition Index made continuous by fitting a linear regression model using relative cover, shelter volume, relative juveniles, and rubble to underpin it.

This method uses four inputs: relative cover, shelter volume, relative juveniles, and rubble.

Arguments

• relative_cover : Relative Coral Cover with dimensions [timesteps ⋅ locations].
• shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• relative_juveniles : Relative juvenile cover with dimensions [timesteps ⋅ locations].
• rubble : Rubble as proportion of location area with dimensions [timesteps ⋅ locations].

Returns

A 2D array of the Reef Tourism Index with dimensions [timesteps ⋅ locations].

reef_tourism_index_no_rubble!(relative_cover::AbstractArray{T,2}, coral_evenness::AbstractArray{T,2}, relative_shelter_volume::AbstractArray{T,2}, relative_juveniles::AbstractArray{T,2}, out_rti::AbstractArray{T,2})::Nothing where {T<:AbstractFloat}

Calculate the Reef Tourism Index (RTI) for a single scenario without rubble as input. This version of the RTI is for ecological models that do not model rubble.

This method uses four inputs: relative cover, coral evenness, relative shelter volume, and relative juveniles.

Arguments

• relative_cover : Relative coral cover with dimensions [timesteps ⋅ locations].
• coral_evenness : Coral evenness with dimensions [timesteps ⋅ locations].
• relative_shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• relative_juveniles : Relative juvenile cover with dimensions [timesteps ⋅ locations].
• out_rti : Output array buffer for the RTI with dimensions [timesteps ⋅ locations].

reef_tourism_index_no_rubble(relative_cover::AbstractArray{T,2}, coral_evenness::AbstractArray{T,2}, relative_shelter_volume::AbstractArray{T,2}, relative_juveniles::AbstractArray{T,2})::AbstractArray{T,2} where {T<:AbstractFloat}

Calculate the Reef Tourism Index (RTI) for a single scenario, without rubble as input. This version of the RTI is for ecological models that do not model rubble.

This method uses four inputs: relative cover, coral evenness, relative shelter volume, and relative juveniles.

The RTI is a continuous version of the Reef Condition Index, fitted with a linear regression model.

Arguments

• relative_cover : Relative coral cover with dimensions [timesteps ⋅ locations].
• coral_evenness : Coral evenness with dimensions [timesteps ⋅ locations].
• relative_shelter_volume : Relative shelter volume with dimensions [timesteps ⋅ locations].
• relative_juveniles : Relative juvenile cover with dimensions [timesteps ⋅ locations].

Returns

A 2D array of the Reef Tourism Index with dimensions [timesteps ⋅ locations].