API

ReefModEngine.DataCube Method

DataCube(data::AbstractArray; kwargs...)::YAXArray

Constructor for YAXArray. When used with axes_names, the axes labels will be UnitRanges from 1 up to that axis length.

Arguments

• data : Array of data to be used when building the YAXArray

• axes_names :

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ReefModEngine._check_deprecated_options Method

_check_deprecated_options(opt::String)::String

Checks option string and updates to latest (renamed) equivalent.

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ReefModEngine._run_batch Method

run_batch(batch_idx::Int64, batch_start::Int64, batch_size::Int64, reps::Int64, rme_results_dir::String, start_year::Int64, end_year::Int64, RCP_scen::String, gcm::String, result_store)::Nothing

Run one batch of repetitions using RME.

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ReefModEngine.append_scenarios! Method

append_scenarios!(rs::ResultStore, reps::Int)::Nothing

Add rows to scenario dataframe in result store.

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ReefModEngine.area_needed Method

area_needed(n_corals::Int64, density::Union{Float64,Vector{Float64}})::Union{Vector{Float64},Float64}

Determine area (in km²) needed to deploy the given the number of corals at the specified density.

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ReefModEngine.concat_RME_datasets Method

concat_RME_datasets(datasets::Vector{Dataset})

Combine RME result datasets along the scenarios dimension to combine scenarios that have been run separately into a single dataset.

Example

results_dataset_300scens = concat_RME_netcdfs( results_dataset_200scens, results_dataset_50scens, results_dataset_50scens )

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ReefModEngine.concat_results! Method

concat_results!(rs::ResultStore, start_year::Int64, end_year::Int64, reps::Int64)::Nothing

Append results for all runs/replicates.

Arguments

• rs : Result store to save data to

• start_year : Collect data from this year

• end_year : Collect data to this year

• reps : Total number of expected replicates

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ReefModEngine.concat_separate_reps Method

concat_separate_reps(results_store_1::ResultStore, result_store_s::ResultStore...)

Concatenate ResultStores that have been saved separately along the scenarios axis. Intended use: When additional scenarios have been run after saving an initial scenario set. All variables and factors such as start_year, end_year, n_reefs must be identical across ResultStores.

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ReefModEngine.create_dataset Method

create_dataset(start_year::Int, end_year::Int, n_reefs::Int, reps::Int)::Dataset

Preallocate and create dataset for result variables. Only constructed when the first results are collected.

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ReefModEngine.deployment_area Method

deployment_area(n_corals::Int64, max_n_corals::Int64, density::Union{Float64, Vector{Float64}}, target_areas::Vector{Float64})::Union{Tuple{Float64,Float64},Tuple{Float64,Vector{Float64}}}

Determine deployment area for the expected number of corals to be deployed.

Arguments

• n_corals : Number of corals,

• max_n_corals : Expected maximum deployment effort (total number of corals in intervention set)

• density : Stocking density per m². In RME versions higher than v1.0.28 density needs to be a vector with each element representing the density per functional group

• target_areas : Available area at target location(s)

Returns

Tuple

• Percent area of deployment

• modified stocking density [currently no modifications are made]

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ReefModEngine.deployment_area Method

deployment_area(max_n_corals::Int64, target_areas::Vector{Float64})::Union{Tuple{Float64,Float64}, Tuple{Float64,Vector{Float64}}}

Determine deployment area for given number of corals and target area, calculating the appropriate deployment density, limiting deployment density to be <40m2 for each coral species.

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ReefModEngine.get_iv_param Method

get_iv_param(iv_name::String, param_name::String)

Return the current value of a parameter of an intervention.

Returns parameter param_name of intervention iv_name. The returned value can either be a number or text depending on the type of parameter. If the intervention does not exist, parameter is not recognized, or value is of the wrong type, an error will be thrown.

Currently supported values for param_name are:

• "second_rs": Secondary reef set name or empty string

• "hours": Number of hours effort

• "rank_data_code1": Data code to rank by or "none"

• "rank_data_code2": Data code to rank by or "none"

• "rank_weight1": Weight for first rank data (0-1)

• "rank_weight2": Weight for second rank data (0-1)

Examples

<Badge type="info" class="source-link" text="source"><a href="https://github.com/open-AIMS/ReefModEngine.jl/blob/2ee6362ac32b7d4779cf94a959b33454646384cc/src/interface.jl#L137-L159" target="_blank" rel="noreferrer">source</a></Badge>

</details>

<details class='jldocstring custom-block' open>
<summary><a id='ReefModEngine.get_param-Tuple{String}' href='#ReefModEngine.get_param-Tuple{String}'><span class="jlbinding">ReefModEngine.get_param</span></a> <Badge type="info" class="jlObjectType jlMethod" text="Method" /></summary>



```julia
get_param(name::String)::Union{Float64,Vector{Float64}}

Return the current value(s) of an RME parameter.

The returned value will be a vector of length 1 or greater.

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ReefModEngine.init_rme Method

init_rme(rme_path::String)::Nothing

Initialize ReefMod Engine for use.

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ReefModEngine.iv_add Method

iv_add(name::String, type::String, reef_set::String, first_year::Int, last_year::Int, year_step::Int, area_pct::Float64, count_per_m2::Union{Float64, Vector{Float64}})

Add an outplant or enrich intervention with deployment parameters.

Additional Arguments for "outplant" and "enrich" types

• area_pct: Percentage of reef area where restoration will occur

• count_per_m2: Corals to add per m² (scalar or 6-element vector for each species)

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ReefModEngine.iv_add Method

iv_add(name::String, type::String, reef_set::String, first_year::Int, last_year::Int, year_step::Int)

Add an intervention to the current run.

Arguments

• name: Name of the intervention (must be unique)

• type: Type of intervention (see types below)

• reef_set: Name of reef set to apply intervention to

• first_year: First year intervention will be applied

• last_year: Last year intervention will be applied

• year_step: Frequency (1=every year, 2=every other year, etc.)

Intervention Types

• cots_control: CSIRO method CoTS control algorithm

• cots_control_basic: Original CoTS control method

• prevent_anchoring: Not implemented (no effect)

• prevent_herbivore_exploitation: Prevent herbivore exploitation

• stabilise: Rubble stabilization

• outplant: Coral outplanting (requires additional parameters)

• enrich: Larval enrichment (requires additional parameters)

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ReefModEngine.load_result_store Method

load_result_store(dir_name::String, n_reps::Int64)::ResultStore

Save ResultStore from saved results.nc and scenarios.csv files to allow modification.

Arguments

• dir_name : Directory where result store files are held.

• n_reps : The number of reps held in resultstore (should not include duplicate reps for counterfactual-only runs).

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ReefModEngine.log_get_reef_data_int Method

log_get_reef_data_int(name::String, reef_index::Int, repeat::Int, iter::Int)

Get reef-level log data from intervention run.

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ReefModEngine.log_get_reef_data_ref Method

log_get_reef_data_ref(name::String, reef_index::Int, repeat::Int, iter::Int)

Get reef-level log data from reference run.

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ReefModEngine.log_get_run_data_int Method

log_get_run_data_int(name::String, repeat::Int, iter::Int)

Get run-level log data from intervention run.

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ReefModEngine.log_get_run_data_ref Method

log_get_run_data_ref(name::String, repeat::Int, iter::Int)

Get run-level log data from reference run.

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ReefModEngine.log_set_all_items_enabled Method

log_set_all_items_enabled(enabled::Bool)

Enable or disable logging of all data items.

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ReefModEngine.log_set_all_reefs_enabled Method

log_set_all_reefs_enabled(enabled::Bool)

Enable or disable logging for all reefs.

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ReefModEngine.log_set_item_enabled Method

log_set_item_enabled(name::String, enabled::Bool)

Enable or disable logging of specific data item.

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ReefModEngine.log_set_reef_enabled Method

log_set_reef_enabled(reef_index::Int, enabled::Bool)

Enable or disable logging for specific reef.

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ReefModEngine.match_id Method

match_id(id::String)::Int64
match_ids(ids::Vector{String})::Vector{Int64}

Find matching index position for the given ID(s) according to ReefMod Engine's reef list.

Note

ReefMod Engine's reef list is in all upper case. The provided IDs are converted to upper case to ensure a match.

Examples

julia> reef_ids()
# 3806-element Vector{String}:
#  "10-330"
#  "10-331"
#  ⋮
#  "23-048"
#  "23-049"

julia> match_id("10-330")
#  1

julia> match_id("23-049")
#  3806

julia> match_ids(["23-048", "10-331"])
#  3805
#  2

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ReefModEngine.n_corals_calculation Method

n_corals_calculation(count_per_year::Float64, target_reef_area_km²::Vector{Float64})::Int64

Calculate total number of corals deployed in an intervention.

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ReefModEngine.preallocate_concat! Method

preallocate_concat(rs, start_year, end_year, reps::Int64)::Nothing

Allocate additional memory before adding an additional result set. Result sets must have the same time frame.

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ReefModEngine.rebuild_RME_dataset Method

rebuild_RME_dataset(
    rs_dataset::Dataset,
    start_year::Int64,
    end_year::Int64,
    n_reefs::Int64,
    n_reps::Int64,
    unique_indices::Vector{Int64}
)

Rebuild a RME dataset that has duplicated scenarios. For example, when RME outputs counterfactual runs with duplicate scenario data.

Arguments

• rs_dataset : The RME dataset with duplicated scenarios.

• start_year : Start year of timesteps dimension.

• end_year : End year of timesteps dimension.

• location_ids : Location IDs to be held in sites dimension.

• n_reps : The intended number of scenarios that should be in the returned dataset (after removing duplicate scenarios).

• unique_indices : The first index of each unique scenario to keep (excludes indices of duplicate scenarios).

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ReefModEngine.reef_areas Method

reef_areas(id_list)

Retrieve reef areas in km² for specified locations.

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ReefModEngine.reef_areas Method

reef_areas()

Retrieve all reef areas in km²

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ReefModEngine.reef_ids Method

reef_ids()::Vector{String}

Get list of reef ids in the order expected by ReefMod Engine.

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ReefModEngine.remove_duplicate_reps Method

remove_duplicate_reps(result_store::ResultStore, n_reps::Int64)

Find the indices of unique scenarios when there are duplicated scenarios and rebuild the scenarios axis in rebuild_RME_dataset() to contain only a single copy of unique scenarios.

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ReefModEngine.reset_rme Method

reset_rme()

Reset ReefModEngine, clearing any and all interventions and reef sets.

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ReefModEngine.rme_version_info Method

rme_version_info()::VersionNumber

Get RME version.

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ReefModEngine.run_init Method

run_init()::Nothing

Convenience function to initialize RME runs.

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ReefModEngine.run_rme Method

run_rme(rme_path::String, n_threads::Int64, reps::Int64, result_path::String; start_year::Int64=2022, end_year::Int64=2099, batch_size::Int64=10, start_batch::Int64=1, RCP_scen::String="SSP 2.45", gcm::String="CNRM_ESM2_1", rnd_seed::Int64=1234)::Nothing

Run counterfactual scenarios with ReefModEngine.jl and save result set to desired directory.

Arguments

• rme_path : Path to REM folder.

• n_threads : Number of threads to be used with RME.

• reps : Total number of repetitions to be run.

• result_path : Path to folder where resultset should be placed.

• start_year : RME run start year.

• end_year : RME run end year.

• batch_size : Number of repetitions to be run in each batch.

• RCP_scen : RCP scenario to be used for RME runs.

• gcm : GCM to be used for RME runs.

• rnd_seed : Random seed.

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ReefModEngine.save_result_store Method

save_result_store(dir_name::String, result_store::ResultStore)::Nothing

Save results to a netcdf file and a dataframe containing the scenario runs. Saved to the given directory. The directory is created if it does not exit.

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ReefModEngine.set_enrichment_deployment! Method

set_enrichment_deployment!(name::String, reefset::String, n_larvae::Int64, max_effort::Int64, first_year::Int64, last_year::Int64, year_step::Int64, area_km2::Vector{Float64}, density::Float64)::Nothing

Set deployment for multiple years at a given frequency.

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ReefModEngine.set_enrichment_deployment! Method

set_enrichment_deployment!(name::String, reefset::String, n_larvae::Int64, year::Int64, area_km2::Vector{Float64}, density::Float64)::Nothing

As set_seeding_deployment() but for larvae enrichment (also known as assisted migration). Set deployment for a single target year.

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ReefModEngine.set_iv_param Method

set_iv_param(name::String, value::Union{Float64, Int64})::Nothing
set_iv_param(name::String, value::Vector{Float64})::Nothing
set_iv_param(name::String, value::String)::Nothing
set_iv_param(iv_name::String, param_name::String, value::String)::Nothing
set_iv_param(iv_name::String, param_name::String, value::Union{Float64, Int64})::Nothing

Set RME intervention parameter by name.

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ReefModEngine.set_option Method

set_option(opt::String, val::Float64)
set_option(opt::String, val::Int)
set_option(opt::String, val::String)

Set RME option.

See RME documentation for full list of available options.

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ReefModEngine.set_outplant_deployment! Method

set_outplant_deployment!(name::String, reefset::String, n_corals::Int64, max_effort::Int64, first_year::Int64, last_year::Int64, year_step::Int64, area_km2::Vector{Float64}, density::Union{Vector{Float64}, Float})::Nothing

Set outplanting deployments across a range of years.

Arguments

• name : Name to assign intervention event

• reefset : Name of pre-defined list of reefs to intervene on

• n_corals : Number of corals to outplant for a given year

• max_effort : Total number of corals to outplant

• first_year : First year to start interventions

• last_year : Final year of interventions

• year_step : Frequency of intervention (1 = every year, 2 = every second year, etc)

• area_km2 : Intervention area [km²]

• density : Stocking density of intervention [corals / m²]

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ReefModEngine.set_outplant_deployment! Method

set_outplant_deployment!(name::String, reefset::String, max_effort::Int64, first_year::Int64, last_year::Int64, year_step::Int64, area_km2::Vector{Float64})::Nothing

Set outplanting deployments across a range of years, automatically determining the coral deployment density to maintain the set grid size.

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ReefModEngine.set_outplant_deployment! Method

set_outplant_deployment!(name::String, reefset::String, n_corals::Int64, year::Int64, area_km2::Vector{Float64}, density::Union{Float64, Vector{Float64}})::Nothing

Set outplanting deployments for a single year.

Arguments

• name : Name to assign intervention event

• reefset : Name of pre-defined list of reefs to intervene on

• n_corals : Number of corals to outplant

• year : Year to intervene

• area_km2 : Area to intervene [km²]

• density : Stocking density of intervention [corals / m²]

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ReefModEngine.set_outplant_deployment! Method

set_outplant_deployment!(name::String, reefset::String, n_corals::Int64, year::Int64, area_km2::Vector{Float64})::Nothing

Set outplanting deployments for a single year, automatically determining the coral deployment density to maintain the set grid size.

Arguments

• name : Name to assign intervention event

• reefset : Name of pre-defined list of reefs to intervene on

• n_corals : Number of corals to outplant

• year : Year to intervene

• area_km2 : Area to intervene [km²]

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ReefModEngine.set_outplant_tolerance! Method

set_outplant_tolerance!(
    iv_name::String,
    dhw_mean::Float64,
    dhw_std::Float64;
    n_groups=6
)

set_outplant_tolerance!(
    iv_name::String,
    dhw_mean::Vector{Float64},
    dhw_std::Vector{Float64};
    n_groups=6
)

Set heat tolerance of outplanting interventions.

Arguments

• iv_name: Name of defined deployment as set by set_outplant_deployment!()

• dhw_mean: Mean of DHW tolerance (for each coral functional group)

• dhw_std: Standard deviation of DHW tolerance (for each coral functional group)

• n_groups: Number of coral groups (default: 6). This should not change unless RME adds more coral groups.

Returns

Nothing

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ReefModEngine.@getRME Macro

Only for use when RME functions return numeric results that are not error codes.

Examples

count_per_m2::Float64 = @getRME ivOutplantCountPerM2("iv_name"::Cstring)::Cdouble

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