Merge pull request #29 from open-AIMS/fix-outplant-function

Fix error when setting outplanting levels due to latest RME expecting density as vector
open-AIMS · Dec 12, 2024 · a6d3cfa · a6d3cfa
2 parents 3ffddb8 + 4256add
commit a6d3cfa
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Showing 3 changed files with 115 additions and 63 deletions.
diff --git a/docs/src/getting_started.md b/docs/src/getting_started.md
@@ -211,8 +211,9 @@ reset_rme()  # Reset RME to clear any previous runs
 # Note: if the Julia runtime crashes, check that the specified data file location is correct
 @RME runCreate(name::Cstring, start_year::Cint, end_year::Cint, RCP_scen::Cstring, gcm::Cstring, reps::Cint)::Cint
 
+# Adding dhw tolerance was removed in v1.0.31
 # Add 3 DHW enhancement to outplanted corals
-set_option("restoration_dhw_tolerance_outplants", 3)
+# set_option("restoration_dhw_tolerance_outplants", 3)
 
 # Create a reef set using the target reefs
 @RME reefSetAddFromIdList("iv_example"::Cstring, target_reef_ids::Ptr{Cstring}, length(target_reef_ids)::Cint)::Cint
@@ -303,7 +304,8 @@ for r in 1:reps
 
     # Note: if the Julia runtime crashes, check that the specified data file location is correct
     @RME runCreate(name::Cstring, start_year::Cint, end_year::Cint, RCP_scen::Cstring, gcm::Cstring, 1::Cint)::Cint
-    @RME setOption("restoration_dhw_tolerance_outplants"::Cstring, 3::Cint)::Cint
+    # Adding dhw tolerance was removed in v1.0.31
+    # @RME setOption("restoration_dhw_tolerance_outplants"::Cstring, 3::Cint)::Cint
 
     # Create a reef set using the target reefs
     @RME reefSetAddFromIdList("iv_example"::Cstring, target_reef_ids::Ptr{Cstring}, length(target_reef_ids)::Cint)::Cint

diff --git a/src/deployment.jl b/src/deployment.jl
@@ -1,41 +1,59 @@
 """
-    deployment_area(n_corals::Int64, max_n_corals::Int64, density::Float64, target_areas::Vector{Float64})::Tuple{Float64,Float64}
+    rme_version_info()::@NamedTuple{major::Int64, minor::Int64, patch::Int64}
+
+Get RME version
+"""
+function rme_version_info()::@NamedTuple{major::Int64, minor::Int64, patch::Int64}
+    rme_ver = @RME version()::Cstring
+    rme_ver = parse.(Int64, split(rme_ver, '.'))
+    return (major=rme_ver[1], minor=rme_ver[2], patch=rme_ver[3])
+end
+
+"""
+    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
+- `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]
 """
-function deployment_area(n_corals::Int64, max_n_corals::Int64, density::Float64, target_areas::Vector{Float64})::Tuple{Float64,Float64}
+function 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}}}
     req_area = area_needed(max_n_corals, density)
 
     # Divide by half (i.e., `* 0.5`) as RME simulates two deployments per year
-    mod_density = (n_corals * 0.5) / (req_area / m2_TO_km2)
-    deployment_area_pct = min((req_area / sum(target_areas)) * 100.0, 100.0)
+    mod_density = area_needed(n_corals, req_area)
+    summed_req_area = sum(req_area)
+    deployment_area_pct = min((summed_req_area / sum(target_areas)) * 100.0, 100.0)
 
     # Adjust grid size if needed to simulate deployment area/percent
     min_cells::Int64 = 3
-    if (RME_BASE_GRID_SIZE[] * req_area / sum(target_areas)) < min_cells
+    if (RME_BASE_GRID_SIZE[] * summed_req_area / sum(target_areas)) < min_cells
         # Determine new grid resolution in terms of number of N by N cells
-        target_grid_size::Float64 = 3.0 * sum(target_areas) / req_area
+        target_grid_size::Float64 = 3.0 * (sum(target_areas) / summed_req_area)
         cell_res::Int64 = ceil(Int64, sqrt(target_grid_size))  # new cell resolution
 
         # RME supported cell sizes (N by N)
         # Determine smallest appropriate grid size when larger grid sizes are set.
         # Larger grid sizes = greater cell resolution, incurring larger runtime costs.
         p::Vector{Int64} = Int64[10, 20, 25, 30, 36, 43, 55, 64, 85, 100]
         n_cells::Int64 = try
-            first(p[p.>=cell_res])
+            first(p[p .>= cell_res])
         catch
-            p[end-1]
+            p[end - 1]
         end
 
         RME_BASE_GRID_SIZE[] = n_cells * n_cells
@@ -49,16 +67,19 @@ function deployment_area(n_corals::Int64, max_n_corals::Int64, density::Float64,
 end
 
 """
-    deployment_area(max_n_corals::Int64, target_areas::Vector{Float64})::Tuple{Float64,Float64}
+    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 to maintain the specified grid size.
 """
-function deployment_area(max_n_corals::Int64, target_areas::Vector{Float64})::Tuple{Float64,Float64}
-
+function deployment_area(
+    max_n_corals::Int64,
+    target_areas::Vector{Float64}
+)::Union{Tuple{Float64,Float64},Tuple{Float64,Vector{Float64}}}
     min_cells::Int64 = 3
-    density::Float64 = 0.0
+    density = 0.0
     req_area::Float64 = 0.0
+
     for d in reverse(0.05:0.1:13.0)
         req_area = area_needed(max_n_corals, d)
 
@@ -71,18 +92,29 @@ function deployment_area(max_n_corals::Int64, target_areas::Vector{Float64})::Tu
     end
 
     if density == 0.0
-        throw(DomainError("Could not determine adequate deployment density: $((RME_BASE_GRID_SIZE[] * req_area / sum(target_areas)))"))
+        throw(
+            DomainError(
+                "Could not determine adequate deployment density: $((RME_BASE_GRID_SIZE[] *sum(req_area) / sum(target_areas)))"
+            )
+        )
     end
 
     @info "Determined min. deployment density to be: $(density) / m²"
-
     deployment_area_pct = min((req_area / sum(target_areas)) * 100.0, 100.0)
 
+    # In RME versions higher than 1.0.28 density needs to be a vector with each element representing density per species
+    rme_version = rme_version_info()
+    density =
+        if (rme_version.major == 1)&&(rme_version.minor == 0)&&(rme_version.patch <= 28)
+            density
+        else
+            fill(density, 6)
+        end
     return deployment_area_pct, density
 end
 
 """
-    set_outplant_deployment!(name::String, reefset::String, n_corals::Int64, year::Int64, area_km2::Vector{Float64}, density::Float64)::Nothing
+    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.
 
@@ -100,13 +132,15 @@ function set_outplant_deployment!(
     n_corals::Int64,
     year::Int64,
     area_km2::Vector{Float64},
-    density::Float64
+    density::Union{Float64, Vector{Float64}}
 )::Nothing
-    set_outplant_deployment!(name, reefset, n_corals, n_corals, year, year, 1, area_km2, density)
+    return set_outplant_deployment!(
+        name, reefset, n_corals, n_corals, year, year, 1, area_km2, density
+    )
 end
 
 """
-    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::Float64)::Nothing
+    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.
 
@@ -130,15 +164,30 @@ function set_outplant_deployment!(
     last_year::Int64,
     year_step::Int64,
     area_km2::Vector{Float64},
-    density::Float64
+    density::Union{Vector{Float64},Float64}
 )::Nothing
     iv_type = "outplant"
 
     area_pct, mod_density = deployment_area(n_corals, max_effort, density, area_km2)
 
-    @RME ivAdd(name::Cstring, iv_type::Cstring, reefset::Cstring, first_year::Cint, last_year::Cint, year_step::Cint)::Cint
+    @RME ivAdd(
+        name::Cstring,
+        iv_type::Cstring,
+        reefset::Cstring,
+        first_year::Cint,
+        last_year::Cint,
+        year_step::Cint
+    )::Cint
     @RME ivSetOutplantAreaPct(name::Cstring, area_pct::Cdouble)::Cint
-    @RME ivSetOutplantCountPerM2(name::Cstring, mod_density::Cdouble)::Cint
+
+    rme_version = rme_version_info()
+    if !((rme_version.major == 1)&&(rme_version.minor == 0)&&(rme_version.patch <= 28))
+        @RME ivSetOutplantCountPerM2(
+            name::Cstring, mod_density::Vector{Cdouble}, length(mod_density)::Cint
+        )::Cint
+    else
+        @RME ivSetOutplantCountPerM2(name::Cstring, mod_density::Cdouble)::Cint
+    end
 
     return nothing
 end
@@ -163,19 +212,11 @@ function set_outplant_deployment!(
     year::Int64,
     area_km2::Vector{Float64}
 )::Nothing
-    set_outplant_deployment!(name, reefset, n_corals, year, year, 1, area_km2)
+    return set_outplant_deployment!(name, reefset, n_corals, year, year, 1, area_km2)
 end
 
 """
-    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_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.
@@ -187,28 +228,36 @@ function set_outplant_deployment!(
     first_year::Int64,
     last_year::Int64,
     year_step::Int64,
-    area_km2::Vector{Float64},
+    area_km2::Vector{Float64}
 )::Nothing
     iv_type = "outplant"
 
     area_pct, mod_density = deployment_area(max_effort, area_km2)
 
-    @RME ivAdd(name::Cstring, iv_type::Cstring, reefset::Cstring, first_year::Cint, last_year::Cint, year_step::Cint)::Cint
+    @RME ivAdd(
+        name::Cstring,
+        iv_type::Cstring,
+        reefset::Cstring,
+        first_year::Cint,
+        last_year::Cint,
+        year_step::Cint
+    )::Cint
     @RME ivSetOutplantAreaPct(name::Cstring, area_pct::Cdouble)::Cint
-    @RME ivSetOutplantCountPerM2(name::Cstring, mod_density::Cdouble)::Cint
+
+    rme_version = rme_version_info()
+    if !((rme_version.major == 1)&&(rme_version.minor == 0)&&(rme_version.patch <= 28))
+        @RME ivSetOutplantCountPerM2(
+            name::Cstring, mod_density::Vector{Cdouble}, length(mod_density)::Cint
+        )::Cint
+    else
+        @RME ivSetOutplantCountPerM2(name::Cstring, mod_density::Cdouble)::Cint
+    end
 
     return nothing
 end
 
 """
-    set_enrichment_deployment!(
-        name::String,
-        reefset::String,
-        n_larvae::Int64,
-        year::Int64,
-        area_km2::Vector{Float64},
-        density::Float64
-    )::Nothing
+    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.
@@ -221,21 +270,13 @@ function set_enrichment_deployment!(
     area_km2::Vector{Float64},
     density::Float64
 )::Nothing
-    set_enrichment_deployment!(name, reefset, n_larvae, n_larvae, year, year, 1, area_km2, density)
+    return set_enrichment_deployment!(
+        name, reefset, n_larvae, n_larvae, year, year, 1, area_km2, density
+    )
 end
 
 """
-    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_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.
 """
@@ -254,7 +295,14 @@ function set_enrichment_deployment!(
 
     area_pct, mod_density = deployment_area(n_larvae, max_effort, density, area_km2)
 
-    @RME ivAdd(name::Cstring, iv_type::Cstring, reefset::Cstring, first_year::Cint, last_year::Cint, year_step::Cint)::Cint
+    @RME ivAdd(
+        name::Cstring,
+        iv_type::Cstring,
+        reefset::Cstring,
+        first_year::Cint,
+        last_year::Cint,
+        year_step::Cint
+    )::Cint
     @RME ivSetEnrichAreaPct(name::Cstring, area_pct::Cdouble)::Cint
     @RME ivSetEnrichCountPerM2(name::Cstring, mod_density::Cdouble)::Cint
 

diff --git a/src/interface.jl b/src/interface.jl
@@ -1,11 +1,13 @@
 """
-    area_needed(n_corals::Int64, density::Float64)::Float64
+    area_needed(n_corals::Int64, density::Union{Float64,Vector{Float64}})::Union{Vector{Float64},Float64}
 
-Determine area (in km²) needed to deploy the given number of corals at the specified density.
+Determine area (in km²) needed to deploy the given the number of corals at the specified density.
 """
-function area_needed(n_corals::Int64, density::Float64)::Float64
+function area_needed(
+    n_corals::Int64, density::Union{Float64,Vector{Float64}}
+)::Union{Vector{Float64},Float64}
     # ReefMod deploys twice a year so halve the number of corals to deploy
-    return ((n_corals * 0.5) / density) * m2_TO_km2  # Convert m² to km²
+    return ((n_corals * 0.5) ./ density) .* m2_TO_km2  # Convert m² to km²
 end
 
 """
@@ -15,7 +17,7 @@ Get list of reef ids in the order expected by ReefMod Engine.
 """
 function reef_ids()::Vector{String}
     n_reefs = 3806
-    reef_id_list = fill("", n_reefs);
+    reef_id_list = fill("", n_reefs)
 
     for i in 1:n_reefs
         reef_id_list[i] = @RME reefId(i::Cint)::Cstring