Update to new output format

examples/24_Output_data.jl

@@ -0,0 +1,119 @@
+# SPDX-License-Identifier: BSD-2-Clause
+
+using DataFrames, CSV, JSON, DataStructures
+
+data = CSV.read("data/Global_plant_climate_envelopes.csv");
+select!(data, Not(:SppID));
+plantlist = JSON.parsefile("data/plant_list_2024-06.json");
+
+species_genus = Dict{String, String}()
+genus_family = Dict{String, String}()
+synonym_to_species = Dict{String, String}()
+species_to_synonyms = Dict{String, Set{String}}()
+binomial_id = Dict{String, Int}()
+name_id = Dict{String, Int}()
+dropped = String[]
+
+df_wfo = DataFrame(rank = String[], binomial = String[], name = String[],
+                   species = Union{Nothing, String}[], genus = Union{Nothing, String}[],
+                   family = Union{Nothing, String}[], order = Union{Nothing, String}[],
+                   phylum = Union{Nothing, String}[], kingdom = Union{Nothing, String}[])
+
+for plant in plantlist
+    if haskey(plant, "role_s")
+        if plant["role_s"] == "accepted"
+            row = (rank = plant["rank_s"], binomial = plant["full_name_string_alpha_s"],
+                   name = plant["full_name_string_plain_s"],
+                   species = get(plant, "placed_in_species_s", nothing),
+                   genus = get(plant, "placed_in_genus_s", nothing),
+                   family = get(plant, "placed_in_family_s", nothing),
+                   order = get(plant, "placed_in_order_s", nothing),
+                   phylum = get(plant, "placed_in_phylum_s", nothing),
+                   kingdom = get(plant, "placed_in_kingdom_s", nothing))
+            if row.rank != "code" && !haskey(binomial_id, row.binomial)
+                push!(df_wfo, row)
+                binomial_id[row.binomial] = nrow(df_wfo)
+                name_id[row.name] = nrow(df_wfo)
+                if row.rank == "species"
+                    species_genus[row.binomial] = row.genus
+                    species_to_synonyms[row.binomial] = Set{String}()
+                elseif plant["rank_s"] == "genus"
+                    genus_family[row.genus] = row.family
+                end
+            end
+        end
+    end
+end
+
+non_species = 0
+for plant in plantlist
+    if haskey(plant, "role_s")
+        if plant["role_s"] == "synonym"
+            if plant["rank_s"] == "species"
+                accepted = plant["accepted_full_name_string_plain_s"]
+                name = plant["full_name_string_alpha_s"]
+                if haskey(binomial_id, accepted)
+                    row = df_wfo[binomial_id[accepted], :]
+                    if row.rank == "species"
+                        if name != accepted && !haskey(binomial_id, name)
+                            synonym_to_species[name] = accepted
+                            push!(species_to_synonyms[accepted], name)
+                        end
+                    elseif row.rank == "subspecies"
+                        label = row.genus * " " * row.species
+                        if name != label && !haskey(binomial_id, name)
+                            synonym_to_species[name] = label
+                            push!(species_to_synonyms[label], name)
+                        end
+                    else
+                        non_species += 1
+                    end
+                elseif haskey(name_id, accepted)
+                    row = df_wfo[name_id[accepted], :]
+                    if row.rank == "species"
+                        if name != row.binomial && !haskey(binomial_id, name)
+                            synonym_to_species[name] = row.binomial
+                            push!(species_to_synonyms[row.binomial], name)
+                        end
+                    elseif row.rank == "subspecies" || row.rank == "variety" || row.rank == "form" || row.rank == "subvariety"
+                        label = row.genus * " " * row.species
+                        if name != label && !haskey(binomial_id, name)
+                            synonym_to_species[name] = label
+                            push!(species_to_synonyms[label], name)
+                        end
+                    else
+                        non_species += 1
+                    end
+                else
+                    push!(dropped, accepted)
+                end
+            end
+        end
+    end
+end
+
+df_climate = copy(data)
+df_climate.species = [get(synonym_to_species, s, s) for s in df_climate.species];
+sort!(df_climate, :species)
+select!(df_climate, Not(:genus))
+select!(df_climate, Not(:family))
+select!(df_climate, Not(:order))
+select!(df_climate, Not(:class))
+select!(df_climate, Not(:phylum))
+spp = df_climate.species;
+duplicates = spp[1:end-1] .== spp[2:end];
+for i in findall(duplicates)
+    n1 = df_climate[i, :numrecords]
+    n2 = df_climate[i+1, :numrecords]
+    for col in names(df_climate)[3:end]
+        df_climate[i, col] = (df_climate[i, col] * n1 +
+                              df_climate[i+1, col] * n2) / (n1 + n2)
+    end
+    df_climate[i+1, :numrecords] = n1 + n2
+end
+push!(duplicates, false);
+deleterows!(df_climate, duplicates);
+@info "Merging $(sum(duplicates)) duplicate species"
+@info "$(nrow(df_climate)) accepted species"
+
+CSV.write("data/climate.csv", df_climate)

examples/Project.toml

@@ -1,12 +1,15 @@
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 ClimatePref = "fca47ed3-1eba-4660-ae9b-41dfe9aa8fbc"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
 JLD = "4138dd39-2aa7-5051-a626-17a0bb65d9c8"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JuliaDB = "a93385a2-3734-596a-9a66-3cfbb77141e6"
 JuliaDBMeta = "2c06ca41-a429-545c-b8f0-5ca7dd64ba19"
 OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"