Merge pull request #33 from EcoJulia/mkb/location_refactor

Adapt to new EcoBase.AbstractPlaces

Manifest.toml

@@ -23,9 +23,9 @@ version = "0.5.1"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "ec61a16eed883ad0cfa002d7489b3ce6d039bb9a"
+git-tree-sha1 = "49269e311ffe11ac5b334681d212329002a9832a"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "1.4.0"
+version = "1.5.1"
 
 [[DataFrames]]
 deps = ["CategoricalArrays", "CodecZlib", "Compat", "DataStreams", "Dates", "InteractiveUtils", "IteratorInterfaceExtensions", "LinearAlgebra", "Missings", "Printf", "Random", "Reexport", "SortingAlgorithms", "Statistics", "StatsBase", "TableTraits", "Tables", "Test", "TranscodingStreams", "Unicode", "WeakRefStrings"]
@@ -47,9 +47,9 @@ version = "0.4.1"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections", "Random", "Serialization", "Test"]
-git-tree-sha1 = "8fc6e166e24fda04b2b648d4260cdad241788c54"
+git-tree-sha1 = "ca971f03e146cf144a9e2f2ce59674f5bf0e8038"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.14.0"
+version = "0.15.0"
 
 [[Dates]]
 deps = ["Printf"]
@@ -65,9 +65,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[EcoBase]]
 deps = ["Compat", "RecipesBase"]
-git-tree-sha1 = "7d05be63ecb77148b3807c89b8977d6397499618"
+path = "/Users/michael/.julia/dev/EcoBase"
 uuid = "a58aae7d-b440-5a11-b283-399458f99aac"
-version = "0.0.4"
+version = "0.0.4+"
 
 [[Future]]
 deps = ["Random"]
@@ -102,9 +102,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[Missings]]
 deps = ["Dates", "InteractiveUtils", "SparseArrays", "Test"]
-git-tree-sha1 = "adc26d2ee85a49c413464110d922cf21efc9d233"
+git-tree-sha1 = "d1d2585677f2bd93a97cfeb8faa7a0de0f982042"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "0.3.1"
+version = "0.4.0"
 
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
@@ -201,10 +201,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 version = "0.4.1"
 
 [[Tables]]
-deps = ["Requires", "Test"]
-git-tree-sha1 = "940944e6b68a35046282897a2218891c7cf14a32"
+deps = ["IteratorInterfaceExtensions", "LinearAlgebra", "Requires", "TableTraits", "Test"]
+git-tree-sha1 = "37be2ed169d5771c1ac8d516d3bcb0093c49966e"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "0.1.12"
+version = "0.1.15"
 
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
@@ -225,6 +225,6 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[WeakRefStrings]]
 deps = ["Missings", "Random", "Test"]
-git-tree-sha1 = "1087e8be380f2c8b96434b02bb1150fc1c511135"
+git-tree-sha1 = "bccf012a0e8815410ad8b6846944a33903992fc3"
 uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
-version = "0.5.3"
+version = "0.5.6"

REQUIRE

@@ -4,7 +4,7 @@ RecipesBase
 DataFrames 0.15
 DataFramesMeta
 StatsBase
-EcoBase 0.0.4
+EcoBase 0.0.5
 RandomBooleanMatrices 0.1.1
 RandomNumbers
 #Phylo

src/Constructor_helperfunctions.jl

@@ -133,7 +133,7 @@ function createsitenames(coords::DataFrames.DataFrame)
 end
 
 creategrid(coords::AbstractMatrix{<:Union{AbstractFloat, Missing}}, tolerance = sqrt(eps())) =
-    GridTopology(gridvar(coords[:,1], tolerance)..., gridvar(coords[:,2], tolerance)...)
+    GridTopology(gridvar(coords[:,1], tolerance), gridvar(coords[:,2], tolerance))
 
 # could allow for n-dimensional binning, using code from StatsBase.Histogram
 function gridvar(x, tolerance = sqrt(eps()))
@@ -158,11 +158,11 @@ function gridvar(x, tolerance = sqrt(eps()))
   min = minimum(sux)
   cellnumber = round(Int, maxrange(sux) / cellsize) + 1
 
-  min, cellsize, cellnumber
+  range(min, step = cellsize, length = cellnumber)
 end
 
 function getindices(coords::AbstractMatrix{<:Union{AbstractFloat, Missing}}, grid::GridTopology, tolerance = 2*sqrt(eps()))
-  index1 = 1 .+ floor.(Int,(coords[:,1] .- grid.xmin) ./ grid.xcellsize .+ tolerance)
-  index2 = 1 .+ floor.(Int,(coords[:,2] .- grid.ymin) ./ grid.ycellsize .+ tolerance)
+  index1 = 1 .+ floor.(Int,(coords[:,1] .- xmin(grid)) ./ xcellsize(grid) .+ tolerance)
+  index2 = 1 .+ floor.(Int,(coords[:,2] .- ymin(grid)) ./ ycellsize(grid) .+ tolerance)
   hcat(index1, index2)
 end

src/Constructors.jl

@@ -56,7 +56,7 @@ function Assemblage(site::P, occ::SpeciesData{D};
 end
 
 function createLocations(coords::AbstractMatrix, cdtype::coordstype = auto,  #by design, this is not type stable, but maybe that is OK for type constructors
-        sitestat = DataFrames.DataFrame(sites = sitenames(occ)))
+        sitestat = DataFrames.DataFrame(sites = 1:size(coords, 1)))
 
     cdtype == pointdata && return Locations{PointData}(PointData(coords), sitestat)
     cdtype == griddata && return Locations{GridData}(GridData(coords), sitestat)

src/DataTypes.jl

@@ -4,25 +4,21 @@
 # Insertion point for defining my own functions. They are mainly abstract
 # over the full type and it's view, so another possibility would be to
 # implement with unions
-abstract type SESpatialData <: EcoBase.AbstractPlaces end
-abstract type SELocations <: EcoBase.AbstractLocations end
+abstract type SESpatialData{T<:EcoBase.AbstractLocationData} <: EcoBase.AbstractPlaces{T} end
+abstract type SELocations{T<:EcoBase.AbstractLocationData} <: EcoBase.AbstractPlaces{T} end
 abstract type SEThings{D <: Real} <: EcoBase.AbstractThings end
 abstract type SEGrid <: EcoBase.AbstractGrid end
-abstract type SEPointData end
+abstract type SEPoints <: EcoBase.AbstractPoints end
 
-abstract type AbstractComMatrix{ D<:Real } end
+abstract type AbstractComMatrix{D<:Real} end
 
 
 # I could implement sitestats as a Dict with several DataFrames to make space for big data sets, but I prefer to not do this now. Example below.
 
 # I could do a lot more with immutable types if I had a clearer view/copy implementation
 mutable struct GridTopology <: EcoBase.AbstractGrid
-    xmin::Number
-    xcellsize::Number
-    xcells::Int
-    ymin::Number
-    ycellsize::Number
-    ycells::Int
+    xs::StepRangeLen{Float64}
+    ys::StepRangeLen{Float64}
 end
 
 mutable struct Bbox
@@ -33,7 +29,7 @@ mutable struct Bbox
 end
 
 # Do I need sitenames here? I think so, they should match those in sitestats, and be separate
-mutable struct PointData <: SEPointData
+mutable struct PointData <: SEPoints
     coords::Matrix{Float64}
 end
 
@@ -42,7 +38,7 @@ mutable struct GridData <: SEGrid
     grid::GridTopology
 end
 
-mutable struct Locations{T<:Union{GridData, PointData}} <: SELocations
+mutable struct Locations{T<:Union{GridData, PointData}} <: SELocations{T}
     coords::T
     sitestats::DataFrames.DataFrame
     function Locations{T}(coords, sitestats = DataFrames.DataFrame(id = 1:size(coords,1))) where T
@@ -73,8 +69,8 @@ end
 SpeciesData(commatrix::ComMatrix{D}, traits) where D<:Real = SpeciesData{D}(commatrix, traits)
 
 # Not really sure what this type is for
-mutable struct SiteData{S} <: SESpatialData where S <: Locations
-    site::S
+mutable struct SiteData{T<:Union{GridData, PointData}} <: SESpatialData{T}
+    site::T
 end
 
 abstract type SEAssemblage{D<:Real, T<:SEThings, P<:SELocations} <: EcoBase.AbstractAssemblage{D, T, P} end

src/DispersionFields.jl

@@ -1,10 +1,10 @@
 
-mutable struct DispersionField <: SESpatialData
+mutable struct DispersionField{T} <: SESpatialData{T}
     site::SELocations
     DFmat::Matrix{Int}
 
     function DispersionField(asm::Assemblage)
         df = asm.occ.occurrences' * asm.occ.occurrences
-        new(asm.site, df)
+        new{typeof(asm.site.coords)}(asm.site, df)
     end
 end

src/GetandSetdata.jl

@@ -1,6 +1,6 @@
 coordinates(asm::SEAssemblage) = coordinates(asm.site)
 coordinates(sd::SiteData) = coordinates(sd.site)
-coordinates(pd::SEPointData) = pd.coords
+coordinates(pd::SEPoints) = pd.coords
 coordinates(l::SELocations) = coordinates(getcoords(l))
 function coordinates(gd::SEGrid)
     index1 = xrange(gd.grid)[gd.indices[:,1]]

src/Gridfunctions.jl

@@ -1,11 +1,11 @@
-xmin(g::GridTopology) = g.xmin
-ymin(g::GridTopology) = g.ymin
-xcellsize(g::GridTopology) = g.xcellsize
-ycellsize(g::GridTopology) = g.ycellsize
-xcells(g::GridTopology) = g.xcells
-ycells(g::GridTopology) = g.ycells
+xmin(g::GridTopology) = minimum(g.xs)
+ymin(g::GridTopology) = minimum(g.ys)
+xcellsize(g::GridTopology) = step(g.xs)
+ycellsize(g::GridTopology) = step(g.ys)
+xcells(g::GridTopology) = length(g.xs)
+ycells(g::GridTopology) = length(g.ys)
 indices(g::SEGrid) = g.indices
-indices(g::SEGrid, idx) = g.indices[:,idx] 
+indices(g::SEGrid, idx) = g.indices[:,idx]
 boundingbox(g::GridTopology) = Bbox(xmin(g), xmax(g), ymin(g), ymax(g))
 
 @forward_func GridData.grid xmin, ymin, xcellsize, ycellsize, cellsize, xcells, ycells, cells, xrange, yrange, xmax, ymax, boundingbox

src/Subsetting.jl

@@ -19,11 +19,11 @@ mutable struct SubGridData <: SEGrid
     grid::GridTopology
 end
 
-mutable struct SubPointData
+mutable struct SubPointData <: SEPoints
     coords::SubArray{Float64,2}
 end
 
-mutable struct SubLocations{T<:Union{SubGridData, SubPointData}} <: SELocations
+mutable struct SubLocations{T<:Union{SubGridData, SubPointData}} <: SELocations{T}
     coords::T
     sitestats::DataFrames.SubDataFrame
 end
@@ -34,7 +34,7 @@ mutable struct SubAssemblage{D <: Real, P <: SubLocations} <: SEAssemblage{D, Su
 end
 
 # TODO delete
-mutable struct SubSiteData{S} <: SESpatialData where S <: SubLocations
+mutable struct SubSiteData{S<:SubLocations} <: SESpatialData{S}
     site::S
 end
 
@@ -55,7 +55,7 @@ function view(com::AbstractComMatrix; species = 1:nspecies(com), sites = 1:nsite
     SubComMatrix(view(com.occurrences, spec, sit), view(com.speciesnames, spec), view(com.sitenames, sit)) #TODO change the order of these in the object to fit the array index order
 end
 
-view(pd::SEPointData, sites) = SubPointData(view(pd.coords, sites, :))
+view(pd::SEPoints, sites) = SubPointData(view(pd.coords, sites, :))
 view(gd::SEGrid, sites) = SubGridData(view(gd.indices, sites, :), gd.grid)
 view(lo::SELocations, sites) = SubLocations{SubGridData}(view(lo.coords, sites), view(lo.sitestats, sites, :))
 view(sp::SESpatialData, sites = 1:nsites(sp)) = SubSiteData(view(sp.site, sites))
@@ -83,7 +83,7 @@ Assemblage(assm::SubAssemblage) = copy(assm)
 
 copy(asm::SEAssemblage) = Assemblage(copy(asm.site), copy(asm.occ))
 copy(sp::SESpatialData) = SiteData(copy(sp.site))
-copy(pd::SEPointData) = PointData(copy(pd.coords), copy(pd.sitestats))
+copy(pd::SEPoints) = PointData(copy(pd.coords), copy(pd.sitestats))
 copy(pd::AbstractComMatrix) = ComMatrix(copy(pd.occurrences), copy(pd.speciesnames), copy(pd.sitenames))
 copy(occ::SEThings) = SpeciesData(copy(occ.commatrix), my_dataframe_copy(occ.traits))
 copy(lo::SELocations) = Locations(copy(lo.coords), my_dataframe_copy(lo.sitestats))
@@ -113,7 +113,7 @@ function subsetgrid(indices, grid)
    ymin = yrange(grid)[minimum(indices[:,2])]
    xcells = maxrange(indices[:,1]) + 1
    ycells = maxrange(indices[:,2]) + 1
-   GridTopology(xmin, grid.xcellsize, xcells, ymin, grid.ycellsize, ycells)
+   GridTopology(range(xmin, step = xcellsize(grid), length = xcells), range(ymin, step = ycellsize(grid), length = ycells))
 end
 
 function show(io::IO, com::SubComMatrix)