Merge branch 'pm/violin_plot' of https://github.com/PaulinaMartin96/MCMCChains.jl into pm/violin_plot

Author: PaulinaMartin96

docs/Project.toml

@@ -3,15 +3,16 @@ CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
-MLJModels = "d491faf4-2d78-11e9-2867-c94bc002c0b7"
+MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 MLJXGBoostInterface = "54119dfa-1dab-4055-a167-80440f4f7a91"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
 
 [compat]
 CategoricalArrays = "0.8, 0.9, 0.10"
 DataFrames = "0.22, 1"
-Documenter = "0.26"
+Documenter = "0.26, 0.27"
 Gadfly = "1.3"
-MLJModels = "0.14"
+MLJBase = "0.18"
 MLJXGBoostInterface = "0.1"
 StatsPlots = "0.14"
+julia = "1.3"

src/chains.jl

@@ -31,9 +31,22 @@ function Chains(
     name_map = (parameters = parameter_names,);
     start::Int = 1,
     thin::Int = 1,
+    iterations::AbstractVector{Int} = range(start; step=thin, length=size(val, 1)),
     evidence = missing,
     info::NamedTuple = NamedTuple()
 )
+    # Check that iteration numbers are reasonable
+    if length(iterations) != size(val, 1)
+        error("length of `iterations` (", length(iterations),
+              ") is not equal to the number of iterations (", size(val, 1), ")")
+    end
+    if !isempty(iterations) && first(iterations) < 1
+        error("iteration numbers must be positive integers")
+    end
+    if !isstrictlyincreasing(iterations)
+        error("iteration numbers must be strictly increasing")
+    end
+
     # Make sure that we have a `:parameters` index and # Copying can avoid state mutation.
     _name_map = initnamemap(name_map)
 
@@ -58,7 +71,7 @@ function Chains(
 
     # Construct the AxisArray.
     arr = AxisArray(val;
-                    iter = range(start, step=thin, length=size(val, 1)),
+                    iter = iterations,
                     var = parameter_names,
                     chain = 1:size(val, 3))
 
@@ -444,17 +457,21 @@ Return the range of iteration indices of the `chains`.
 Base.range(chains::Chains) = chains.value[Axis{:iter}].val
 
 """
-    setrange(chains::Chains, range)
+    setrange(chains::Chains, range::AbstractVector{Int})
 
 Generate a new chain from `chains` with iterations indexed by `range`.
 
 The new chain and `chains` share the same data in memory.
 """
-function setrange(chains::Chains, range::AbstractRange{<:Integer})
+function setrange(chains::Chains, range::AbstractVector{Int})
     if length(chains) != length(range)
         error("length of `range` (", length(range),
               ") is not equal to the number of iterations (", length(chains), ")")
     end
+    if !isempty(range) && first(range) < 1
+        error("iteration numbers must be positive integers")
+    end
+    isstrictlyincreasing(range) || error("iteration numbers must be strictly increasing")
 
     value = AxisArray(chains.value.data;
                       iter = range, var = names(chains), chain = MCMCChains.chains(chains))
@@ -574,8 +591,7 @@ function header(c::Chains; section=missing)
     # Return header.
     return string(
         ismissing(c.logevidence) ? "" : "Log evidence      = $(c.logevidence)\n",
-        "Iterations        = $(first(c)):$(last(c))\n",
-        "Thinning interval = $(step(c))\n",
+        "Iterations        = $(range(c))\n",
         "Number of chains  = $(size(c, 3))\n",
         "Samples per chain = $(length(range(c)))\n",
         ismissing(wall) ? "" : "Wall duration     = $(round(wall, digits=2)) seconds\n",
@@ -725,8 +741,11 @@ _cat(dim::Int, cs::Chains...) = _cat(Val(dim), cs...)
 
 function _cat(::Val{1}, c1::Chains, args::Chains...)
     # check inputs
-    thin = step(c1)
-    all(c -> step(c) == thin, args) || throw(ArgumentError("chain thinning differs"))
+    lastiter = last(c1)
+    for c in args
+        first(c) > lastiter || throw(ArgumentError("iterations have to be sorted"))
+        lastiter = last(c)
+    end
     nms = names(c1)
     all(c -> names(c) == nms, args) || throw(ArgumentError("chain names differ"))
     chns = chains(c1)
@@ -735,7 +754,7 @@ function _cat(::Val{1}, c1::Chains, args::Chains...)
     # concatenate all chains
     data = mapreduce(c -> c.value.data, vcat, args; init = c1.value.data)
     value = AxisArray(data;
-                      iter = range(first(c1); length = size(data, 1), step = thin),
+                      iter = mapreduce(range, vcat, args; init=range(c1)),
                       var = nms,
                       chain = chns)
 

src/constructors.jl

@@ -63,7 +63,8 @@ function Base.Array(
 end
 
 function to_matrix(chain::Chains)
-    return Matrix(reshape(permutedims(chain.value.data, (1, 3, 2)), :, size(chain, 2)))
+    x = permutedims(chain.value.data, (1, 3, 2))
+    return Matrix(reshape(x, size(x, 1) * size(x, 2), size(x, 3)))
 end
 
 function to_vector(chain::Chains)
@@ -79,4 +80,3 @@ function to_vector_of_matrices(chain::Chains)
     data = chain.value.data
     return [Matrix(data[:, :, i]) for i in axes(data, 3)]
 end
-

src/fileio.jl

@@ -22,5 +22,5 @@ function readcoda(output::AbstractString, index::AbstractString)
     value[:, i] = out[inds, 2]
   end
 
-  Chains(value, start=first(window), thin=step(window), names=names)
+  Chains(value; iterations=window, names=names)
 end

src/rstar.jl

@@ -18,12 +18,11 @@ verbosity level.
 
 # Example
 ```jldoctest rstar; output = false, filter = r".*"s
-using MLJModels
+using MLJBase, MLJXGBoostInterface
 
-XGBoost = @load XGBoostClassifier verbosity=0
 chn = Chains(fill(4, 100, 2, 3))
 
-Rs = rstar(XGBoost(), chn; iterations=20)
+Rs = rstar(XGBoostClassifier(), chn; iterations=20)
 R = round(mean(Rs); digits=0)
 
 # output

src/utils.jl

@@ -96,7 +96,7 @@ function merge_union(a::NamedTuple{an}, b::NamedTuple{bn}) where {an,bn}
                 :(getfield(b, $(QuoteNode(n))))
             end
         end
-        
+
         return :(NamedTuple{$names,$types}(($(values...),)))
     else
         names = Base.merge_names(an, bn)
@@ -113,7 +113,7 @@ function merge_union(a::NamedTuple{an}, b::NamedTuple{bn}) where {an,bn}
                 getfield(b, n)
             end
         end
-        
+
         return NamedTuple{names,types}(values)
     end
 end
@@ -179,8 +179,8 @@ function concretize(x::AbstractArray)
         return x
     else
         xnew = map(concretize, x)
-        T = mapreduce(typeof, promote_type, xnew)
-        if T <: eltype(xnew)
+        T = mapreduce(typeof, promote_type, xnew; init=Union{})
+        if T <: eltype(xnew) && T !== Union{}
             return convert(AbstractArray{T}, xnew)
         else
             return xnew
@@ -196,3 +196,17 @@ function concretize(x::Chains)
         return Chains(concretize(value), x.logevidence, x.name_map, x.info)
     end
 end
+
+function isstrictlyincreasing(x::AbstractVector{Int})
+    return isempty(x) || _isstrictlyincreasing_nonempty(x)
+end
+
+_isstrictlyincreasing_nonempty(x::AbstractRange{Int}) = step(x) > 0
+function _isstrictlyincreasing_nonempty(x::AbstractVector{Int})
+    i = first(x)
+    for j in Iterators.drop(x, 1)
+        j > i || return false
+        i = j
+    end
+    return true
+end

test/Project.toml

@@ -24,7 +24,7 @@ UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 AbstractMCMC = "2.2.1, 3.0"
 DataFrames = "0.22.4, 1.0"
 Distributions = "0.24.12, 0.25"
-Documenter = "0.26"
+Documenter = "0.26, 0.27"
 FFTW = "1.1"
 IteratorInterfaceExtensions = "1"
 KernelDensity = "0.6.2"

test/arrayconstructor_tests.jl

@@ -67,6 +67,11 @@ using MCMCChains, Test
         Array(chns[:a])
         Array(chns, [:parameters])
         Array(chns, [:parameters, :internals])
+
+        # empty chain: #317
+        empty_chain = chns[Symbol[]]
+        @test isempty(MCMCChains.to_matrix(empty_chain))
+        @test isempty(Array(empty_chain))
     end
     @testset "Accuracy" begin
         nchains = 5

test/concatenation_tests.jl

@@ -46,58 +46,60 @@ end
     chn = Chains(rand(10, 5, 2), ["a", "b", "c", "d", "e"], Dict(:internal => ["d", "e"]))
     chn1 = Chains(rand(5, 5, 2), ["a", "b", "c", "d", "e"], Dict(:internal => ["a", "b"]))
 
-    # incorrect thinning
-    @test_throws ArgumentError vcat(chn, Chains(rand(2, 5, 2); thin = 2))
+    # incorrect iterations
+    @test_throws ArgumentError vcat(chn, Chains(rand(2, 5, 2)))
 
     # incorrect names
-    @test_throws ArgumentError vcat(chn, Chains(rand(10, 5, 2), ["a", "b", "c", "d", "f"]))
+    @test_throws ArgumentError vcat(chn, Chains(rand(10, 5, 2), ["a", "b", "c", "d", "f"]; start=11))
 
     # incorrect number of chains
-    @test_throws ArgumentError vcat(chn, Chains(rand(10, 5, 3), ["a", "b", "c", "d", "e"]))
+    @test_throws ArgumentError vcat(chn, Chains(rand(10, 5, 3), ["a", "b", "c", "d", "e"]; start=11))
 
     # concate the same chain
-    chn2 = vcat(chn, chn)
+    chn_shifted = setrange(chn, 11:20)
+    chn2 = vcat(chn, chn_shifted)
     @test chn2.value.data == vcat(chn.value.data, chn.value.data)
     @test size(chn2) == (20, 5, 2)
     @test names(chn2) == names(chn)
     @test range(chn2) == 1:20
     @test chn2.name_map == (parameters = [:a, :b, :c], internal = [:d, :e])
-    
-    chn2a = cat(chn, chn)
+
+    chn2a = cat(chn, chn_shifted)
     @test chn2a.value == chn2.value
     @test chn2a.name_map == chn2.name_map
     @test chn2a.info == chn2.info
 
-    chn2b = cat(chn, chn; dims = Val(1))
+    chn2b = cat(chn, chn_shifted; dims = Val(1))
     @test chn2b.value == chn2.value
     @test chn2b.name_map == chn2.name_map
     @test chn2b.info == chn2.info
 
-    chn2c = cat(chn, chn; dims = 1)
+    chn2c = cat(chn, chn_shifted; dims = 1)
     @test chn2c.value == chn2.value
     @test chn2c.name_map == chn2.name_map
     @test chn2c.info == chn2.info
 
     # concatenate a different chain
-    chn3 = vcat(chn, chn1)
+    chn1_shifted = setrange(chn1, 11:15)
+    chn3 = vcat(chn, chn1_shifted)
     @test chn3.value.data == vcat(chn.value.data, chn1.value.data)
     @test size(chn3) == (15, 5, 2)
     @test names(chn3) == names(chn)
     @test range(chn3) == 1:15
     # just take the name map of first argument
     @test chn3.name_map == (parameters = [:a, :b, :c], internal = [:d, :e])
-    
-    chn3a = cat(chn, chn1)
+
+    chn3a = cat(chn, chn1_shifted)
     @test chn3a.value == chn3.value
     @test chn3a.name_map == chn3.name_map
     @test chn3a.info == chn3.info
 
-    chn3b = cat(chn, chn1; dims = Val(1))
+    chn3b = cat(chn, chn1_shifted; dims = Val(1))
     @test chn3b.value == chn3.value
     @test chn3b.name_map == chn3.name_map
     @test chn3b.info == chn3.info
 
-    chn3c = cat(chn, chn1; dims = 1)
+    chn3c = cat(chn, chn1_shifted; dims = 1)
     @test chn3c.value == chn3.value
     @test chn3c.name_map == chn3.name_map
     @test chn3c.info == chn3.info

test/diagnostic_tests.jl

@@ -15,6 +15,12 @@ val = hcat(val, rand(1:2, niter, 1, nchains))
 
 # construct a Chains object
 chn = Chains(val, start = 1, thin = 2)
+@test_throws ErrorException Chains(val; start=0, thin=2)
+@test_throws ErrorException Chains(val; start=niter, thin=-1)
+@test_throws ErrorException Chains(val; iterations=1:(niter - 1))
+@test_throws ErrorException Chains(val; iterations=range(0; step=2, length=niter))
+@test_throws ErrorException Chains(val; iterations=niter:-1:1)
+@test_throws ErrorException Chains(val; iterations=ones(Int, niter))
 
 # Chains object for discretediag
 val_disc = rand(Int16, 200, nparams, nchains)
@@ -29,18 +35,26 @@ chn_disc = Chains(val_disc, start = 1, thin = 2)
     @test keys(chn) == names(chn) == [:param_1, :param_2, :param_3, :param_4]
 
     @test range(chn) == range(1; step = 2, length = niter)
+    @test range(chn) == range(Chains(val; iterations=range(chn)))
+    @test range(chn) == range(Chains(val; iterations=collect(range(chn))))
 
     @test_throws ErrorException setrange(chn, 1:10)
+    @test_throws ErrorException setrange(chn, 0:(niter - 1))
+    @test_throws ErrorException setrange(chn, niter:-1:1)
+    @test_throws ErrorException setrange(chn, ones(Int, niter))
     @test_throws MethodError setrange(chn, float.(range(chn)))
 
-    chn2 = setrange(chn, range(1; step = 10, length = niter))
-    @test range(chn2) == range(1; step = 10, length = niter)
-    @test names(chn2) === names(chn)
-    @test chains(chn2) === chains(chn)
-    @test chn2.value.data === chn.value.data
-    @test chn2.logevidence === chn.logevidence
-    @test chn2.name_map === chn.name_map
-    @test chn2.info == chn.info
+    chn2a = setrange(chn, range(1; step = 10, length = niter))
+    chn2b = setrange(chn, collect(range(1; step = 10, length = niter)))
+    for chn2 in (chn2a, chn2b)
+        @test range(chn2) == range(1; step = 10, length = niter)
+        @test names(chn2) === names(chn)
+        @test chains(chn2) === chains(chn)
+        @test chn2.value.data === chn.value.data
+        @test chn2.logevidence === chn.logevidence
+        @test chn2.name_map === chn.name_map
+        @test chn2.info == chn.info
+    end
 
     chn3 = resetrange(chn)
     @test range(chn3) == 1:niter

test/rstar_tests.jl

@@ -1,5 +1,6 @@
 using MCMCChains
-using MLJModels
+using MLJBase
+using MLJXGBoostInterface
 using Test
 
 N = 1000
@@ -8,8 +9,7 @@ colnames = ["a", "b", "c", "d", "e", "f", "g", "h"]
 internal_colnames = ["c", "d", "e", "f", "g", "h"]
 chn = Chains(val, colnames, Dict(:internals => internal_colnames))
 
-XGBoost = @load XGBoostClassifier
-classif = XGBoost()
+classif = XGBoostClassifier()
 
 @testset "R star test" begin
     # Compute R* statistic for a mixed chain.

test/runtests.jl

@@ -22,7 +22,7 @@ Random.seed!(0)
     if VERSION >= v"1.3" && Sys.WORD_SIZE == 64
         # run tests related to rstar statistic
         println("Rstar")
-        Pkg.add("MLJModels")
+        Pkg.add("MLJBase")
         Pkg.add("MLJXGBoostInterface")
         @time include("rstar_tests.jl")