Merge pull request #61 from JuliaAI/dev

For a 0.1.11 release

Author: ablaom

Project.toml

@@ -1,7 +1,7 @@
 name = "CategoricalDistributions"
 uuid = "af321ab8-2d2e-40a6-b165-3d674595d28e"
 authors = ["Anthony D. Blaom <[email protected]>"]
-version = "0.1.10"
+version = "0.1.11"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"

README.md

@@ -82,7 +82,7 @@ Arrays of `UnivariateFinite` distributions are defined using the same
 constructor. Broadcasting methods, such as `pdf`, are optimized for
 such arrays:
 
-```
+```julia
 julia> v = UnivariateFinite(["no", "yes"], [0.1, 0.2, 0.3, 0.4], augment=true, pool=data)
 4-element UnivariateFiniteArray{Multiclass{3}, String, UInt32, Float64, 1}:
  UnivariateFinite{Multiclass{3}}(no=>0.9, yes=>0.1)
@@ -119,7 +119,6 @@ julia> pdf(v, L)
  0.0  0.6  0.4
 ```
 
-
 ## Measures over finite labeled sets
 
 There is, in fact, no enforcement that probabilities in a
@@ -128,7 +127,6 @@ to a type `T` for which `zero(T)` is defined. In particular
 `UnivariateFinite` objects implement arbitrary non-negative, signed,
 or complex measures over a finite labeled set.
 
-
 ## What does this package provide?
 
 - A new type `UnivariateFinite{S}` for representing probability
@@ -144,7 +142,7 @@ or complex measures over a finite labeled set.
 - Implementations of `rand` for generating random samples of a
   `UnivariateFinite` distribution.
 
-- Implementations of the `pdf`, `logpdf` and `mode` methods of
+- Implementations of the `pdf`, `logpdf`, `mode` and `modes` methods of
   Distributions.jl, with efficient broadcasting over the new array
   type.
 

src/CategoricalDistributions.jl

@@ -16,7 +16,7 @@ using Random
 
 const Dist = Distributions
 
-import Distributions: pdf, logpdf, support, mode
+import Distributions: pdf, logpdf, support, mode, modes
 
 include("utilities.jl")
 include("types.jl")
@@ -28,7 +28,7 @@ include("arithmetic.jl")
 export UnivariateFinite, UnivariateFiniteArray, UnivariateFiniteVector
 
 # re-eport from Distributions:
-export pdf, logpdf, support, mode
+export pdf, logpdf, support, mode, modes
 
 # re-export from ScientificTypesBase:
 export Multiclass, OrderedFactor

src/arrays.jl

@@ -271,7 +271,7 @@ Base.Broadcast.broadcasted(
     c::Missing) where {S,V,R,P,N} = Missings.missings(P, length(u))
 
 
-## PERFORMANT BROADCASTING OF mode:
+## PERFORMANT BROADCASTING OF mode(s):
 
 function Base.Broadcast.broadcasted(::typeof(mode),
                                     u::UniFinArr{S,V,R,P,N}) where {S,V,R,P,N}
@@ -298,6 +298,26 @@ function Base.Broadcast.broadcasted(::typeof(mode),
     return reshape(mode_flat, size(u))
 end
 
+function Base.Broadcast.broadcasted(::typeof(modes),
+                                    u::UniFinArr{S,V,R,P,N}) where {S,V,R,P,N}
+    dic = u.prob_given_ref
+
+    # using linear indexing:
+    mode_flat = map(1:length(u)) do i
+        max_prob = maximum(dic[ref][i] for ref in keys(dic))
+        M = R[]
+
+        # see comment for in broadcasted(::mode) above
+        throw_nan_error_if_needed(max_prob)
+        for ref in keys(dic)
+            if dic[ref][i] == max_prob
+                push!(M, ref)
+            end
+        end
+        return u.decoder(M)
+    end
+    return reshape(mode_flat, size(u))
+end
 
 ## EXTENSION OF CLASSES TO ARRAYS OF UNIVARIATE FINITE
 

src/methods.jl

@@ -120,7 +120,7 @@ end
 # TODO: It would be useful to define == as well.
 
 """
-    Dist.pdf(d::UnivariateFinite, x)
+    Distributions.pdf(d::UnivariateFinite, x)
 
 Probability of `d` at `x`.
 
@@ -178,15 +178,31 @@ function Dist.mode(d::UnivariateFinite)
     return d.decoder(m)
 end
 
+function Dist.modes(d::UnivariateFinite{S,V,R,P}) where {S,V,R,P}
+    dic = d.prob_given_ref
+    p = values(dic)
+    max_prob = maximum(p)
+    M = R[] # modes
+
+    # see comment in `mode` above
+    throw_nan_error_if_needed(max_prob)
+    for (x, prob) in dic
+        if prob == max_prob
+            push!(M, x)
+        end
+    end
+    return d.decoder(M)
+end
+
+const ERR_NAN_FOUND = DomainError(
+    NaN,
+    "`mode(s)` is invalid for a `UnivariateFinite` distribution "*
+    "with `pdf` containing `NaN`s"
+)
+
 function throw_nan_error_if_needed(x)
     if isnan(x)
-        throw(
-            DomainError(
-                NaN,
-                "`mode` is invalid for `UnivariateFininite` distribution "*
-                "with `pdf` containing `NaN`s"
-            )
-        )
+        throw(ERR_NAN_FOUND)
     end
 end
 

test/arrays.jl

@@ -10,7 +10,7 @@ import Random
 using Missings
 using ScientificTypes
 
-import CategoricalDistributions: classes
+import CategoricalDistributions: classes, ERR_NAN_FOUND
 import CategoricalArrays.unwrap
 
 rng = StableRNG(111)
@@ -198,10 +198,10 @@ end
     probs = rand(rng, n)
     u = UnivariateFinite(probs, augment = true, pool=missing)
     supp = Distributions.support(u)
-    modes = mode.(u)
-    @test modes isa CategoricalArray
+    _modes = mode.(u)
+    @test _modes isa CategoricalArray
     expected = [ifelse(p > 0.5, supp[2], supp[1]) for p in probs]
-    @test all(modes .== expected)
+    @test all(_modes .== expected)
 
     # multiclass
     rng = StableRNG(554)
@@ -220,7 +220,48 @@ end
         ],
         pool=missing
     )
-    @test_throws DomainError mode.(unf_arr)
+    @test_throws ERR_NAN_FOUND mode.(unf_arr)
+end
+
+@testset "broadcasting modes" begin
+    # binary
+    rng = StableRNG(668)
+    probs = rand(rng, n)
+    u = UnivariateFinite(probs, augment = true, pool=missing)
+    supp = Distributions.support(u)
+    _modes = modes.(u)
+    @test _modes isa Vector{<:CategoricalArray}
+    expected = [ifelse(p > 0.5, [supp[2]], [supp[1]]) for p in probs]
+    @test all(_modes .== expected)
+
+    # multiclass, bimodal
+    rng = StableRNG(554)
+    P   = rand(rng, n, c)
+    M, M_idx = findmax(P, dims=2)
+    M_idx = getindex.(M_idx, 2)
+    for i in axes(P,1)
+        m = M[i]
+        j = M_idx[i]
+        while j == M_idx[i]
+            j = rand(axes(P,2))
+        end
+        P[i,j] = m
+    end
+    P ./= sum(P, dims=2)
+    u   = UnivariateFinite(P, pool=missing)
+    expected = modes.([u...])
+    @test all(modes.(u) .== expected)
+
+    # `mode` broadcasting of `Univariate` objects containing `NaN` in probs.
+    unf_arr = UnivariateFinite(
+        [
+            0.1 0.2 NaN 0.1 NaN;
+            0.2 0.1 0.1 0.4 0.2;
+            0.3 NaN 0.2 NaN 0.3
+        ],
+        pool=missing
+    )
+    @test_throws ERR_NAN_FOUND modes.(unf_arr)
 end
 
 @testset "cat for UnivariateFiniteArray" begin

test/methods.jl

@@ -9,7 +9,7 @@ import Random
 rng = StableRNG(123)
 using ScientificTypes
 
-import CategoricalDistributions: classes
+import CategoricalDistributions: classes, ERR_NAN_FOUND
 
 v = categorical(collect("asqfasqffqsaaaa"), ordered=true)
 V = categorical(collect("asqfasqffqsaaaa"))
@@ -19,8 +19,10 @@ A, S, Q, F = V[1], V[2], V[3], V[4]
 @testset "set 1" begin
 
     # ordered (OrderedFactor)
-    dict = Dict(s=>0.1, q=> 0.2, f=> 0.7)
+    dict = Dict(s=>0.1, q=>0.2, f=>0.7)
     d    = UnivariateFinite(dict)
+    dict_bimodal = Dict(a=>0.1, s=>0.1, q=>0.4, f=>0.4)
+    d_bimodal    = UnivariateFinite(dict_bimodal)
     @test classes(d) == [a, f, q, s]
     @test classes(d) == classes(s)
     @test levels(d) == levels(s)
@@ -45,6 +47,7 @@ A, S, Q, F = V[1], V[2], V[3], V[4]
     @test logpdf(d, 'f') ≈ log(0.7)
     @test isinf(logpdf(d, a))
     @test mode(d) == f
+    @test modes(d_bimodal) == [f, q]
 
     @test UnivariateFinite(support(d), [0.7, 0.2, 0.1]) ≈ d
 
@@ -72,7 +75,7 @@ A, S, Q, F = V[1], V[2], V[3], V[4]
     @test isapprox(freq[q]/N, ffreq[q]/N)
 
     # unordered (Multiclass):
-    dict = Dict(S=>0.1, Q=> 0.2, F=> 0.7)
+    dict = Dict(S=>0.1, Q=>0.2, F=>0.7)
     d    = UnivariateFinite(dict)
     @test classes(d) == [a, f, q, s]
     @test classes(d) == classes(s)
@@ -178,7 +181,21 @@ end
 
     # `mode` of `Univariate` objects containing `NaN` in probs.
     unf = UnivariateFinite([0.1, 0.2, NaN, 0.1, NaN], pool=missing)
-    @test_throws DomainError mode(unf)
+    @test_throws ERR_NAN_FOUND mode(unf)
+end
+
+@testset "Univariate modes, bimodal" begin
+    v = categorical(1:101)
+    p = rand(rng,101)
+    p[24] = 2*maximum(p)
+    p[42] = p[24]
+    p = p/sum(p)
+    d = UnivariateFinite(v, p)
+    @test modes(d) == [24, 42]
+
+    # `mode` of `Univariate` objects containing `NaN` in probs.
+    unf = UnivariateFinite([0.1, 0.2, NaN, 0.1, NaN], pool=missing)
+    @test_throws ERR_NAN_FOUND modes(unf)
 end
 
 @testset "UnivariateFinite methods" begin