Merge pull request #3 from JuliaAI/dev

For a 0.1.1 release
JuliaAI · May 25, 2023 · be112a3 · be112a3
2 parents 780c7ec + 87a9d66
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diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
 Manifest.toml
-docs/src/_auto_generated_list_of_measures.md
+docs/src/auto_generated_list_of_measures.md
 .ipynb_checkpoints
 *~
 #*

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "StatisticalMeasures"
 uuid = "a19d573c-0a75-4610-95b3-7071388c7541"
 authors = ["Anthony D. Blaom <[email protected]>"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
@@ -13,16 +13,19 @@ LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
 ScientificTypesBase = "30f210dd-8aff-4c5f-94ba-8e64358c1161"
 StatisticalMeasuresBase = "c062fc1d-0d66-479b-b6ac-8b44719de4cc"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [weakdeps]
 LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
+ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
 
 [extensions]
 LossFunctionsExt = "LossFunctions"
+ScientificTypesExt = "ScientificTypes"
 
 [compat]
 CategoricalArrays = "0.10"
@@ -33,6 +36,7 @@ LossFunctions = "0.10"
 MacroTools = "0.5"
 OrderedCollections = "1"
 PrecompileTools = "1.1"
+ScientificTypes = "3"
 ScientificTypesBase = "3"
 StatisticalMeasuresBase = "0.1"
 StatsBase = "0.33, 0.34"

diff --git a/README.md b/README.md
@@ -1,14 +1,12 @@
 # StatisticalMeasures.jl
 
-&#128679;
-
 Measures (metrics) for statistics and machine learning.
 
 [![Build Status](https://github.com/JuliaAI/StatisticalMeasures.jl/workflows/CI/badge.svg)](https://github.com/JuliaAI/StatisticalMeasures.jl/actions)
 [![Coverage](https://codecov.io/gh/JuliaAI/StatisticalMeasures.jl/branch/master/graph/badge.svg)](https://codecov.io/github/JuliaAI/StatisticalMeasures.jl?branch=master)
 [![Docs](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliaai.github.io/StatisticalMeasures.jl/dev/)
 
-[List](https://juliaai.github.io/StatisticalMeasures.jl/dev/_auto_generated_list_of_measures.html#aliases) of provided measures and their aliases thereof.
+[List](https://juliaai.github.io/StatisticalMeasures.jl/dev/auto_generated_list_of_measures#aliases) of provided measures and their aliases thereof.
 
 Powered by
 [StatisticalMeasuresBase.jl](https://juliaai.github.io/StatisticalMeasuresBase.jl/dev/).

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -4,6 +4,7 @@ CategoricalDistributions = "af321ab8-2d2e-40a6-b165-3d674595d28e"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 LossFunctions = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
+ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
 ScientificTypesBase = "30f210dd-8aff-4c5f-94ba-8e64358c1161"
 StatisticalMeasures = "a19d573c-0a75-4610-95b3-7071388c7541"
 StatisticalMeasuresBase = "c062fc1d-0d66-479b-b6ac-8b44719de4cc"

diff --git a/docs/make.jl b/docs/make.jl
@@ -3,6 +3,7 @@ using StatisticalMeasures
 using StatisticalMeasures.StatisticalMeasuresBase
 using StatisticalMeasures.LearnAPI
 using ScientificTypesBase
+using ScientificTypes
 
 const REPO="github.com/JuliaAI/StatisticalMeasures.jl"
 
@@ -20,7 +21,7 @@ makedocs(;
     pages=[
         "Overview" => "index.md",
         "Examples of usage" => "examples_of_usage.md",
-        "The Measures" => "_auto_generated_list_of_measures.md",
+        "The Measures" => "auto_generated_list_of_measures.md",
         "Confusion Matrices" => "confusion_matrices.md",
         "Receiver Operator Characteristics" => "roc.md",
         "Tools" => "tools.md",

diff --git a/docs/make_tools.jl b/docs/make_tools.jl
@@ -39,7 +39,7 @@ function alias_table()
 end
 
 function write_measures_page(path=PATH_TO_DOCS_SRC)
-    pagename = "_auto_generated_list_of_measures.md"
+    pagename = "auto_generated_list_of_measures.md"
     pagepath = joinpath(path, pagename)
     traits_given_constructor = measures()
     all_constructors = keys(traits_given_constructor) |> collect

diff --git a/docs/src/examples_of_usage.md b/docs/src/examples_of_usage.md
@@ -35,7 +35,7 @@ bacc == BalancedAccuracy() == BalancedAccuracy(adjusted=false)
 - [Probabilistic regression](@ref)
 - [Custom multi-target measures](@ref)
 - [Using losses from LossFunctions.jl](@ref)
-
+- [Measure search (experimental feature)](@ref)
 
 ## Binary classification
 
@@ -333,3 +333,23 @@ Wrap again, as shown in the preceding section, to get a multi-target version.
 
 For distance-based loss functions, wrapping in `Measure` is not strictly
 necessary, but does no harm.
+
+
+## Measure search (experimental feature)
+
+```@example 29
+using StatisticalMeasures
+using ScientificTypes
+
+y = rand(3)
+yhat = rand(3)
+options = measures(yhat, y, supports_weights=true)
+```
+
+```@example 29
+options[LPLoss]
+```
+
+```@example 29
+measures("Matthew")
+```
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -2,7 +2,7 @@
 <script async defer src="https://buttons.github.io/buttons.js"></script>
 
 <div style="font-size:1.4em;font-weight:bold;">
-  <a href="https://juliaai.github.io/StatisticalMeasures.jl/dev/_auto_generated_list_of_measures.html#aliases"
+  <a href="https://juliaai.github.io/StatisticalMeasures.jl/dev/auto_generated_list_of_measures#aliases"
     style="color: #9558B2;">List of measures</a>           &nbsp;|&nbsp;
   <a href="examples_of_usage"
     style="color: #389826;">Examples</a>
@@ -19,7 +19,7 @@ Measures (metrics) for statistics and machine learning</span>
 # Overview
 
 This package defines common measures (metrics) for classification and regression problems
-in statistics and machine learning. To see if your favorite measures is implemented, see
+in statistics and machine learning. To see if your favorite measure is implemented, see
 [this list](@ref aliases). Some multi-target measures are included, but see also [Custom
 multi-target measures](@ref).
 

diff --git a/docs/src/tools.md b/docs/src/tools.md
@@ -3,7 +3,7 @@
 | method                                        | description                                                                          |
 |:----------------------------------------------|:-------------------------------------------------------------------------------------|
 | [`measurements`](@ref)`(measure, ...)`        | for obtaining per-observation measurements, instead of aggregated ones               |
-| [`measures()`](@ref)                          | dictionary of traits keyed on measure constructors                                   |
+| [`measures()`](@ref)                          | dictionary of traits keyed on measure constructors, with filter options              |
 | [`unfussy(measure)`](@ref)                    | new measure without argument checks¹                                                 |
 | [`multimeasure`](@ref)`(measure; options...)` | wrapper to broadcast measures over multiple observations                             |
 | [`robust_measure(measure)`](@ref)             | wrapper to silently treat unsupported weights as uniform                             |

diff --git a/ext/LossFunctionsExt.jl b/ext/LossFunctionsExt.jl
@@ -31,8 +31,6 @@ loss(measure) = measure
 #     show(io, mime, loss(measure))
 # Base.show(io::IO, measure::LossFunctionType) = show(io, loss(measure))
 
-println("############### LOADED ###############")
-
 # # DISTANCE LOSS TYPE
 
 @trait(

diff --git a/ext/ScientificTypesExt.jl b/ext/ScientificTypesExt.jl
@@ -0,0 +1,41 @@
+module ScientificTypesExt
+using ScientificTypes
+import ScientificTypes.Tables
+using StatisticalMeasures
+import StatisticalMeasuresBase.MLUtils
+import Distributions
+import LearnAPI
+
+# # HELPERS
+
+guess_observation_scitype(y) = guess_observation_scitype(y, Val(Tables.istable(y)))
+guess_observation_scitype(y, ::Val{false}) = MLUtils.getobs(y, 1) |> scitype
+guess_observation_scitype(table, ::Val{true}) =
+    MLUtils.getobs(table, 1) |> collect |> scitype
+
+
+# # MEASURE SEARCH BASED ON ARGUMENTS
+
+StatisticalMeasures.measures(y; kwargs...) = filter(measures(; kwargs...)) do (_, metadata)
+    guess_observation_scitype(y) <: metadata.observation_scitype
+end
+
+function StatisticalMeasures.measures(yhat, y; trait_filters...)
+    y_scitype = guess_observation_scitype(y)
+    yhat_scitype = guess_observation_scitype(yhat)
+    filter(measures(; trait_filters...)) do (_, metadata)
+        requirement1 = y_scitype <: metadata.observation_scitype
+        proxy = metadata.kind_of_proxy
+        requirement2 = if proxy == LearnAPI.LiteralTarget()
+            yhat_scitype <: metadata.observation_scitype
+        elseif proxy == LearnAPI.Distribution()
+            yhat_scitype <: Density{<:y_scitype}
+        else
+            false
+        end
+        requirement3 = !Tables.istable(y) || metadata.can_consume_tables
+        requirement1 && requirement2 && requirement3
+    end
+end
+
+end # module
diff --git a/src/StatisticalMeasures.jl b/src/StatisticalMeasures.jl
@@ -43,14 +43,16 @@ include("precompile.jl")
 
 # remove after julia LTS supports pkg extensions:
 if !isdefined(Base, :get_extension)
-  include("../ext/LossFunctionsExt.jl")
+    include("../ext/LossFunctionsExt.jl")
+    include("../ext/ScientificTypesExt.jl")
 end
 
 const MEASURES_FOR_EXPORT = let measures = measures()
     ret = Symbol[]
     for C in keys(measures)
         push!(ret, Symbol(C))
         for alias  in measures[C].aliases
+            alias == "precision" && continue
             push!(ret, Symbol(alias))
         end
     end

diff --git a/src/confusion_matrices.jl b/src/confusion_matrices.jl
@@ -607,6 +607,10 @@ function Base.show(stream::IO, m::MIME"text/plain", cm::ConfusionMatrix{N}
     write(stream, take!(iob))
 end
 
+function Base.show(stream::IO, cm::ConfusionMatrix{N}) where N
+    mat = matrix(cm, warn=false)
+    print(stream, "ConfusionMatrix{$N}($(repr(mat)))")
+end
 
 # ## STATISTICAL FUNCTIONS ON CONFUSION MATRICES
 

diff --git a/src/docstrings.jl b/src/docstrings.jl
@@ -112,7 +112,7 @@ function docstring(signature; body="", footer="", scitype="")
     API.can_report_unaggregated(m) &&
         (ret *= "\n\nMeasurements are aggregated. "*
         "To obtain a separate measurement for each observation, "*
-        "use the syntax `measurements(m, ŷ, y)`. ")
+        "use the syntax `measurements($m_str, ŷ, y)`. ")
     ret *= "Generally, an observation `obs` in `MLUtils.eachobs(y)` is expected to satisfy "*
         "`ScientificTypes.scitype(obs)<:`$scitype. "
     # if kind_of_proxy == LearnAPI.LiteralTarget()

diff --git a/src/functions.jl b/src/functions.jl
@@ -163,7 +163,7 @@ end
 
 # # FUNCTIONS ON MATRICES INTERPRETED AS CONFUSION MATRICES
 
-clean(s) = join(split(s, "_"), " ")
+clean(s) = join(split(last(split(s, ".")), "_"), " ")
 function docstring(measure; sig="(m)", name=clean(measure), binary=false, the=false)
     footer = binary ?
         "The first index corresponds to the \"negative\" class, "*

diff --git a/src/probabilistic.jl b/src/probabilistic.jl
@@ -103,7 +103,8 @@ Core implementation: [`Functions.auc`](@ref).
 
 $INVARIANT_LABEL
 """,
-    scitype = ""
+    scitype = "",
+    footer="See also [`roc_curve`](@ref). ",
 )
 
 "$AreaUnderCurveDoc"

diff --git a/src/registry.jl b/src/registry.jl
@@ -4,17 +4,96 @@ const ERR_BAD_CONSTRUCTOR = ArgumentError(
     "Constructor must have a zero argument method. "
 )
 
+const ERR_BAD_KWARG(trait) = ArgumentError(
+    "`$trait` is not a valid measure trait name. You must choose one of these: "*
+        "$(API.OVERLOADABLE_TRAITS_LIST). "
+)
+
 """
-    StatisticalMeasusures.measures()
+    measures(; trait_options...)
 
 *Experimental* and subject to breaking behavior between patch releases.
 
 Return a dictionary, `dict`, keyed on measure constructors provided by
-StatisticalMeasures.jl. The value of `dict[constructor]` provides information about
-traits shared by all measures constructed using the syntax `constructor(args...)`.
+StatisticalMeasures.jl. The value of `dict[constructor]` provides information about traits
+(measure "metadata") shared by all measures constructed using the syntax
+`constructor(args...)`.
+
+# Trait options
+
+One can filter on the basis of measure trait values, as shown in this example:
+
+```
+using StatisticalMeasures
+import ScientificTypesBase.Multiclass
+
+julia> measures(
+    observation_scitype = Union{Missing,Multiclass},
+    supports_class_weights = true,
+)
+```
+
+---
+
+    measures(y; trait_filters...)
+    measures(yhat, y; trait_filters...)
+
+*Experimental* and subject to breaking behavior between patch releases.
+
+Assuming, ScientificTypes.jl has been imported, find measures that can be applied to data
+with the specified data arguments `(y,)` or `(yhat, y)`. It is assumed that the arguments
+contain multiple observations (have types implementing `MLUtils.getobs`).
+
+Returns a dictionary keyed on the constructors of such measures. Additional
+`trait_filters` are the same as for the zero argument `measures` method.
+
+```julia
+using StatisticalArrays
+using ScientificTypes
+
+julia> measures(rand(3), rand(3), supports_weights=false)
+LittleDict{Any, Any, Vector{Any}, Vector{Any}} with 1 entry:
+  RSquared => (aliases = ("rsq", "rsquared"), consumes_multiple_observations = true, can_re…
+```
+
+*Warning.* Matching is based only on the *first* observation of the arguments provided,
+and must be interpreted carefully if, for example, `y` or `yhat` are vectors with `Union`
+or other abstract element types.
+
+"""
+measures(; trait_options...) = filter(TRAITS_GIVEN_CONSTRUCTOR) do (_, metadata)
+    trait_value_pairs = collect(trait_options)
+    traits = first.(trait_value_pairs)
+    for trait in traits
+        trait in API.OVERLOADABLE_TRAITS || throw(ERR_BAD_KWARG(trait))
+    end
+    all(trait_value_pairs) do pair
+        trait = first(pair)
+        value = last(pair)
+        getproperty(metadata, trait) == value
+    end
+end
 
 """
-measures() = TRAITS_GIVEN_CONSTRUCTOR
+    measures(needle::Union{AbstractString,Regex}; trait_options...)
+
+*Experimental* and subject to breaking behavior between patch releases.
+
+Find measures that contain `needle` in their document string.  Returns a dictionary keyed
+on the constructors of such measures.
+
+```
+julia> measures("Matthew")
+LittleDict{Any, Any, Vector{Any}, Vector{Any}} with 1 entry:
+  MatthewsCorrelation => (aliases = ("matthews_correlation", "mcc"), consumes_multiple_obse…
+```
+"""
+function measures(needle::Union{AbstractString,Regex}; trait_options...)
+    filter(measures(; trait_options...)) do (constructor, _)
+        doc = Base.Docs.doc(constructor) |> string
+        occursin(needle, doc)
+    end
+end
 
 """
     StatisticalMeasures.register(constructor, aliases=String[])

diff --git a/src/tools.jl b/src/tools.jl
@@ -54,3 +54,4 @@ function API.check_pools(
     end
     return nothing
 end
+
diff --git a/test/ScientificTypesExt.jl b/test/ScientificTypesExt.jl
@@ -0,0 +1,29 @@
+using ScientificTypes
+using ScientificTypes.Tables
+
+n = 10
+p = 3
+y    = rand(p, n)
+yhat = rand(p, n)
+t = y'       |> Tables.table |> Tables.columntable
+that = yhat' |> Tables.table |> Tables.columntable
+
+ms = measures(t)
+@test all(ms) do (_, metadata)
+    AbstractVector{Continuous} <: metadata.observation_scitype
+end
+
+ms = measures(that, t)
+@test all(ms) do (_, metadata)
+    AbstractVector{Continuous} <: metadata.observation_scitype
+end
+
+y = categorical(rand("ab", n))
+yhat = UnivariateFinite(levels(y), rand(n), augment=true, pool=y)
+ms2 = measures((yhat, y))
+@test all(ms2) do (_, metadata)
+    Multiclass{2} <: metadata.observation_scitype &&
+        metadata.kind_of_proxy == LearnAPI.Distribution()
+end
+
+@test isempty(intersect(keys(ms), keys(ms2)))
Original file line number	Diff line number	Diff line change
Expand Up		@@ -54,3 +54,4 @@ function API.check_pools(
		end
		return nothing
		end